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Cartograph Commands
AIMS Commands
VIP commands
SiGraph commands
Connectomist commands
NMR commands
Cartograph Commands
AIMS Commands
VIP commands
SiGraph commands
Connectomist commands
NMR commands
cartoFSLmatToTrm.py
Usage: cartoFSLmatToTrm.py [options]
Transforms a FSL registration matrix (.mat, but _not_ a matlab file) into an
AIMS .trm transformation file, and converts coordinates systems from FSL to
AIMS.
Options:
-h, --help show this help message and exit
-i INPUT, --input=INPUT
input .mat FSL transformation
-o OUTPUT, --output=OUTPUT
output .trm AIMS transformation
-s SOURCE, --source=SOURCE
transformation source image
-d DESTINATION, --destination=DESTINATION
transformation destination image
cartoGraphAddAttributeFromCsv.py
Usage: cartoGraphAddAttributeFromCsv.py [options]
Add an attritute to some nodes of a graph. The attribute stem from a csv file
with an header. Each line of this file is a pair of node-name value
Options:
-h, --help show this help message and exit
-i FILE Input graph
-o FILE Output graph (default=out.arg)
-j FILE Input csv file
-k STRING graph key attribute: the attribute name which identifies the
graph nodes (default=name)
-l STRING graph value attribute: the attribute name of the graph nodes
that will be used to store the value,
(default=custom_num_val)
-m STRING|INT table (csv) column name|number which contains keys to be
matched with attribute name of the graph (default=0, first
column)
-n STRING|INT csv column name|number which contains values to be set with
attribute name of the graph (default=1, second column)
-q, --quiet don't print status messages to stdout
cartoGraphAddAttributeFromCsv.py -i input_fold_graph.arg -j stats-values.csv
cartoGraphCat.py
Usage: cartoGraphCat.py [options]
Graphs concatenation
Options:
-h, --help show this help message and exit
-o OUTPUT, --output=OUTPUT
output graph
-i FILENAME, --input=FILENAME
input graph(s)
cartoGraphTransform.py
Usage: cartoGraphTransform.py [options]
Apply transformations to ROI graph nodes. Several transformations can apply to
different regions specified by their name. Currently only ROI bucket graphs
are handled, and no resampling is done (each voxel is transformed with no more
processing, which may result in holes and/or unconnected regions if scaling
factors are superior to 1.)
Options:
-h, --help show this help message and exit
-i INPUT, --input=INPUT
input graph
-o OUTPUT, --output=OUTPUT
output graph [default: <INPUT>]
-t TRANSFO, --transformation=TRANSFO
transformation file. Any -t option must correspond to
a -n option
-n NAME, --name=NAME ROI name to apply transformation to. Any -n option
must correspond to a -t option
cartoLinearComb.py
Usage: cartoLinearComb.py [options]
Apply a formula to a set of homogeneous images (homogeneous means all of the
same data type)
Options:
-h, --help show this help message and exit
-o OUTPUT, --output=OUTPUT
output volume
-f FORMULA, --formula=FORMULA
image formula, ex: ( I1 * 2 + I2 * I3 ) / 1.2
-i FILENAME, --input=FILENAME
input volume(s)
cartoSetMinf.py
Usage: cartoSetMinf.py [options]
set/create properties in a .minf header
Options:
-h, --help show this help message and exit
-i INPUT, --inpput=INPUT
input .minf
-p PROPERTY, --property=PROPERTY
property to set
-v VALUE, --value=VALUE
property value (12, or "toto", or [ 1.2, 12 ]. Be
careful to put two quotes around numeric expressions
that are meant to be strings (one quote for the shell,
one for pyhton: "'12.5'") otherwise they will be taken
as numbers. Multiple property/value pairs are allowed
but must have matching numbers
-e EXPRESSION, --expression=EXPRESSION
expression to apply, ex: attributes.update( { "toto" :
12, "tutu" : [ 1.2, 12.5 ] } , or del attributes[
"toto" ]
Aims3DPointCloud
Aims3DPointCloud
----------------
Generates cloud of 3D points
Options :
-i | --input <string>
input coordinates file
-o | --output <filename: mesh of VOID>
output mesh
-r | --radius <FLOAT>
sphere radius
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsActivPixel2Volume
AimsActivPixel2Volume
---------------------
Convert an Activ pixel list file into a volume
Options :
-i <file name (read only): volume of S16>
origin file
-p <string>
activ pixels list file
[ -o <filename: volume of S16> ]
output image [default=input]
[ -l <S16> ]
filling value [default=255]
[ -x <FLOAT> ]
value of translation along x axis [default=0.0]
[ -y <FLOAT> ]
value of translation along y axis [default=0.0]
[ -z <FLOAT> ]
value of translation along z axis [default=0.0]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsAdaptiveSelVoxel
---------------------------------------------------------------------------
AimsAdaptiveSelVox-TD -i[nput] < input file Image >
--grd[adient] < input file Gradient Norm >
-o[output] < fileout (NO EXTENSION) >
--tIma [threshold IMAGE] <seuil % Short >
--tGrd [threshold GRADIENT] <seuil % Short >
--psg < Prob 'sans' gradient <float> >
--pagMin < Prob 'avec' gradient MIN float >
--pagMax < Prob 'avec' gradient MAX float >
[-h[elp]]
---------------------------------------------------------------------------
Create an image of selected voxel
---------------------------------------------------------------------------
AimsAddNoise2Data
AimsAddNoise2Data
-----------------
Add gaussian or uniform noise to data
Options :
-i | --input <string>
input data file
-o | --output <string>
output data file
[ -m | --mean <FLOAT> ]
mean of the Gaussian distribution [default=0.0]
[ -s | --sigma <FLOAT> ]
standard deviation of the Gaussian distribution
[ -u | --uniform <boolean> ]
take a uniform distribution rather than gaussian
[ -I | --Inferior <FLOAT> ]
lowest value of uniform distribution
[ -S | --Superior <FLOAT> ]
highest value of uniform distribution
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsAffineRegister
AimsAffineRegister
------------------
Registration according to Mutual Information Method
Options :
[ -f <vector of string> ]
freedom degrees (Tx, Ty, Tz, Rx, Ry, Rz, Sx, Sy, Sz, Cx, Cy, Cz)
[ -r <string> ]
source S16 reference data
[ -t <string> ]
source S16 test data (to register)
[ -o <string> ]
destination S16 data
[ -l <string> ]
logger
[ --Tx <FLOAT> ]
init Translation coord
[ --Ty <FLOAT> ]
init Translation coord
[ --Tz <FLOAT> ]
init Translation coord
[ --Rx <FLOAT> ]
init Rotation coord
[ --Ry <FLOAT> ]
init Rotation coord
[ --Rz <FLOAT> ]
init Rotation coord
[ --Sx <FLOAT> ]
init Scaling coord
[ --Sy <FLOAT> ]
init Scaling coord
[ --Sz <FLOAT> ]
init Scaling coord
[ --Cx <FLOAT> ]
init Shear coord
[ --Cy <FLOAT> ]
init Shear coord
[ --Cz <FLOAT> ]
init Shear coord
[ --dTx <FLOAT> ]
increment for variable Tx
[ --dTy <FLOAT> ]
increment for variable Ty
[ --dTz <FLOAT> ]
increment for variable Tz
[ --dRx <FLOAT> ]
increment for variable Rx
[ --dRy <FLOAT> ]
increment for variable Ry
[ --dRz <FLOAT> ]
increment for variable Rz
[ --dSx <FLOAT> ]
increment for variable Sx
[ --dSy <FLOAT> ]
increment for variable Sy
[ --dSz <FLOAT> ]
increment for variable Sz
[ --dCx <FLOAT> ]
increment for variable Cx
[ --dCy <FLOAT> ]
increment for variable Cy
[ --dCz <FLOAT> ]
increment for variable Cz
[ --dir <string> ]
output filename for direct transform parameter
[ --inv <string> ]
output filename for inverse transform parameter
[ --interpolation <string> ]
interpolation nearest/linear/spline [default=linear]
[ --optimizer <string> ]
optimizer powell/random/single [default=powell]
[ --pdfcalc <string> ]
pdf calculus mode direct/pv [default=direct]
[ --gcinit <string> ]
init with GravCenter yes/no [default=yes]
[ --index <string> ]
index to be optimized mi/cr [default=mi]
[ --refstartpyr <LONG> ]
start resolution level of the multiresolution optimization for ref
[ --refendpyr <LONG> ]
end resolution level of the multiresolution optimization for ref
[ --teststartpyr <LONG> ]
start resolution level of the multiresolution optimization for test
[ --testendpyr <LONG> ]
end resolution level of the multiresolution optimization for test
[ --serialnum <LONG> ]
number of the frame to consider for ref
[ --pays_size <LONG> ]
half size the volume generated if algo=other activated
[ --graylevel <LONG> ]
numb of classes in histogram pdf estimation [def.=64]
[ --masksize <LONG> ]
size of the gaussian convolution mask in pdf estimation for Mutual
Information [default=5]
[ --error <FLOAT> ]
tolerance on results [default=0.00001]
[ --seuiltest <FLOAT> ]
relative thresh applied prior to grav cent estimation
[ --seuilref <FLOAT> ]
relative thresh applied prior to grav cent estimation
[ --verbosity <LONG> ]
verbose level
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
terminate called after throwing an instance of 'carto::user_interruption'
what(): user interruption
AimsAmyloidDensity
AimsAmyloidDensity
------------------
Interpolation of plaques
Options :
-i <file name (read only): volume of S16>
Input proba plaques image
-m <file name (read only): volume of S16>
Input Binary Mask
[ -r <DOUBLE> ]
Radius of STRUCT ELEMT
-o <filename: volume of DOUBLE>
Output image
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsAmyloidDetection
AimsAmyloidDetection
--------------------
Detection of plaques
Options :
-i <file name (read only): volume of RGB>
Input RGB image
-o <filename: volume of RGB>
Output RGB proba image
-d <filename: N3bio7DpyDataE>
Output features data file
[ -s <S32> ]
Shape paremeter [Default=10]
[ -a <FLOAT> ]
Maximal area [Default=0.05]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsAmyloidFiltering
AimsAmyloidFiltering
--------------------
Filtering Amyloid Plaques detected
Options :
-rgb <file name (read only): volume of RGB>
Input original RGB image
-bin <file name (read only): volume of S16>
Input detected AP binary image
-mask <file name (read only): volume of S16>
Input tissue mask binary image
[ -ms <S32> ]
Mimimal AP size [Defaut: 2]
[ -Ms <S32> ]
Maximal AP size [Default: 1000]
[ -a <FLOAT> ]
Maximal anisotropy accepted [Default: 3]
-d <filename: N3bio7DpyDataE>
Output AP final DPY file
-o <filename: volume of S16>
Output AP final image
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsAmyloidLoadAvgDistNeigh
AimsAmyloidLoadAvgDistNeigh
---------------------------
Interpolation of plaques
Options :
[ -i <file name (read only): volume of S16> ]
Input proba plaques image
[ -m <file name (read only): volume of S16> ]
Input Binary Mask
[ -o <filename: volume of DOUBLE> ]
Output image
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsAmyloidLoadInvSurfVor
AimsAmyloidLoadInvSurfVor
-------------------------
Interpolation of plaques
Options :
[ -i <file name (read only): volume of S16> ]
Input proba plaques image
[ -m <file name (read only): volume of S16> ]
Input Binary Mask
[ -o <filename: volume of DOUBLE> ]
Output image
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsAmyloidMRIDetection
AimsAmyloidMRIDetection
-----------------------
Detection of plaques
Options :
[ -i <file name (read only): volume of RGB> ]
Input RGB image
[ -o <filename: volume of RGB> ]
Output RGB proba image
[ -d <string> ]
Output features data file
[ -s <S32> ]
Shape paremeter [Default=10]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsApplyVectorField
AimsApplyVectorField
--------------------
Apply a vector field to a simple mesh or to all meshes of a fold graph
Options :
-i | -input <string>
input mesh/graph data
[ -o | -output <string> ]
output mesh/graph (default: trans_input)
-t | -target <string>
target volume header
-v | -vectorfield <string>
vector field prefix (will add .x, .y and .z)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsAreaNbConnectCompRatio
AimsAreaNbConnectCompRatio
--------------------------
Evolution of the Area/Nb connected comp Ratio
Options :
-i <file name (read only): volume of FLOAT>
Input image
[ -m <file name (read only): volume of FLOAT> ]
mask image
[ -n <S32> ]
number of bins [default : 255]
[ -r <string> ]
Text output
-d <filename: volume of FLOAT>
Data array output
-o <filename: volume of FLOAT>
Thresholded image
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsAttributedViewer
AimsAttributedViewer: cannot connect to X server
AimsAverage
AimsAverage
-----------
Averages several volume files or several images / slices of a file
Options :
-o <string>
output data
[ -t | --type <string> ]
output data type (S16, U8, FLOAT, ...)
[ -d | --dir <string> ]
if specified, perform averaging inside each file along this direction (x, y,
z or t)
[ -n | --num <string> ]
if a direction is specified, gives the volume or slice numbers to process.
ex: 2-20,24,26 (no space between numbers)
-i | --output | --input <vector of string>
input volumes
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsAxialProjection
AimsAxialProjection
-------------------
Colliculi parameters projection
Options :
[ -i <file name (read only): volume of S16> ]
input image
[ -m <file name (read only): volume of S16> ]
mask image
[ -o <filename: volume of DOUBLE> ]
output image
[ -p <string> ]
output parameters (ASCII)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsBinaryBorder
AimsBinaryBorder
----------------
Binary border computing
Options :
-i <file name (read only): volume of U8>
Input grey-level image
[ -c <U8> ]
Connexity 4 or 8 [default : 4]
-o <filename: volume of U8>
Output image
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsBlockMatching
AimsBlockMatching
-----------------
Compute registrations between two 2D or 3D volumes
Options :
-r <string>
input reference data
-t <string>
input test data
[ -o <string> ]
output data
[ -m <string> ]
initialisation motion (default = identity)
[ -n <string> ]
output motion (default = <test data directory>/<test>_TO_<ref>.trm)
[ --start <S32> ]
starting pyramid level (default = auto)
[ --stop <S32> ]
end pyramid level (default = auto)
[ --transfo <S32> ]
transformation type : 1 for rigid, 2 for similitude, 3 for affine (default
= 1)
[ --Xsize <S16> ]
x size of the bloc in voxel (default = 4)
[ --Ysize <S16> ]
y size of the bloc in voxel (default = 4)
[ --Zsize <S16> ]
z size of the bloc in voxel (default = 4)
[ --cutVar <DOUBLE> ]
% initial de blocs de plus forte variance conserves (default=auto)
[ --stopVar <DOUBLE> ]
minimum de ce % de blocs conserves (default=auto)
[ --%kept <DOUBLE> ]
% de blocs de plus faibles residus conserves pour l'estimation robuste
(default=0.5)
[ --correlThresh <DOUBLE> ]
threshold on the similarity criterion norm (default=-1, no threshold)
[ --lthRef <DOUBLE> ]
low grey level threshold on ref image (default = -100000)
[ --hthRef <DOUBLE> ]
high grey level threshold on ref image (default = +100000)
[ --lthTest <DOUBLE> ]
low grey level threshold on test image (default = -100000)
[ --hthTest <DOUBLE> ]
high grey level threshold on test image (default = +100000)
[ --iter <S32> ]
maximum number of iterations per pyramid level (default=3)
[ --field <string> ]
Displacement field
[ --Info <string> ]
list all the initial parameters : y or n (default=y)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsBorderCrop
AimsBorderCrop
--------------
Border croping
Options :
-i <file name (read only): volume of RGB>
Input RGB image
[ -b <U8> ]
Border_value, default : 255 (white)]
-o <filename: volume of RGB>
Output image
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsBorderGenerate
AimsBorderGenerate
------------------
Generate border around image
Options :
-i <string>
input data
[ -m <string> ]
mask for data
[ -bx <FLOAT> ]
border size (in mm) for x dimension
[ -by <FLOAT> ]
border size (in mm) for y dimension
[ -bz <FLOAT> ]
border size (in mm) for z dimension
[ -bv <string> ]
border value to use
[ -u <boolean> ]
use background instead of border when it is possible
[ -hxyz <boolean> ]
homogenize x, y and z borders using the maximum border size
[ -om <string> ]
output motion
-o <string>
output image
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsBorderInfo
AimsBorderInfo
--------------
Border info
Options :
-i <string>
Input image
[ -b <VECTOR_OF_3_S16> ]
Border width, default : (10 ,10 ,10)
[ -t <string> ]
Smoothing filter type: mea[n], med[ian], min[imum], max[imum], maj[ority]
(default = median)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsBorderLineProj
AimsBorderLineProj
------------------
Compute direct assess to image border
Options :
-i <file name (read only): volume of S16>
Input image
[ -o <string> ]
Output projection image [Default: extension *.proj added]
[ -od <string> ]
Output distance image [Default: extension *.dist added]
-bv <S16>
Background value
[ -m <string> ]
Mask image [Compute value if mask!=0]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsBoundingBox
AimsBoundingBox
---------------
Optical bounding box computation and resampling
Options :
[ -i <file name (read only): { Volume of DOUBLE, Volume of FLOAT, Volume of S16,
Volume of S32, Volume of S8, Volume of U16, Volume of U32, Volume of U8 }>
Input optical volume image ]
[ -o <string> ]
Output optical volume image with border
[ -b <string> ]
Output bounding box
[ -t <string> ]
Output transfo bounding box
[ --factor <S32> ]
Resample factor [Default : 1]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsBuildDti
AimsBuildDti
------------
Estimation of the Tensor Diffusion from a diffusion MR image
Options :
-i <file name (read only): volume of S16>
Diffusion image
[ -b <FLOAT> ]
bvalue used during acquisition (default = read from image)
[ -dti <filename: bucket of DTITENSOR> ]
DTI tensor output file name (default = not saved)
[ -m <string> ]
Mask of brain or white matter
[ -tr <filename: volume of FLOAT> ]
trace output file (default = not saved)
[ -vr <filename: volume of FLOAT> ]
volume ratio output file (default = not saved)
[ -fa <filename: volume of FLOAT> ]
fractional anisotropy output file (default = not saved)
[ -dir <filename: volume of POINT3DF> ]
directions output file (default = not saved)
[ -rgb <filename: volume of RGB> ]
RGB directions output file (default = not saved)
[ -em <filename: volume of U8> ]
Binary mask of bad voxels (default = not saved)
[ -g <FLOAT> ]
gamma diffusion coefficient for protons (default=42,57e6 . 2 Pi)
[ -r <boolean> ]
when a point is NOT_POSITIVE_MATRIX, replace by an isotropic tensor which
mean diffusivity is estimated on the N26 neighborhood of the point rather
than the mean diffusivity equal to trace / 3.0
[ --correct <FLOAT> ]
correct sites with negative eigen value
[ -verbose <boolean> ]
show as much information as possible
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsBuildIndex
AimsBuildIndex
--------------
Extract trace,frationnal and relative anisotropy, volume ratio, directions,
coherence index, lattice index, linear, planar and spherical measures from
dtitensor bucket
Options :
-i | --input <file name (read only): bucket of DTITENSOR>
source dtitensor bucket
[ -o | --output <string> ]
destination base file name
-x <S32>
dimensions of output images
-y <S32>
dimensions of output images
-z <S32>
dimensions of output images
[ --trace <boolean> ]
calculate trace <fileout_trace.ima>
[ --l1 <boolean> ]
calculate largest eigenvalue <fileout_lambda1.ima>
[ --l2 <boolean> ]
calculate second eigenvalue <fileout_lambda2.ima>
[ --l3 <boolean> ]
calculate third eigenvalue <fileout_lambda3.ima>
[ --fa <boolean> ]
calculate fractionnal anisotropy <fileout_fa.ima>
[ --vr <boolean> ]
calculate volume ratio <fileout_vr.ima>
[ --dir <boolean> ]
calculate the main direction <fileout_dir.ima>
[ --ra <boolean> ]
calculate relative anisotropy <fileout_ra.ima>
[ --ci <boolean> ]
calculate coherence index <fileout_ci.ima>. NB: This index is computed in
2D which seems meaningless
[ --li <boolean> ]
calculate lattice index <fileout_li.ima>
[ --m <boolean> ]
calculate linear, planar and spherical measures <fileout_linear.ima>,
<fileout_planar.ima>, <fileout_spherical.ima>
--all <boolean>
calculate all maps
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsBvalue
AimsBvalue
----------
B matrices for diffusion tensor sequence parameters
Options :
-i | --input <string>
source EPI sequence
-o | --output <string>
output volume name
[ -e | --eps <FLOAT> ]
integration relative error [1e-5]
[ -j | --jmax <S32> ]
maximum iteration number during integration [22]
[ -k <S32> ]
interpolation order for Romberg integration [10]
[ -a | --agrad <S32> ]
save gradients gx,gy,gz and their integrals
[ -g | --gamma <FLOAT> ]
gamma diffusion coefficient for protons [default=42,57e6 . 2 Pi]
[ -b | --bipolar <S32> ]
bipolar gradients [default=no]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsCenterSlices
AimsCenterSlices
----------------
Command that stacks images and uses gravity centers to coalign images
Options :
-i <list of string>
input files (1 minimum)
[ -dx <S32> ]
dx dimension [Default: input]
[ -dy <S32> ]
dy dimension [Default: input]
[ -z <FLOAT> ]
z thickness [Default: input]
[ -resol <FLOAT> ]
scan resolution [Default: input voxelsize]
[ -rx <FLOAT> ]
scan resolution for X [Default: input X voxelsize]
[ -ry <FLOAT> ]
scan resolution for Y [Default: input Y voxelsize]
[ -vs <string> ]
voxel size unit (mm or dpi) [Default: dpi]
[ -usegc <boolean> ]
uses gravity center to center slices [Default: true]
[ -ratio <FLOAT> ]
seuil = % max [default 0.15 = 15%]
[ -v <string> ]
values of interest high/low [Default=low]
-o <string>
output image
[ -t <string> ]
output translations list [default=not written]
[ -m <string> ]
output motion base name [default=not written]
[ -c <U8> ]
Channel to use to process multi-channel image
Possible types and values:
type : RGB or RGBA
values: 0=red, 1=green, 2=blue, 3=norm
type : HSV
values: 0=hue, 1=saturation, 2=value, 3=norm
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsChamferDistanceMap
AimsChamferDistanceMap
----------------------
Chamfer distance map on a volume
Options :
-i | --input <file name (read only): volume of S16>
source volume
-o | --output <filename: volume of FLOAT>
destination volume
[ -x | --xmask <S32> ]
X size of the distance mask [default=3]
[ -y | --ymask <S32> ]
Y size of the distance mask [default=3]
[ -z | --zmask <S32> ]
Z size of the distance mask [default=3]
[ -f | --factor <FLOAT> ]
chamfer multiplication factor [default=50]
[ -s | --side <string> ]
OUTSIDE, INSIDE, SIGNED [default=SIGNED]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsCheck2DCoordinates
AimsCheck2DCoordinates
----------------------
[UNCOMPLETE DEBUG FUNCTION] Check that a 2D surface-based coordinate system is
OK (unicity)
Options :
-m | --mesh <string>
input mesh
-x | --xcoord <string>
latitude texture
-y | --ycoord <string>
longitude texture
-o | --out <string>
output sign texture
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsClosing
AimsClosing
-----------
Chamfer closing on a volume
Options :
-i | --input <file name (read only): volume of S16>
source volume
-o | --output <filename: volume of S16>
destination volume
-r | --radius <FLOAT>
radius of the structuring element
[ -x | --xmask <S32> ]
X size of the distance mask [default=3]
[ -y | --ymask <S32> ]
Y size of the distance mask [default=3]
[ -z | --zmask <S32> ]
Z size of the distance mask [default=3]
[ -f | --factor <FLOAT> ]
chamfer multiplication factor [default=50]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsClusterArg
AimsClusterArg
--------------
Builds a graph (cluster graph) from an image
Options :
-i | --input <file name (read only): { Volume of FLOAT, Volume of S16, Volume
of U8 }> input data
[ -o | --output <string> ]
output .arg graph file (default: <input>.arg)
[ -g | --graphtype <string> ]
graph type to produce: c (cluster) or f (cortical folds). default: cluster
[ -t | --trans <string> ]
transformation matrix to Talairach space (default: none)
[ -c | --connectivity <string> ]
connectivity type (4xy / 4xz / 4yz / 6 / 8xy / 8xz / 8yz / 18 / 26),
default: 18
[ -s | --size <S32> ]
min cluster size (default: 0)
[ -b | --binarize <boolean> ]
binarize volume (after thresholding) before processing connectivity stuff
[ -l | --lowth <FLOAT> ]
lower threshold, values under this one are set to zero (background)
(default: none)
[ -u | --upth <FLOAT> ]
upper threshold, values above this one are set to zero (background)
(default: none)
[ -m | --mesh <boolean> ]
make cluster meshes (default: y)
[ --deciMaxClearance <FLOAT> ]
maximum clearance of the decimated mesh expected is <clearance> mm
[default=5.]
[ --deciMaxError <FLOAT> ]
maximum error distance from the original mesh expected is <error> mm ,
[default=0.1]
[ --minFacetNumber <U32> ]
minimum number of facets to allow decimation [default=50]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsCompareSPMtToPrimalSketch
AimsCompareSPMtToPrimalSketch
-----------------------------
Select blobs in a PS that are the closest to selected activations in a SPMt -
EXPERIMENTAL. Blobs that are selected are given the activation label in their
'name' attribute
Options :
-p | --primal <file name (read only): Graph>
PS graph
-s | --spmt <file name (read only): volume of S16>
spmt image
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsComposeTransformation
AimsComposeTransformation
-------------------------
Composes two Aims/anatomist transformations: M1 x M2 [Possibility to use a list
of motions with -i option]
Options :
[ -i <list of string> ]
M1: 1st input transformation
[ -j <string> ]
M2: 2nd input transformation [option]
[ -o <string> ]
output transformation (default: same as 1st input)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsConformalMapping
AimsConformalMapping
--------------------
Spherical conformal parameterization of a mesh
Options :
-i | --input <string>
input mesh
[ -dt | --deltat <FLOAT> ]
time step (recommended : 0.1, nothing above that for stability)
[ -de | --deltae <FLOAT> ]
energy variation threshold for convergence (recommended : 0.001)
-o | --output <string>
output mesh
-l | --lat <string>
latitude texture
-L | --lon <string>
longitude texture
[ -t | --tuette <string> ]
Tuette map precomputed mesh
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsConnectComp
AimsConnectComp
---------------
Extract connected components of a binary data volume
Options :
-i | --input <file name (read only): { Bucket of S16, Bucket of VOID, Volume of
S16 }> input SHORT binary volume
-o | --output <string>
output labelled connected components volume
[ -c | --connectivity <string> ]
connectivity 4xy / 4xz / 4yz / 6 / 8xy / 8xz / 8yz / 18 / 26 [default=26]
[ -s | --size <ULONG> ]
minimum size of the seeds [default=0]
[ -n <ULONG> ]
number of components kept [default=all]
[ -b <boolean> ]
force binary mode [default=false]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsConstraintCleaner
AimsConstraintCleaner
---------------------
Cortical Constraints Cleaning (for cortical surface coordinate system)
Options :
-m | --inMesh <string>
input Mesh
-t | --inTexCingularPole <string>
input Texture Cingular Pole
-p | --inTexPoles <string>
Poles Textures
-x | --inTexMer <string>
input Texture Meridian Constraints
-y | --inTexPar <string>
input Texture Parallel Constraints
-f | --inCorrFile <string>
input Constraint Correspondance File
-g | --inProjFile <string>
input Projected constraint Correspondance File
-a | --outMer <string>
outut Texture Cleaned Meridian Constraints
-b | --outPar <string>
output Texture Cleaned Parallel Constraints
-i | --constraint_distance <FLOAT>
constraint distance parameter
-j | --curvature <FLOAT>
curvature parameter
-k | --elasticity <FLOAT>
elasticity parameter
-c | --context <S32>
context
-s | --side <string>
side (left or right)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsConvexHull
AimsConvexHull
--------------
Build triangulation of the convex hull of a list of points
Options :
-i <string>
file containing 3D points. The file is an ASCII text file. The first line
should indicate the number of points, the other lines are each one of the
points, with x, y, z coordinates separated by spaces. Actually the line
breaks are nor needed but the order of values should be respected.
-o <filename: mesh of VOID>
output mesh file
[ -s <boolean> ]
add symetric directions
[ --ascii <boolean> ]
output mesh file in ASCII (if supported by the output format)
[default:binary]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsCoordinateGridMesh
AimsCoordinateGridMesh
----------------------
generate iso-parameter lines from a mesh and textures
Options :
-m | --mesh <string>
input mesh
-x | --xcoord <string>
latitude texture (or -x for sulci)
-y | --ycoord <string>
longitude texture (or -y for sulci)
-c | --coord <string>
coordinates (r=regular, c=constraints, s=sillon)
-o | --out <string>
output mesh
[ -d | -diameter <FLOAT> ]
tubes diameter (default=0.25)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsCoordinatesTextureToMesh
AimsCoordinatesTextureToMesh
----------------------------
Creates a mesh from 3 coordinates textures (x,y and z)
Options :
-i | --inputMesh <string>
input mesh
-x | --inputx <string>
texture_x
-y | --inputy <string>
texture_y
-z | --inputz <string>
texture_z
-o <string>
output mesh
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsCoordinatesToIndex
AimsCoordinatesToIndex
----------------------
get the index of a point from its 2D surface coordinates
Options :
-i | --inputMesh <string>
input mesh
-l | --lat <string>
latitude texture
-L | --lon <string>
longitude texture
-x <FLOAT>
latitude
-y <FLOAT>
longitude
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsCoordinatesToTexture
AimsCoordinatesToTexture
------------------------
Create 3 textures of node coordinates
Options :
-i | --inputMesh <string>
input mesh
-x | --outx <string>
texture_x
-y | --outy <string>
texture_y
-z | --outz <string>
texture_z
-l | --local <S32>
local coordinates transo (yes=1, default=0)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsCorrectImages
AimsCorrectImages
-----------------
Correct pixels intensity in the overlapping region of a pair of images (Mosaic
reconstruction)
Options :
-ref <string>
Input reference image (Top or Left)
-test <string>
Input test image (Bottom or Right)
-tx <S32>
translation along X axis
-ty <S32>
translation along Y axis
-d <S32>
mosaicing direction axis
1 : Horizontal
2 : Vertical
-type <S32>
Data type :
S16 : 1
U8 : 2
FLOAT : 3
RGB : 4
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsCorrectionEpi
AimsCorrectionEpi
-----------------
Correction of echoplanar distortions in DW MR image
Base on a model of geometric distortion characterized by:
- a scaling S,
- a translation T0,
- a shearing T1
Options :
-t2 <file name (read only): volume of S16>
T2 image
-dw <file name (read only): volume of S16>
Diffusion-weighted image
-o <filename: volume of S16>
Corrected Diffusion-weighted image
[ -divider <S32> ]
divider for subresolution calculations (default=1)
[ -levels <S32> ]
number of graylevels in MI calculations (default=64)
[ -smoothing <string> ]
pdf smoothing deriche/discrete (default=discrete)
[ -sigma <FLOAT> ]
discrete : gaussian mask size (default=3)
deriche : gaussian std dev. (default=3.0mm)
[ -deltaS <FLOAT> ]
variation of S (default=0.05)
[ -deltaT0 <FLOAT> ]
variation of T0 (default=1.00)
[ -deltaT1 <FLOAT> ]
variation of T1 (default=0.01)
[ -error <FLOAT> ]
tolerance on results (default=0.005)
[ -memMap <boolean> ]
memory mapping activated (default=no)
[ -parameters <string> ]
(S,T0,T1) parameter text file name [default=not saved]
[ -verbose <boolean> ]
show as much information as possible
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsCorticalReferential
AimsCorticalReferential
-----------------------
Diffusion of mesh-based coordinates with constraints
Options :
-i <string>
input Surface Mesh
-p <string>
input Texture Parallel Constraints
-m <string>
input Texture Meridian Constraints
-l <string>
input Texture Corpus Callosum Pole
-r <string>
input Texture Poles
-c <FLOAT>
Max difference stop criterium for the diffusion process ( default = 1e-6 )
-d <FLOAT>
Iterative step ( default = 0.2 )
-b <S32>
Context (in order to swap 0/360 around central sulcus if necessary)
-f <S32>
process choice : 1 latitude only 2 longitude only 3 none 0 latitude and
longitude
-t <FLOAT>
data-driven weight
-a <S32>
Beta Map (1=Yes, 0=No)
-x <string>
output Latitude Texture
-y <string>
output Longitude Texture
[ --insula <boolean> ]
do parameterize insula
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsCorticalThickness
AimsCorticalThickness
---------------------
AimsMeshMedianSurface
Options :
-i <string>
White Hemisphere Mesh
-e <string>
Grey/CSF Hemisphere Mesh
[ -v <string> ]
Neighbours table file (from "arrival" mesh)
-d <U32>
Process direction (int -> ext || ext -> int)
[ -vout <string> ]
Output file in case the neighbours table would not be available and should
be computed (6th order by default)
[ -o <string> ]
Output width texture
[ -v2 <string> ]
[DEBUG ONLY] Neighbours table file (from "other arrival" mesh)
[ -m <string> ]
If provided, saves the created median mesh used for thickness computation
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsCreateFieldsFromMotion
AimsCreateFieldsFromMotion
--------------------------
Create the resampling field from a motion
Options :
-m <string>
Input motion
-r <string>
Reference image
-o <string>
Output field
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsCreateTexture
AimsCreateTexture
-----------------
Map a volume on the mesh in the normal direction
Options :
-m | --mesh <file name (read only): mesh of VOID>
input_mesh
-v | --volume <string>
input_volume
-t | --texture | -o <string>
output_texture
[ --ascii <boolean> ]
write texture file in ASCII [default=false]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsCurvature2d
AimsCurvature2d
---------------
2D curvature of an intensity image f(x,y) = I
Options :
-i | --input <file name (read only): volume of S16>
source matrix
-o | --output <filename: volume of FLOAT>
destination float matrix
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsCurvature3d
AimsCurvature3d
---------------
2D curvature of an intensity image f(x,y) = I
Options :
-i | --input <file name (read only): volume of S16>
source matrix
-o | --output <filename: volume of FLOAT>
destination float matrix
[ -g | --gaussian <boolean> ]
use gaussian curvature [default=mean]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsCylinder
AimsCylinder
------------
2D curvature of an intensity image f(x,y) = I
Options :
-e | --eigen <file name (read only): volume of POINT3DF>
source eigen vectors file
[ -o | --output <filename: mesh of VOID> ]
output mesh file [default=<eigen>.mesh]
[ -m | --mask <file name (read only): volume of U8> ]
mask on the eigen vectors file
[ -a | --aniso <file name (read only): volume of FLOAT> ]
anisotropy file to give a length
[ -x <S32> ]
(x,y,z),(X,Y,Z) defines a sub-volume of interest
[ -y <S32> ]
[ -z <S32> ]
[ -X <S32> ]
[ -Y <S32> ]
[ -Z <S32> ]
[ -t | --topLength <FLOAT> ]
maximum length of the cylinders [default=3.0]
[ -r | --radius <FLOAT> ]
radius of the cylinders [default=0.2]
[ -n <S32> ]
number of division on 2 disk faces of the cylinders [default=6]
[ -l <S32> ]
number of triangles on each division [default=2]
[ -g <FLOAT> ]
lower threshold for anisotropy; an eigen vector is valid if its anisotropy
is greater or equal to <g> [default=0.5]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsDanielssonDist
-------------------------------------------------------------------------
AimsDanielssonDistanceMap -i[nput] <filein>
-o[utput] <fileout>
[-s[ide] <S>] [-h[elp]]
-------------------------------------------------------------------------
Danielsson's distance map on a volume
-------------------------------------------------------------------------
filein : source volume
fileout : destination volume
S : OUTSIDE, INSIDE, SIGNED [default=SIGNED]
-------------------------------------------------------------------------
AimsData2Jpeg
-------------------------------------------------------------------------
AimsData2Jpg -i[nput] <input>
-o[utput] <output>
-d[ir] <dir>
[-s[lice] <slice>]
[-t[ime] <time> ]
[-b[egin] <begin>]
[-e[nd] <end>]
[-m[in] <minimum>]
[-M[ax] <maximum>]
[-c[olormap] <cmap>]
[-I[ncrement] <inc>]
[-h[elp]]
-------------------------------------------------------------------------
JPEG or PostScript grab on data
( S8, U8, S16, U16, S32, U32, FLOAT, DOUBLE )
-------------------------------------------------------------------------
input : input data file
output : output file name for *.jpg or *.ps file
dir : direction of the slice ('x', 'y' or 'z')
slice : index of the slice to grab [default=all slices]
time : time of the volume where to select slice [default=0]
begin : start the grab from the beginth slice [default=0]
end : stop the grab at the endth slice [default=dim-1]
minimum : lower float threshold on data
maximum : upper float threshold on data
cmap : color map file [default=greyscale]
inc : increment of slices between two grabs
Structure of the cmap file :
ncolor |=> number of entries
R G B |=> 1st color
R G B |=> 2nd color
. . .
. . .
. . .
. . .
R G B |=> last color
-------------------------------------------------------------------------
AimsDilation
-------------------------------------------------------------------------
AimsDilation -i[nput] <filein>
-o[utput] <fileout>
-e[radius] <radius>
[-x[mask] <xxx>] [-y[mask] <yyy>] [-z[mask] <zzz>]
[-f[actor] <fff>]
[-h[elp]]
-------------------------------------------------------------------------
Morphological dilation
-------------------------------------------------------------------------
filein : source volume
fileout : destination volume
radius : radius of the structuring element
xxx : X size of the distance mask [default=3]
yyy : Y size of the distance mask [default=3]
zzz : Z size of the distance mask [default=3]
fff : chamfer multiplication factor [default=50]
-------------------------------------------------------------------------
AimsDistordDti
-------------------------------------------------------------------------
AimsDistordDti -R[eference] <ref>
-d[istorded] <dist>
--S <S>
--T0 <T0>
--T1 <T1>
[--interpolator <interpolator>]
[-h[elp]]
-------------------------------------------------------------------------
Distord DTI
-------------------------------------------------------------------------
ref : source S16 data
dist : distorded S16 data
S : magnification
T0,T1 : translation T = T0 + T1 * x
interpolator : nearest/linear/spline [default=linear]
-------------------------------------------------------------------------
AimsDivide
------------------------------------------------------------------
AimsDivide -n[um] <i1>
-d[en] <i2>
-o[utput] <fileout>
[-t[ype] <datatype>]
[-h[elp]]
------------------------------------------------------------------
Division I1/I2
------------------------------------------------------------------
i1 : numerator data
i2 : denominator data
fileout : destination data
datatype: output data type (S16, U8, ...). Default = i1 type
------------------------------------------------------------------
AimsDtiBck2Vol
------------------------------------------------------------------
AimsDtiBck2Vol -i[nput] <bucket>
[-o[utput] <dti>]
[-x <dimx> -y <dimy> -z <dimz>]
[-h[elp]]
------------------------------------------------------------------
Convert a DTI bucket to a FLOAT tensor image
------------------------------------------------------------------
bucket : input DTI bucket data
dti : destination FLOAT tensor data [default=bucket]
dimx,dimy,
dimz : dimensions of the destination volume
------------------------------------------------------------------
AimsElevationMap
AimsElevationMap
----------------
Convert 2D data in surface
Options :
-i <file name (read only): { Volume of DOUBLE, Volume of FLOAT, Volume of S16,
Volume of S32, Volume of S8, Volume of U16, Volume of U32, Volume of U8 }>
Input 2D short image
-o <filename: mesh of VOID>
Output surface
[ -of <filename: mesh of VOID> ]
Output flat surface [default: not written]
[ -ob <filename: mesh of VOID> ]
Output border surface [default: not written]
[ -s <FLOAT> ]
Scale factor (intensity)
[ --inv <boolean> ]
Inverse grey level [default=no]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsEntropicThresholding
AimsEntropicThresholding
------------------------
Entropic thresholding
Options :
-i <file name (read only): volume of U8>
Input grey-level image
[ -b <S32> ]
Binary threshold or not [default : 0]
[ -min <U8> ]
Minimal value of the entropic threshold [default : 1]
[ -max <U8> ]
Minimal value of the entropic threshold [default : 255]
-o <filename: volume of U8>
Output image
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsEqualizer
-------------------------------------------------------------------------
AimsEqualizer -i [eference] <ref>
-o [utput] <fileout>
[-h[elp]]
-------------------------------------------------------------------------
AimsErosion
-------------------------------------------------------------------------
AimsErosion -i[nput] <filein>
-o[utput] <fileout>
-e[radius] <radius>
[-x[mask] <xxx>] [-y[mask] <yyy>] [-z[mask] <zzz>]
[-f[actor] <fff>]
[-h[elp]]
-------------------------------------------------------------------------
Morphological erosion
-------------------------------------------------------------------------
filein : source volume
fileout : destination volume
radius : radius of the structuring element
xxx : X size of the distance mask [default=3]
yyy : Y size of the distance mask [default=3]
zzz : Z size of the distance mask [default=3]
fff : chamfer multiplication factor [default=50]
-------------------------------------------------------------------------
AimsExactDepthArea
AimsExactDepthArea
------------------
Compute the Exact Geodesic Depth Map
Options :
-im | --inputMesh <string>
mesh
-it | --inputTexContour <string>
input texture (contour area)
-ot | --inputTexDepth <string>
output texture (depth map)
-v | --inputValue <S32>
texture value contour
[ -c | --constraint <S32> ]
constraintType:
"0" -> no constraint
"1" -> constrained sulci
"2" -> constrained gyri
"3" -> Exact geodesic path
"4" -> Euclidian distance
"5" -> z value
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsExtractGyrus
AimsExtractGyrus
----------------
Extract a particular gyrus from a mesh and its gyri texture
Options :
-m | --mesh <string>
input mesh
-t | --tex <string>
gyri texture
-g | --gyrus <FLOAT>
gyrus index
-lat | --latitude <string>
latitude texture
-lon | --longitude <string>
longitude texture
-o | --out <string>
output gyrus name pattern
[ -dt <FLOAT> ]
diffusion time step (default=0.01)
[ -delta <FLOAT> ]
diffusion stoping criterion (default=0.0001)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsFFD
AimsFFD
-------
Estimation of FFD deformation
Options :
[ -r <string> ]
Input reference image
[ -t <string> ]
Input test image
[ -o <string> ]
Output image
[ -l <string> ]
List of VOID bucket
[ -d <string> ]
Rigid initial displacement <ref_TO_test>
[ -initFFD <string> ]
Initial FFD field <ctrlshift.ima>
[ -initDEP <string> ]
Initial Displacement field <Ex: derived from BlockMatching>
[ -icx <S32> ]
Initial number of control knots / X
[ -icy <S32> ]
Initial number of control knots / Y
[ -icz <S32> ]
Initial number of control knots / Z
[ -fcx <S32> ]
Final number of control knots / X
[ -fcy <S32> ]
Final number of control knots / Y
[ -fcz <S32> ]
Final number of control knots / Z
[ -ix <S16> ]
Increment number of control knots / X
[ -iy <S16> ]
Increment number of control knots / Y
[ -iz <S16> ]
Increment number of control knots / Z
[ -scoef <S32> ]
Reduction of the coefficient / pyramid level [default=1= cste]
[ -sfin <FLOAT> ]
Threshold of the last pyramid level < Gain min [default=0.01]>
[ -interFile <boolean> ]
To write all intermediates files [default=false]>
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsFFD2d
AimsFFD2d
---------
Estimation of FFD2d deformation
Options :
[ -r <string> ]
Input reference image
[ -t <string> ]
Input test image
[ -o <string> ]
Output image
[ -l <string> ]
List of VOID bucket
[ -d <string> ]
Rigid initial displacement <ref_TO_test>
[ -initFFD <string> ]
Initial FFD field <ctrlshift.ima>
[ -initDEP <string> ]
Initial Displacement field <Ex: derived from BlockMatching>
[ -icx <S32> ]
Initial number of control knots / X
[ -icy <S32> ]
Initial number of control knots / Y
[ -fcx <S32> ]
Final number of control knots / X
[ -fcy <S32> ]
Final number of control knots / Y
[ -ix <S16> ]
Increment number of control knots / X
[ -iy <S16> ]
Increment number of control knots / Y
[ -scoef <S32> ]
Reduction of the coefficient / pyramid level [default=1= cste]
[ -sfin <FLOAT> ]
Threshold of the last pyramid level < Gain min [default=0.01]>
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsFFDApply
AimsFFDApply
------------
*** Apply FFD ***
Options :
-i <string>
Input image
[ -d <string> ]
Input control knots grid
[ -m <string> ]
Input affine transformation [Test_TO_Ref.trm]
[ -bv <S16> ]
Background value to use
-o <string>
Output image
[ -b <string> ]
Output bucket knots
[ -g <string> ]
Output grid mesh
[ -c <string> ]
Output compression volume
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsFFDApply2d
AimsFFDApply2d
--------------
*** Apply FFD2d ***
Options :
[ -i <file name (read only): volume of S16> ]
Input image
[ -d <file name (read only): volume of POINT2DF> ]
Input control knots grid
[ -o <filename: volume of S16> ]
Output image
[ -b <filename: bucket of VOID> ]
Output bucket knots
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsFileConvert
AimsFileConvert
---------------
Performs file format and data conversion
Options :
-i | --input <file name (read only): { Bucket of DTITENSOR, Bucket of S16,
Bucket of VOID, Mesh of VOID, Mesh4 of VOID, Motion of VOID, Segments of
VOID, Texture of FLOAT, Texture of POINT2DF, Texture of S16, Texture of S32,
Texture of U32, Texture of unsigned integer, Volume of CDOUBLE, Volume of
CFLOAT, Volume of DOUBLE, Volume of FLOAT, Volume of HSV, Volume of
POINT3DF, Volume of RGB, Volume of RGBA, Volume of S16, Volume of S32,
Volume of S8, Volume of U16, Volume of U32, Volume of U8, Volume of
VECTOR_OF_3_SHORT, Volume of VECTOR_OF_6_FLOAT }> input data filename to
convert
-o | --output <string>
output filename
[ -e | --encoding <S32> ]
set the data encoding for any output file.
0 : Binary (default)
1 : ASCII
2 : Base64 binary (for gifti format only)
3 : Base64 compressed binary (for gifti format only)
[ -n | --normal <boolean> ]
write normal in output file
[ -r | --rescale <boolean> ]
rescale output values to amplitude of output format (if output format is an
integer variant)
[ --imin <DOUBLE> ]
specify input minimum value for rescaling.
[ --imax <DOUBLE> ]
specify input maximum value for rescaling.
[ --omin <DOUBLE> ]
specify output minimum value for rescaling.
[ --omax <DOUBLE> ]
specify output maximum value for rescaling.
[ --itypelimits <boolean> ]
uses input type limits instead of dynamic min max to rescale data dynamic.
[ -f | --format <string> ]
force a specific output format (GIS, VIDA, ...) (default: guessed by the
output filename extension)
[ -t | --type <string> ]
output data type (only applicable to volumes or textures of scalars,
default: same as input)
[ -c | --change | --otype <string> ]
change object type in addition to data type, currently only applicable to
Bucket of VOID <-> Volume
[ -x | --xdim <U32> ]
(for output volumes only) forces output volume dimension
[ -y | --ydim <U32> ]
(for output volumes only) forces output volume dimension
[ -z | --zdim <U32> ]
(for output volumes only) forces output volume dimension
[ --orient <string> ]
change/force output volume voxels orientation on disk (if the output format
supports it), with different syntaxes:
--orient "flipx yflip": flips orientations of x and y axes.
--orient neuro or --orient neurological or --orient left-to-right: force
neuro orientation.
--orient radio or --orient radiological or --orient right-to-left: force
radio orientation.
--orient "-1 1 -1": set a flip matrix flipping x and z axes.
--orient "-1 0 0 0 1 0 0 0 -1": same by specifying the full rotation
matrix.
--orient "-1 0 0 255 0 1 0 0 0 0 -1 123 0 0 0 1": same by specifying the
full 4x4 matrix.
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsFileInfo
AimsFileInfo
------------
Give information about a data file (any file Aims can read)
Options :
-i | --input <string>
input data file
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose | -v [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsFlattenCortex
AimsFlattenCortex
-----------------
Create a flat representation of a cortical mesh if it has been parameterised
Options :
-m | --mesh <string>
input mesh
-x | --xcoord <string>
latitude texture
-y | --ycoord <string>
longitude texture
-t | --tex <string>
texture
-om | --outM <string>
output mesh
-oi | --outI <string>
output ima
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsFlip
AimsFlip
--------
Image flip
Options :
-i | --input <string>
input image to flip
-o | --output <string>
output flipped image
-m <string>
flip image XX, YY, ZZ, XXYY, XXZZ, YYZZ, XXYYZZ, or flip axes : XY, XZ, YZ
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsFoldArgAtt
AimsFoldArgAtt
--------------
Builds cortical folds graph attributes - replaces VipFoldArgAtt
Options :
-i <file name (read only): volume of S16>
skeleton image
-g <file name (read only): Graph>
fold graph
[ -o <filename: Graph> ]
output fold graph [default: input]
[ -m <string> ]
transformation to Talairach [default: none]
[ -n | --nomesh <boolean> ]
don't generate meshes
[ --apc <string> ]
set AC/PC/IH points in graph from a .APC file [default: don't set them]
[ -li <S16> ]
'inside' label on skeleton image [default: 0]
[ -lo <S16> ]
'outside' label on skeleton image [default: 11]
[ --graphversion <string> ]
output graph version [default: 4.2]
[ --threads <S32> ]
limit threads usage. code: 0: one thread per CPU; 1: mono-threaded; n>0:
use exactly n threads; -n: use one thread per CPU, up to n max. Default: 0.
Note: no effect on Windows, threading is disabled
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsFoldsGraphOverSegmentation.py
Usage: AimsFoldsGraphOverSegmentation.py [options]
Split fold nodes that are too big into smaller pieces
Options:
-h, --help show this help message and exit
-i GRAPH_NAME, --input=GRAPH_NAME
input graph
-o OUTPUT_GRAPH_NAME, --output=OUTPUT_GRAPH_NAME
output graph
-l LENGTH, --length=LENGTH
target length of split pieces [default: 20mm]
-m MINSIZE, --minsize=MINSIZE
minimum size (in voxels) of split pieces [default: 50]
AimsFoldsGraphThickness.py
Usage: AimsFoldsGraphThickness.py [options]
Processing of Cortical thickness attributes in Cortical Folds Graph
Options:
-h, --help show this help message and exit
-i GRAPH_NAME, --input=GRAPH_NAME
input graph
-c HEMI_CORTEX_NAME, --cortex=HEMI_CORTEX_NAME
segmented cortex volume (LCR + Grey)
-g GW_INTERFACE_NAME, --gw=GW_INTERFACE_NAME
segmented cortex volume (Grey, White, LCR)
-w WHITE_MESH_NAME, --white=WHITE_MESH_NAME
white mesh
-l HEMI_MESH_NAME, --lcr=HEMI_MESH_NAME
hemi mesh (Grey-LCR interface)
-o OUTPUT_GRAPH_NAME, --output=OUTPUT_GRAPH_NAME
output graph
-m OUTPUT_MID_INTERFACE_NAME, --mid=OUTPUT_MID_INTERFACE_NAME
output mid_interface (optional)
-s OUTPUT_LCR_GREY_WHITE_NAME, --savelgw=OUTPUT_LCR_GREY_WHITE_NAME
output volume of lcr, grey and white matter for the
use of computing thickness (optional)
-v VORONOI, --voronoi=VORONOI
sulci voronoi diagram, optional, recalculated if not
provided
AimsFovAdapt
AimsFovAdapt
------------
Adapt FOV of a volume according to reference volume FOV
Options :
[ -i <file name (read only): { Volume of DOUBLE, Volume of FLOAT, Volume of RGB,
Volume of RGBA, Volume of S16, Volume of S32, Volume of S8, Volume of U16,
Volume of U32, Volume of U8 }> Input image to be cropped ]
[ -r <file name (read only): { Volume of DOUBLE, Volume of FLOAT, Volume of RGB,
Volume of RGBA, Volume of S16, Volume of S32, Volume of S8, Volume of U16,
Volume of U32, Volume of U8 }> Input image Reference ]
[ -bv <string> ]
border value to use
[ -o <string> ]
Output image cropped
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsFovCentering
AimsFovCentering
----------------
Generate .trm file to center FOV
Options :
-i <string>
Input image 1
-j <string>
Input image 2
[ --inv <boolean> ]
Generate inverted motion
[ -o <string> ]
Output motion
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsFovSplit
AimsFovSplit
------------
Premier program rats
Options :
-i <list of string>
input files (1 minimum)
[ -o <vector of string> ]
output file names (give as many as you want of rats if the automatic names
do not suit you)
[ -r <U32> ]
Nbre de rat [default: number of output file names, of by default : 4 rats]
[ -m <S32> ]
Taille minimale des composantes connexes [default: 1000]
[ -t <FLOAT> ]
Seuil initial de recherche [default: 20000]
[ -p <FLOAT> ]
Pas de d�r�ent du seuil [default: 10]
[ --binary <boolean> ]
Image used to split is almost binary
[ -d <string> ]
dirname
[ -u <boolean> ]
perform unlink
[ -a <string> ]
attenuation file name
[ --a2split <boolean> ]
use attenuation file to split
-gcA <vector of FLOAT>
Force first gravity center(optional) : must set others too
-gcB <vector of FLOAT>
Force second gravity center(optional) : must set others too
-gcC <vector of FLOAT>
Force third gravity center(optional) : must set others too
-gcD <vector of FLOAT>
Force fourth gravity center(optional) : must set others too
[ -verbose <boolean> ]
yields some more info
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsFovSplit: user interruption
AimsFrontDistanceMap
AimsFrontDistanceMap
--------------------
Chamfer distance map by front propagation
Propagation starts from voxels with any value not in (<forbidden>, <domain>)
and propagates inside voxels with value <domain>. All voxel values different
from <forbidden> and <domain> are considered to be the seed (zero distance)
Options :
-i | --input <file name (read only): { Bucket of FLOAT, Bucket of S16, Bucket
of VOID, Volume of FLOAT, Volume of S16 }> source label data
-o | --output <string>
output distance map
[ -d | --domain <DOUBLE> ]
valid domain label where to propagate the diagram [default=0]
[ -f | --forbidden <DOUBLE> ]
forbidden domain [default=-1]
[ -x | --xmask <S32> ]
X size of the distance mask [default=3]
[ -y | --ymask <S32> ]
Y size of the distance mask [default=3]
[ -z | --zmask <S32> ]
Z size of the distance mask [default=3]
[ -F | --factor <FLOAT> ]
chamfer multiplication factor [default=50]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsFunctionProjection
AimsFunctionProjection
----------------------
AimsFunctionProjection : first computes anatomically-informed
kernels from one anatomy and uses them to project some functional
data onto a cortical mesh
Options :
-op <S32>
0 : computes convolution kernels from one anatomy ; 1 : projects functional
volumes onto the surface (using kernels)
-m <string>
Grey/white matter mesh (.mesh)
[ -d <string> ]
Convolution kernels (.ima) to be used for projection (-op=1)
[ -d1 <string> ]
4D functional volume (.ima/.img) to project onto the mesh (-op=1)
[ -i <S32> ]
Size of computed kernels (integer)
[ -vx <FLOAT> ]
X-resolution of kernels (float)
[ -vy <FLOAT> ]
Y-resolution of kernels (float)
[ -vz <FLOAT> ]
Z-resolution of kernels (float)
[ -g <FLOAT> ]
Geodesic decay (in mm;default = 5.0)
[ -n <FLOAT> ]
Normal decay (in mm;default = 2.0)
[ -t <S32> ]
For computing convolution kernels (-op=0), selects the cortical thickness
evaluation method : 0 for 3mm constant (only for now)
-o <string>
Output file : convolution kernels (-op=0) or projection texture (-op=1)
[ -I <S32> ]
[DEBUG] Index of a precise kernel to be computed
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsGL2Activity
inv_log10 = 0.434294
AimsGL2Activity
---------------
Convert a grey level image to an activity image
Options :
[ -i <string> ]
input grey level image
[ -o <string> ]
output activity image
[ -d <S32> ]
polynome degree for fit (default = 4)
[ -s <S32> ]
1=use classic standards, 0=indicate your standards (default = 1)
[ -c <S32> ]
1=conversion niveaux de gris en D.O, 0=non conversion (default = 1)
[ -gl <A200_c> ]
input grey level standard data
[ -act <A200_c> ]
input activity standard data
[ -input <S32> ]
specify command line input for grey level and activity is enabled (default
= 1)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsGTMDump
----------------------------------------------------------------
AimsGTMDump -i[nput] <filein>
-h[elp]
----------------------------------------------------------------
Dump Gtm
----------------------------------------------------------------
filein : origin Roi file (arg format)
----------------------------------------------------------------
AimsGaussianSmoothing
----------------------------------------------------------------
AimsGaussianSmoothing -i[nput] <filein>
-o[utput] <fileout>
[-x[sigma] <sigmaX>]
[-y[sigma] <sigmaY>]
[-z[sigma] <sigmaZ>]
[-h[elp]]
----------------------------------------------------------------
3D Deriche's recursive gaussian smoothing filter
----------------------------------------------------------------
filein : origin file
fileout : output file
sigmaX : X standard deviation of the gaussian function
[default=largest voxel size]
sigmaY : Y standard deviation [default=same as sigmaX]
sigmaZ : Z standard deviation [default=same as sigmaX]
for a 2D image, set zsigmat to 0
----------------------------------------------------------------
AimsGaussianSmoothing1d
----------------------------------------------------------------
AimsGaussianSmoothing1d -i[nput] <filein>
-o[utput] <fileout>
-d[irection] <dir>
[-s[igma] <sigma>]
[-h[elp]]
----------------------------------------------------------------
1D Deriche's recursive gaussian smoothing filter
----------------------------------------------------------------
filein : origin file
fileout : output file
dir : direction of smooting (x/y/z)
sigma : standard deviation of the gaussian function
[default=corresponding voxel size]
----------------------------------------------------------------
AimsGeodesicPath
AimsGeodesicPath
----------------
Compute the shortest path between two vertex
Options :
-i | --input <string>
mesh
-s | --source <U32>
index of source vertex
-t | --target <U32>
index of target vertex
-o | --output <string>
output file without extension file specified (.tex or .mesh)
[ -c | --constraint <S32> ]
constraintType:
"0" -> no constraint
"1" -> constrained sulci
"2" -> constrained gyri
"3" -> Exact geodesic path
[ -st | --strain <S32> ]
strain parameter (3 by default)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsGetTransformation.py
Usage: AimsGetTransformation.py [options]
extract an affine transformation information in an object header into a
transformation file
Options:
-h, --help show this help message and exit
-i FILE, --input=FILE
object to get transformation from (volume, mesh, etc).
-o TRMFILE, --output=TRMFILE
output transformation file (*.trm)
-n TRANSNUM, --number=TRANSNUM
get transformation information as the n-th
transformation. Default: -1, last one in list
-d DESTINATION, --destination=DESTINATION
set destination referential name/UUID. Default: try to
get it from the referentials info of the input file
header
-s SOURCE, --source=SOURCE
set source referential name/UUID. Default: try to get
it from the referential info of the input file header
AimsGraphComplete
AimsGraphComplete
-----------------
Completes missing attributes in graphs (cortical folds graphs generally)
Options :
-i | -input <file name (read only): Graph>
input graph
[ -o | -output <filename: Graph> ]
output (completed) graph [default=input]
[ --dversion <string> ]
set data graph version
[ --mversion <string> ]
set model graph compatibility version
[ --forceversion <boolean> ]
force data/model graph versions [default: only if newer]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsGraphConvert
AimsGraphConvert
----------------
Performs graph storage conversion or volume-S16 labels volume to graph
conversion
Options :
-i | -input <string>
input data graph
[ -o | -output <string> ]
output data graph (default: same as input)
[ -b | -basename <string> ]
directory where to put sub-data in (default: <input>.data)
[ -g | -global <boolean> ]
save sub-objects in 'global' mode (1 file for all objects of same type)
[ -l | -local <boolean> ]
save sub-objects in 'local' mode (each object with a specific file)
(contradictory with -g)
[ -c | -copy <string> ]
copy attribute (use with -d)
[ -d | -dest <string> ]
destination attribute (for use with -c)
[ -s | -syntax <string> ]
syntax of elements involved by copy operations (use with -c and -d)
[default: no filtering]
[ --volume <boolean> ]
convert buckets to volume of labels
[ --bucket <boolean> ]
convert volumes of labels to buckets
[ --roi <boolean> ]
Output graph will be a roi graph, and all unnamed regions will be named by
their roi label
[ --substitution <string> ]
Graph substitution file for syntax and label
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsGraphExtractTransformation
AimsGraphExtractTransformation
------------------------------
Extracts the Talairach transformation in a graph file and write it as an
Aims/Anatomist transformation file
Options :
-i | -input <string>
input data graph
[ -o | -output <string> ]
output transformation (default: <input>TOtalairach.trm)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsGraphMerge
AimsGraphMerge
--------------
Merge 2 graphs (cortical folds graphs generally)
Options :
-i | -input1 <file name (read only): Graph>
input graph1
-k | -key <string>
matching key
-j | -input2 <file name (read only): Graph>
input graph2
[ -o | -output <filename: Graph> ]
output (merge) graph [default=input]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsGraphMesh
AimsGraphMesh
-------------
Performs graph storage conversion and sub-buckets meshing
This command is an improved version of AimsGraphConvert
Options :
-i | -input <file name (read only): Graph>
input data graph
[ -o | -output <filename: Graph> ]
output data graph (default: same as input)
[ -b | -basename <string> ]
directory where to put sub-data in (default: <output>.data)
[ -g | -global <boolean> ]
save sub-objects in 'global' mode (1 file for all objects of same type)
[ -l | -local <boolean> ]
save sub-objects in 'local' mode (each object with a specific file)
(contradictory with -g)
[ -m | -mesh <vector of string> ]
mesh some objects into the given attribute
Needs at least one -mb option (default: aims_Tmtktri)
[ -mb | -meshbucket <vector of string> ]
mesh buckets of given attribute (experts manips). Needs also a -m option.
Specify several -mb <attrib> to mesh several buckets(default: all)
[ -f <U32> ]
minimum number of facets to mesh (default 50)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsGraphTransferLabels
AimsGraphTransferLabels
-----------------------
Transfers labelling from a buckets graph to another graph.
Graph structures don't need to match, transfer is based on a Voronoi diagram
Options :
-i | --input1 <file name (read only): Graph>
input graph to set labels into
-j | --input2 <file name (read only): Graph>
input labelled graph to take labels from
[ -o | --output <filename: Graph> ]
output labelled graph [default=input]
[ -l | --label <string> ]
label attribute [default=name]
[ -v | --voronoi <filename: volume of S16> ]
output voronoi diagram (in input2 space) [default=not saved]
[ -m | --map <string> ]
output labels map file [default=not saved]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsGroupGyri
AimsGroupGyri
-------------
Group some of the original cortical gyri to get a new gyri model.
Options :
-m | --mesh <string>
input mesh
-i | --in <string>
input gyri texture
-o | --out <string>
output gyri texture
-g | --grouping <string>
grouping model file
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsGyriRegularization
AimsGyriRegularization
----------------------
Build a regularized version of gyri from the 2D coordinate system
Options :
-m | --mesh <string>
input mesh
-i | --in <string>
input gyri texture
-o | --out <string>
output gyri texture
[ -w | --weight <FLOAT> ]
data-driven term weight
[ -a | --anneal <S32> ]
annealing (0=no, ICM; 1=yes
[ -s | --smooth <S32> ]
Smoothing of probability maps (default=80)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsGyriStuff
AimsGyriStuff
-------------
Creation de gyri utilisant le systeme de coordonnees surfacique
AimsCorticalReferential
Options :
-x | --inLon <string>
input Longitude Texture
-y | --inLat <string>
input Latitude Texture
-a | --inCor <string>
input Correspondance File
-o | --outTex <string>
output texture
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsHJEvolution2d
--------------------------------------------------------------------------
AimsHJEvolution2d -i[nput] <filein>
-o[output] <fileout>
-e[poch] <epoch>
[-t[ime] <timestep>]
[-f[0] <F0>]
-F[1] <F1>
[-s[tep] <savingstep>]
[-u[radius] <tuberadius>]
[-m[orphology] <typeMorpho>]
[-h[elp]]
--------------------------------------------------------------------------
2D Hamilton-Jacobi evolution of a binary short image f(x,y)
Fast tubular method
--------------------------------------------------------------------------
filein : input SHORT binary data
fileout : prefix name for output SHORT data
epoch : number of evolving iterations to proceed
timestep : time step in seconds [default=0.1]
F0,F1 : speed function F = F0 + F1.K [default F0=-1.0 / F1=-1.0]
F0<0 : erosion / F0>0 : dilation
savingtep : number of time iterations between 2 backups [default=1]
uradius : radius of the evolving tube [default=12]
typeMorpho: type of morphologic evolution
0 -> -F0.||DPhi||
1 -> -F0.||DPhi||.dist(x,y)
2 -> -F0.||DPhi||.(1.0 + 0.5 * dist(x,y))
--------------------------------------------------------------------------
AimsHJEvolution3d
--------------------------------------------------------------------------
AimsHJEvolution3d -i[nput] <filein>
-o[output] <fileout>
[-d[istmap] <filedist>
-e[poch] <epoch>
[-t[ime] <timestep>]
[-f[0] <F0>]
-F[1] <F1>
[-s[tep] <savingstep>]
[-u[radius] <tuberadius>]
[-c[urvature] <typeCurv>]
[-m[orphology] <typeMorpho>]
[-h[elp]]
--------------------------------------------------------------------------
3D Hamilton-Jacobi evolution of a binary short image f(x,y,z)
Fast tubular method
--------------------------------------------------------------------------
filein : input SHORT binary volume
fileout : prefix name for output SHORT volumes
filedist : distance map volume
epoch : number of evolving iterations to proceed
timestep : time step in seconds [default=0.1]
F0,F1 : speed function F = F0 + F1.K [default F0=-1.0 / F1=-1.0]
F0<0 : erosion / F0>0 : dilation
savingtep : number of time iterations between 2 backups [default=1]
uradius : radius of the evolving tube [default=12]
typeCurv : mean, gaussian, mean-gaussian, min, max
[default=mean-gaussian]
typeMorpho: type of morphologic evolution
0 -> -F0.||DPhi||
1 -> -F0.||DPhi||.dist(x,y,z)
2 -> -F0.||DPhi||.(1.0 + 0.5 * dist(x,y,z))
--------------------------------------------------------------------------
AimsHeightFiltering
AimsHeightFiltering
-------------------
Height filtering
Options :
-i <file name (read only): volume of U8>
Input grey-level image
-height <U8>
Height of the filter
[ -b <S32> ]
Binary threshold or not [default : 0]
[ -c <U8> ]
Connexity 4 or 8 [default : 4]
-o <filename: volume of U8>
Output image
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsHippocampicReferential
AimsHippocampicReferential
--------------------------
Transformation to hippocampic referential
Options :
-o <string>
Output motion file
--ac <vector of FLOAT>
Anterior commissure (mm)
--pc <vector of FLOAT>
Posterior commissure (mm)
--ih <vector of FLOAT>
Inter hemispheric point (mm)
[ --angle <FLOAT> ]
rotation angle in degrees (default 30°)
[ --axis <string> ]
rotation axis 'x', 'y' or 'z' (default x)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsIcmSpaghetti
-------------------------------------------------------------------------
AimsIcmSpaghetti -i[nput] <input>
-o[utput] <output>
[-a[lpha] <alpha>]
[-m[odifAngle] <modifAngle>]
[-n[eighborAngle] <neighborAngle>]
[-s[ampling] <sampling>]
[-M[axIter] <iteration>]
[-h[elp]]
-------------------------------------------------------------------------
Regularization of the tensor maps with a Spaghetti Markov Field
-------------------------------------------------------------------------
input : bucket of dtitensor to be regularized
output : result of the regularization
alpha : energy balancing [default=1.0]
V = V(spaghetti) + alpha x V(attachment)
modifAngle : maximum angle in degrees between the direction of a
neighbor of a voxel and the spin of that voxel
[default=45deg]
neighborAngle : maximum angle in degrees beetween 2 spins to be
considered in the same fiber
[default=46deg]
sampling : minimum number of discrete unit vectors uniformly
distributed on a unit sphere
[default=162]
iteration : stop the ICM after a maximum number of iterations
[default=30]
-------------------------------------------------------------------------
AimsIcmSpaghettiN
-------------------------------------------------------------------------
AimsIcmSpaghettiN -i[nput] <input>
-o[utput] <output>
[-a[lpha] <alpha>]
[-m[odifAngle] <modifAngle>]
[-n[eighborAngle] <neighborAngle>]
[-s[ampling] <sampling>]
[-M[axIter] <iteration>]
[--neighbor <nneighbor>]
[-h[elp]]
-------------------------------------------------------------------------
Regularization of the tensor maps with a Spaghetti Markov Field
-------------------------------------------------------------------------
input : bucket of dtitensor to be regularized
output : result of the regularization
alpha : energy balancing [default=1.0]
V = V(spaghetti) + alpha x V(attachment)
modifAngle : maximum angle in degrees between the direction of a
neighbor of a voxel and the spin of that voxel
[default=45deg]
neighborAngle : maximum angle in degrees beetween 2 spins to be
considered in the same fiber
[default=46deg]
sampling : minimum number of discrete unit vectors uniformly
distributed on a unit sphere
[default=162]
iteration : stop the ICM after a maximum number of iterations
[default=30]
nneighbor : number of neighbor by semi-conic neighborhood
[default=all]
-------------------------------------------------------------------------
AimsIcosaList
-------------------------------------------------------------------------
AimsIcosaList -d[irection] <dir>
-o[utput] <output>
[-e[psilon] <eps>]
[-a[ll]]
[-h[elp]]
-------------------------------------------------------------------------
Output a file with coordinates of discrete spheric distribution
-------------------------------------------------------------------------
dir : number of discrete directions
output : output ASCII file
all : all directions (+d and -d)
(useful for DTI where +d and -d are equivalent
eps : error on dot product (+d).(-d) [default=1e-6]
-------------------------------------------------------------------------
AimsImageGLBlobStats
Here we go !
AimsImageGLBlobStats
--------------------
Compute every scale and corresponding grey-level blob measurements from an
image
Options :
-i <string>
input data
-m <string>
mask
[ -t1 <FLOAT> ]
scale min (default=1.0)
-t2 <FLOAT>
scale max
-p <string>
stats file name pattern
-s <S32>
smoother (0 : Gaussian, 1 : diffusion)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsImagePrimalSketch
AimsImagePrimalSketch
---------------------
ScaleSpace d'une image au format FLOAT
Options :
-i | --input <string>
inputImage
-m | --mask <string>
mask
-os | --output-scales <string>
output scalespace filename
-ob | --output-blobs <string>
output blobs filename
[ -t1 | --scalemin <FLOAT> ]
minimum scale (default=1.0)
-t2 | --scalemax <FLOAT>
maximum scale
-s | --smoother <S32>
smoother (0 : Gaussian, 1 : diffusion; default=0)
[ -dt | --deltat <FLOAT> ]
time step (for diffusion only; default=0.1)
[ -f | --stats <string> ]
name of file containing statistics for blob measurements normalisation
[ -sj | --subject <string> ]
subject name (default : inputImage)
[ -og | --graph <string> ]
primal sketch graph
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsImageScaleSpace
AimsImageScaleSpace
-------------------
ScaleSpace d'une image...
Options :
-i | --input <string>
inputImage
-o | --output <string>
output filename pattern
-tm | --scalemax <FLOAT>
maximum scale
-s | --smoother <S32>
smoother (0 : Gaussian, 1 : diffusion
-dt | --deltat <FLOAT>
time step
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsImageSmoothing
AimsImageSmoothing
------------------
Image smoothing by diffusion or recursive filtering
Options :
-i | --input <string>
input Image
-o | --output <string>
output Image
-t | --scale <FLOAT>
scale
-s | --smoother <S32>
smoother (0 : Gaussian, 1 : isotropic diffusion, 2 : Perona-Malik)
[ -dt | --deltat <FLOAT> ]
time step (diffusion only; default=0.1)
[ -k | --gradient <FLOAT> ]
gradient bound (0-1), Perona-Malik only, default=0.98
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsIndexCluster
AimsIndexCluster
----------------
Automatically index SPMclusters using an atlas segmentation
--> compute Vol_cluster (mm3) / ROI
only for volumes of labels (same dim + voxel_size)
ROIs must have same label in both volumes
Options :
[ -r <file name (read only): { Volume of DOUBLE, Volume of FLOAT, Volume of S16,
Volume of S32, Volume of S8, Volume of U16, Volume of U32, Volume of U8 }>
Input atlas data ]
[ -t <string> ]
Input cluster data
[ -o <string> ]
Output textfile
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsIndividSlices
AimsIndividSlices
-----------------
Individualize and stack slices from multiple scan
Options :
-i <string>
Input original image
[ -pi <string> ]
Input preprocessed image
[ -f <string> ]
force a specific output format (GIS, TIFF, ...) (default: GIS)
[ -c <U8> ]
Channel to use to process multi-channel image
Possible types and values:
type : RGB or RGBA
values: 0=red, 1=green, 2=blue, 3=norm
type : HSV
values: 0=hue, 1=saturation, 2=value, 3=norm
-n <S32>
Number of slices
[ --dimsizes <vector of S32> ]
Dimensions sizes
[ --dimorders <vector of S32> ]
Dimensions orders
[ -nostack <boolean> ]
Specify that individualized slices must not be stacked.
In that case, individualized slices are stored in the output directory.
-z <FLOAT>
Inter slice space (in mm)
-res <S32>
Scan resolution (in dpi)
[ -dx <S32> ]
X dimension of the final volume
[ -dy <S32> ]
Y dimension of the final volume
[ -lt <S32> ]
Lower threshold [manual activation]
[ -ht <S32> ]
Higher threshold [manual activation]
-ms <S32>
Minimal surface of slices [in mm2]
[ -sn <U8> ]
First slice number (use only with -nostack option)
[ -nm <string> ]
Output image name (use only with -nostack option)
[ -tf <FLOAT> ]
Test fraction to use for dimension and surface variations
[ -o <string> ]
Output stacked image or directory (depending on -nostack option)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsIndividStackSlices
AimsIndividStackSlices
----------------------
Individualize and stack slices from multiple scan
Options :
-i <string>
Input original image
[ -pi <string> ]
Input preprocessed image
-n <S32>
Number of slices
[ --dimsizes <vector of S32> ]
Dimensions sizes
[ --dimorders <vector of S32> ]
Dimensions orders
-z <FLOAT>
Inter slice space (in mm)
-res <S32>
Scan resolution (in dpi)
[ -dx <S32> ]
X dimension of the final volume
[ -dy <S32> ]
Y dimension of the final volume
[ -lt <S32> ]
Lower threshold [manual activation]
[ -ht <S32> ]
Higher threshold [manual activation]
-ms <S32>
Minimal surface of slices [in mm2]
[ -o <string> ]
Output labelled image
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsInflate
AimsInflate
-----------
Gonflement d'une surface (tri ou mesh)
Options :
-i | --input <string>
input
[ -t | --time <S32> ]
evolution time
-o | --output <string>
output filename
[ -Kn | --Knormal <FLOAT> ]
normal force weight (default=0.01)
[ -Ksp | --Kspring <FLOAT> ]
spring force weight (default=0.01)
[ -Ksm | --Ksmooth <FLOAT> ]
smoothing force weight (default=0.5)
[ -B | --Bound <FLOAT> ]
bound for the force computation (default=5000.0)
[ -S | --Sequence <boolean> ]
to save the inflating sequence
-c | --curvature <string>
mean curvature file name
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsInterSliceNormalize
AimsInterSliceNormalize
-----------------------
Normalize the intensity through 3D volume
Options :
-i <string>
input data
[ -o <string> ]
output data
[ -m <string> ]
input mask
[ -s <S32> ]
starting slice
[ -f <FLOAT> ]
multiplication factor
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsInterlaceVolumes
AimsInterlaceVolumes
--------------------
Interlacing multiple volumes in resulting one
Options :
[ -i <vector of string> ]
Input volumes to interlace
[ -o <string> ]
Output interlaced volume
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsInterpolateVolumeToSurface
AimsInterpolateVolumeToSurface
------------------------------
Projection d'un volume sur une surface par interpolation des noeuds de la
surface dans le volume
Options :
-im | --inMesh <string>
input Mesh
-iv | --inVol <string>
input Volume
-o | --outTex <string>
output Texture
-t | --type <S32>
type d'interpolation (default: 0=trilinŽaire, 1=plus proche voisin
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsInvertTransformation
AimsInvertTransformation
------------------------
Inverts an Aims/anatomist transformation
Options :
-i <string>
input transformation
[ -o <string> ]
output (inverted) transformation (default: <input>_inverted.trm)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsKMeans
-------------------------------------------------------------------------
AimsKMeans -f[ile] <data file>
-g[ile2] <data file>
-i[nput] <image>
-o[utput]
-n[umber]
[-h[elp]]
-------------------------------------------------------------------------
Image des classes produite par le kmeans
-------------------------------------------------------------------------
file : nom fichier containing the classification
file2 : nom fichier des donnees initiales
input : nom image segmentee
fileout : nom image sortie des classes
number : number of vectors
-------------------------------------------------------------------------
AimsKMeansImageSegmentation
AimsKMeansImageSegmentation
---------------------------
K means based automatic segmentation
Options :
-i <string>
dynamic series file
-o <string>
fileout segmentation image filename
-c <S32>
number of classes
-r <S32>
number of runs
[ -m <string> ]
input mask of organism of interest (example: brain mask)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsLZHCompress
-------------------------------------------------------------------------
AimsLZHCompress -i[nput] <filein>
[-o[utput] <fileout>]
[-d]
[-h[elp]]
-------------------------------------------------------------------------
LZH light compressor
-------------------------------------------------------------------------
filein : source file
fileout : destination file [default=filein.lzh]
d : decompress [default=compress]
-------------------------------------------------------------------------
AimsLabelSelector
AimsLabelSelector
-----------------
Selects ROI labels from a nomenclature
(to be used as input for ROI and morphometry commands)
Options :
[ -m | --model <string> ]
Load a model
[ -n | --nomenclature | --hierarchy <string> ]
Load a nomenclature hierarchy
[ -p | --presel <string> ]
Load a pre-made selection
[ -b | --batch <boolean> ]
Batch mode: process the input selection/model if possible and immediately
outputs a selection without user interaction
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsLightenAtlas
AimsLightenAtlas
----------------
Lighten anatomical probabilistic atlas
Options :
-i <string>
Probabilistic atlas image with one region per frame
-o <string>
Lightened atlas image
[ -s <string> ]
Sum of the lightened atlas image
[ -r <FLOAT> ]
Radius around a point in the structure within which a point with a 1
probability
to belong to the structure is supposed to exist (default : 8 mm)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsLinearComb
------------------------------------------------------------------
AimsLinearComb -i <i1> [-a <num1>] [-b <den1>]
[-j <i2> [-c <num2>] [-d <den2>]]
[-e <cst>]
-o[utput] <fileout>
[-t[ype] <datatype>
[-h[elp]]
------------------------------------------------------------------
Linear combination a.I1/b + c.I2/d + e
Note : a,b,c,d,e must be real
------------------------------------------------------------------
i1 : first data (volume or texture)
num1 : multiplicative coefficient for the first data [1.0]
den1 : divisor coefficient for the first data [1.0]
i2 : second data (volume or texture)
(if none, linear combination a.I1/b)
num2 : multiplicative coefficient for the second data[1.0]
den2 : divisor coefficient for the second data [1.0]
cst : constant offset value [default=0.0]
fileout : destination data
datatype: data type of the destination volume/texture (S16, U8, ...)
[default=type of in1]
For texture, i1, i2 and fileout must have the same type
------------------------------------------------------------------
AimsMIBucketRegister
-------------------------------------------------------------------------
AimsMIBucketRegister -r[eference] <ref (bucket_SHORT file)>
-t[est] <test >
-o[utput] <fileout>
[--serialnum <sn>]
[--Tx <Tx>]
[--Ty <Ty>]
[--Tz <Tz>]
[--dTx <dTx>]
[--dTy <dTy>]
[--dTz <dTz>]
[--Rx <Rx>]
[--Ry <Ry>]
[--Rz <Rz>]
[--dRx <dRx>]
[--dRy <dRy>]
[--dRz <dRz>]
[--interpolation <method>]
[--optimization <algo>]
[--pdfcalc <mode>]
[--gcinit <mode>]
[--index <index>]
[--pays_size <pays_size>]
[--graylevel <nl>]
[--masksize <ms>]
[--error <epsilon>]
[-h[elp]]
-------------------------------------------------------------------------
Registration according to Mutual Information Method
-------------------------------------------------------------------------
ref : source S16 reference data
test : source S16 test data (to register)
fileout : destination S16 data
sn : number of the frame to consider for ref [default 0]
: relevant for dynamic series ref images
Tx, Ty, Tz : Init Translaction coord [default=0.0,0.0]
Rx, Ry, Rz : Init Rotation coord [default=0.0,0.0]
dWw : Increment for variable Ww [default=heuristics in code]
method : interpolation nearest/linear/spline [default=linear]
algo : optimaizer powell/random/single [default=powell]
single --> get a one shot evaluation
random --> sample cost value in a given area
powell --> cost minimization with powell algorithm
index : index to be optimized mi/cr [default=mi]
Mutual Information --> mi
Correlation Ratio --> cr
mode : Pdf calculus mode : direct(def) ou pv
pays_size : Half size the volume generated if algo=other activated
nl : numb of classes in histogram pdf estimation [def.=64]
ms : size of the gaussian convolution mask in pdf estimation
for Mutual Information [default=5]
seuilref : relative thresh applied prior to grav cent estimation
seuiltest :
epsilon : tolerance on results [default=0.00001]
gcinit : Init with GravCenter : "yes" (def.) or "no"
-------------------------------------------------------------------------
AimsMIRegister
AimsMIRegister
--------------
Registration according to Mutual Information Method
Options :
-r | --reference <file name (read only): volume of S16>
source S16 reference volume
-t | --test <file name (read only): volume of S16>
source S16 test volume to register)
[ --dir <filename: AffineTransformation3d> ]
test_TO_ref: output transfomation filename [default=<test>_TO_<ref>.trm]
[ --inv <filename: AffineTransformation3d> ]
ref_TO_test: output transfomation filename [default=<ref>_TO_<test>.trm]
[ -l | --logger <string> ]
output log file
[ --serialnum <S32> ]
number of the frame to consider for ref [default 0], relevant for dynamic
series ref images
[ --Tx <FLOAT> ]
Init Translaction coord [default=0.]
[ --Ty <FLOAT> ]
Init Translaction coord [default=0.]
[ --Tz <FLOAT> ]
Init Translaction coord [default=0.]
[ --dTx <FLOAT> ]
Increment for variable Tx [default=heuristics in code]
[ --dTy <FLOAT> ]
Increment for variable Ty [default=heuristics in code]
[ --dTz <FLOAT> ]
Increment for variable Tz [default=heuristics in code]
[ --Rx <FLOAT> ]
Init Rotation coord [default=0.]
[ --Ry <FLOAT> ]
Init Rotation coord [default=0.]
[ --Rz <FLOAT> ]
Init Rotation coord [default=0.]
[ --dRx <FLOAT> ]
Increment for variable Rx [default=heuristics in code]
[ --dRy <FLOAT> ]
Increment for variable Ry [default=heuristics in code]
[ --dRz <FLOAT> ]
Increment for variable Rz [default=heuristics in code]
[ --interpolation <string> ]
interpolation nearest/linear/spline [default=linear]
[ --optimization <string> ]
optimaizer powell/random/single [default=powell]
single --> get a one shot evaluation
random --> sample cost value in a given area
powell --> cost minimization with powell algorithm
[ --pdfcalc <string> ]
Pdf calculus mode : direct ou pv [default=pv]
[ --gcinit <string> ]
Init with GravCenter: yes/no [default=yes]
[ --index <string> ]
index to be optimized mi/cr [default=mi]
Mutual Information --> mi
Correlation Ratio --> cr
[ --refstartpyr <S32> ]
level of the multiresolution optimization:
start resolution level for ref
[ --refendpyr <S32> ]
level of the multiresolution optimization:
end resolution level for ref
[ --teststartpyr <S32> ]
level of the multiresolution optimization:
start resolution level for tes
[ --testendpyr <S32> ]
level of the multiresolution optimization:
end resolution level for tes
[ --pays_size <S32> ]
Half size the volume generated if optimization=other activated
[ --graylevel <S32> ]
numb of classes in histogram pdf estimation [default=64]
[ --masksize <S32> ]
size of the gaussian convolution mask in pdf estimation for Mutual
Information [default=5]
[ --error <FLOAT> ]
tolerance on results [default=0.01]
[ --threshref | --seuilref <FLOAT> ]
relative thresh applied prior to grav cent estimation
[ --threshtest | --seuiltest <FLOAT> ]
relative thresh applied prior to grav cent estimation
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsManualBiasCorrection
-------------------------------------------------------------------------
AimsManualBiasCorrection -i[nput] <filein>
-o[utput] <fileout>
-d[irection] <direction : x, y, or z>
-f[irst] <first slice value>
-l[ast] <last slice value>
-------------------------------------------------------------------------
Morphological dilation
-------------------------------------------------------------------------
filein : source volume
fileout : destination volume
direction: direction of bias correction : x axis, y axis, ou z axis
f : first slice white matter level
l : last slice white matter level
-------------------------------------------------------------------------
AimsManualRegistration
----------------------------------------------------------------
AimsManualRegistration
-f[rom] < .arg file >
-t[o] < .arg file >
-o[utput] < displacement file: from_TO_to.trm >
--l[oose] < loose or point to point registration>
--transfo < 1=rigide, 2=simi, 3=affine (default=1)>
[-h[elp]]
----------------------------------------------------------------
Compute manual registration
Both arg files can be filled with anatomist roi module, but must
- contain only one point per region
- region must be correctly ordered : same roi_label or order
of creation for appariated points in both graphs
----------------------------------------------------------------
.arg file: voi type file
--loose condition: registration with two points plus a point
defining a plane (inter-hemispheric plane)
----------------------------------------------------------------
AimsMask
AimsMask
--------
Mask an image with another one
Options :
-i <string>
origin file
-o <string>
output file
-m <string>
S16 mask
[ --inv <boolean> ]
use inverse mask image (default=no)
[ -d <string> ]
Default values for masked pixels [default=0]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMaskContour
AimsMaskContour
---------------
Contour image visualization
Options :
-i <string>
Input mask image
[ -ic <boolean> ]
Generate input contour [default=true]
[ -oc <boolean> ]
Generate output contour [default=true]
-o <string>
Output contour image
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMaskPhantom
----------------------------------------------------------------
AimsMaskPhantom -i[nput] <filein>
[-o[utput] <fileout>]
[--centerX <cx>]
[--centerY <cy>]
[--centerZ <cz>]
[--radius <R>]
[--withSphere]
--bandX <bx>
--bandW <bw>
[-r[eader] <reader>]
[-h[elp]]
----------------------------------------------------------------
Special masking of DTI Phantom for Anne Darquie
----------------------------------------------------------------
filein : origin file
fileout : output file [default=filein]
cx, cy, cz, R : center and radius of the sphere for masking
Eddy current [default=no masking]
--withSphere : mask Eddy Current with sphere [default=no]
bx, bw : x-coordinate and width of the band to mask the
air buble
----------------------------------------------------------------
AimsMassCenter
AimsMassCenter
--------------
Computes position of the mass center of the image
Options :
-i | --input <file name (read only): { Volume of FLOAT, Volume of S16, Volume
of S8, Volume of U8 }> input data
[ -b | --binary <boolean> ]
consider input image as binary data
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMaxAndSumProjection
AimsMaxAndSumProjection
-----------------------
Maximum and Sum Intensity Projection
Options :
-i <string>
Input file
[ -s <string> ]
Output sum projection file
[ -m <string> ]
Output maximum projection file
[ -f <S32> ]
Number of frames (required for PET dynamic data, default = 1)
-p <string>
Projection plane 'a' for Axis, 'c' for Coronal, 's' for Sagittal
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMeanCurvFlow
--------------------------------------------------------------------------
AimsMeanCurvFlow -i[nput] <filein>
-o[output] <fileout>
-e[poch] <epoch>
-F[1] <F1>
[-t[ime] <timestep>]
[-s[tep] <savingstep>]
[-u[radius] <tuberadius>]
[-c[urvature] <typeCurv>]
[-r[eader] <reader>]
[-h[elp]]
--------------------------------------------------------------------------
3D Hamilton-Jacobi evolution of a binary short image f(x,y,z)
Fast tubular method - Mean Curvature Flow
Ut = - F1.K.||DU||
--------------------------------------------------------------------------
filein : input SHORT binary volume
fileout : prefix name for output SHORT volumes
epoch : number of evolving iterations to proceed
timestep : time step in seconds [default=0.1]
F1 : speed function F = F1.K [default F1=-1.0]
savingtep : number of time iterations between 2 backups [default=1]
uradius : radius of the evolving tube [default=12]
typeCurv : mean, gaussian, mean-gaussian, min, max
[default=mean-gaussian]
--------------------------------------------------------------------------
AimsMedianSmoothing
---------------------------------------------------------------------------
AimsMedianSmoothing -i[nput] < input file Image SHORT >
-o[output] < fileout (NO EXTENSION) >
--dx[dimemsion] < X direction > [default=3]
--dy[dimemsion] < Y direction > [default=3]
--dz[dimemsion] < Z direction > [default=1]
[-h[elp]]
---------------------------------------------------------------------------
Filtering inline command
---------------------------------------------------------------------------
dx, dy, dz : mask form (2/3 dimensions) ODD NUMBER !!!
---------------------------------------------------------------------------
AimsMedianSubSampling
AimsMedianSubSampling
---------------------
Median image subsampling
Options :
-i <string>
Input image to subsample
[ -rx <S32> ]
X dimension to aggregate
[ -ry <S32> ]
Y dimension to aggregate
[ -rz <S32> ]
Z dimension to aggregate
-o <string>
Output image
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMerge
----------------------------------------------------------------
AimsMerge -i[nput] <filein>
-M[ask] <mask>
-o[utput] <fileout>
-m[ode] <mm>
[-l[abel] <label>]
[-v[alue] <value>]
[-h[elp]]
----------------------------------------------------------------
Merge a data and a byte label data
----------------------------------------------------------------
filein : origin file
fileout : output file
mask : label file
mm : mode that can be
sv --> same values
oo --> one to one
ao --> all to one
om --> one to maximum plus 1
am --> all to maximum plus 1
label : only label to get into account
value : replacement value
----------------------------------------------------------------
AimsMerge2Rgb
AimsMerge2Rgb
-------------
Merge 3 AimsData<byte> files to an AimsData<AimsRGB>
Options :
-r <string>
input U8 data R channel
-g <string>
input U8 data G channel
-b <string>
input U8 data B channel
-o <string>
output data
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMergeLabel
AimsMergeLabel
--------------
Merge several label data into a new label data
Options :
-i <list of string>
input label data filename list
[ -b <list of S16> ]
background labels for label data (default=-1)
-o <string>
output label data filename
[ -bo <S16> ]
background label for output label data (default=-1)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMesh
AimsMesh
--------
Extracts triangulation in a label short volume
Options :
-i | --input | -input <string>
input short volume label (level 0 is assumed to be the background)
[ -o | --output | -output <string> ]
output mesh prefix name (extension will determine the format)
[default=filein]
[ -l | --label | -label <S32> ]
labelInf: extracts only label in [<labelInf>;<labelSup>]
[ -L | --Label | -Label <S32> ]
labelSup: extracts only label in [<labelInf>;<labelSup>]
[ -S | --Surface | -Surface <FLOAT> ]
minimum surface of the interfaces to extract [default=0.0 mm^2]
[ --smooth <boolean> ]
smoothes the mesh [default=no smoothing]
[ --smoothIt <S32> ]
smoothing number of iterations [default=10]
[ --smoothRate <FLOAT> ]
smoothing moving factor at each iteration [default=0.2]
[ --smoothAngle <FLOAT> ]
smoothing feature angle in degrees between 0 and 180 degrees, [default=180]
[ --decimation <S32> ]
decimate the mesh [default=no decimation]
[ --deciReductionRate <FLOAT> ]
expected % decimation reduction rate [default=99%]
[ --deciMaxClearance <FLOAT> ]
maximum clearance of the deci
[ --deciMaxError <FLOAT> ]
maximum error distance from the original mesh (mm) [default=10.0]
[ --deciAngle <FLOAT> ]
feature angle (degrees), between 0 and 180 [default=180]
[ --split <boolean> ]
split the surface corresponding to one connected component into
sub-surfaces, each corresponding to an interface between 2 different
components [default=no splitting]
[ --minFacetNumber <S32> ]
minimum number of facets to allow decimation [default=50]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMesh2Ascii
usage : AimsMesh2Ascii filein.mesh fileout.txt
AimsMesh2SSGraph
AimsMesh2SSGraph [-p prim.arg] [-s surftype] [-b] [-t trans] [-g growmode] in.mesh inflate.mesh outgraph.arg irm.ima textures...
Makes a primal sketch graph from a mesh and a set of smoothed textures
Options :
-p prim.arg : make also the corresponding primal sketch graph
-s surftype : tore (default) or surface
-b : blobs are already extracted, don't search for them
(textures are labels)
-t trans : initial translation of extracted surfaces (default: 0)
-g growmode : mesh growing mode along scales: scale (default), translate, or pushnormal
AimsMesh2Sphere
AimsMesh2Sphere
---------------
Build a spherical coordinate system on a mesh
Options :
-i <file name (read only): mesh of VOID>
input mesh
-o <filename: mesh of VOID>
result
[ -t <filename: texture of POINT2DF> ]
output 2D coord texture
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMeshArea
AimsMeshArea
------------
Prints a mesh surface area
Options :
-i | --input <file name (read only): mesh of VOID>
input mesh
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMeshAverage
-------------------------------------------------------------------------
AimsMeshAverage -m[esh] <input_mesh>]
-o[utput] <output_mesh>
-v[ariability <output_texture>
[-h[elp]]
-------------------------------------------------------------------------
Average a time serie mesh.
WARNING : Be sure that the nodes at different time serie correspond to the same point...
-------------------------------------------------------------------------
input_mesh : input time serie mesh
output_mesh : output mean mesh
output_texture : variability
-------------------------------------------------------------------------
AimsMeshBlobExtract
-------------------------------------------------------------------------
AimsMeshBlobExtract -i[nput] <meshfilein>
-t[exture] <input_texture>
[-T[ime] <time serie> default = 0]
[-o[utput] <output_texture>]
[-h[elp]]
-------------------------------------------------------------------------
Extract blobs
-------------------------------------------------------------------------
meshfilein : input *.tri or *.mesh file
output_texture : output *.tex file (blobs)
input_texture : object definition
-------------------------------------------------------------------------
AimsMeshBrain
AimsMeshBrain
-------------
Computes the brain surface from a segmented image and saves it in a triangles
mesh format file
Options :
-i | --input | -input <string>
input volume label (short int data), level 0 is assumed to be the back
[ -o | --output | -output <string> ]
output file name for the mesh [default: same basename as input]
[ --deciMaxClearance <FLOAT> ]
maximum clearance expected in the resulting mesh, in mm [default= 5]
[ --deciMaxError <FLOAT> ]
maximum error distance from the original data, in mm [default = 3]
[ --minFacetNumber <U32> ]
minimum number of facets to allow decimation [default=50]
[ --internalinterface <boolean> ]
mesh the internal interface of the main object [default=false]
[ --ascii <boolean> ]
write file in ASCII mode if the format supports it [default=binary]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMeshCC2Arg
-------------------------------------------------------------------------
AimsMeshCC2Arg -i[nput] <meshfilein>
-v[olume] <input_volume>
-t[exture] <input_texture>
[-o[utput] <output_arg>]
[-h[elp]]
-------------------------------------------------------------------------
Converts Connected Component texture to graph
-------------------------------------------------------------------------
meshfilein : input *.tri or *.mesh file
input_volume : for voxel sizes
output_arg : output *.arg file
input_texture : CC definition
-------------------------------------------------------------------------
AimsMeshConnectedComponent
-------------------------------------------------------------------------
AimsMeshConnectedComp -i[nput] <meshfilein>
-t[exture] <input_texture>
[-T[hreshold] <default:0>]
[-m[ode] <default:0>]
[-o[utput] <output_dist_texture>]
[--tri]
[--ascii]
[-h[elp]]
-------------------------------------------------------------------------
Label Connected Component
-------------------------------------------------------------------------
meshfilein : input *.tri or *.mesh file
output_dist_texture : output *.tex file (distance)
threshold : applied on input texture
mode : 1: lesser than threshold, 0: greater [default=0]
input_texture : object definition
tri : mesh in *.tri format [default=*.mesh]
ascii : write *.tex file in ASCII [default=binar]
-------------------------------------------------------------------------
AimsMeshCoordinatesToDecimated
AimsMeshCoordinatesToDecimated
------------------------------
Transfer 2D coordinates of a mesh to a decimated version of this mesh
Options :
-i | --input <string>
input mesh
-d | --deci <string>
decimatedMesh
-ix | --inputx <string>
input x coordinate
-iy | --inputy <string>
input y coordinate
-ox | --outputx <string>
output x coordinate
-oy | --outputy <string>
output y coordinate
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMeshCurvature
AimsMeshCurvature
-----------------
Estime the mean curvature of a mesh
Options :
-i | --input <string>
input file
-o | --output <string>
output texture
-m | --method <string>
method: "fem" -> finite elements, "boix" -> Boix, "barycenter" ->
barycenter, "boixgaussian" -> Boix Gaussian
[ -r | --ratio <FLOAT> ]
proportion (%) of point to be thresholded
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMeshCut
AimsMeshCut
-----------
Cuts a mesh by a plane
Options :
-i | --input <file name (read only): mesh of VOID>
input mesh
-o | --output <filename: mesh of VOID>
output cutout mesh
-a <FLOAT>
plane equation coef: a
-b <FLOAT>
plane equation coef: b
-c <FLOAT>
plane equation coef: c
-d <FLOAT>
plane equation coef: d
[ -p | --plane <filename: mesh of VOID> ]
output plane intersection mesh
[ --border <filename: Segments of VOID> ]
output border polygon
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMeshDecimation
AimsMeshDecimation
------------------
Decimates a triangulation
Options :
-i | --input <file name (read only): mesh of VOID>
input triangulation
[ -o | --output <filename: mesh of VOID> ]
output triangulation
[ --smooth <S32> ]
smoothes the mesh [default is no smoothing]
[ --smoothIt <S32> ]
smoothing number of iterations [default=10]
[ --smoothRate <FLOAT> ]
smoothing moving factor at each iteration [default=0.2]
[ --smoothAngle <FLOAT> ]
smoothing feature angle in degrees, between 0 and 180 degree, [default=180]
[ --deciReductionRate <FLOAT> ]
decimation reduction rate expected in % [default=99%]
[ --deciMaxClearance <FLOAT> ]
maximum clearance of the decimated mesh expected in mm [default=10]
[ --deciMaxError <FLOAT> ]
maximum error distance from the original mesh in mm [default=10]
[ --deciAngle <FLOAT> ]
feature angle in degrees, between 0 and 180: angle formed by local mesh
edges above which edges are preferably not smoothed [default=180: no
filtering]
[ --ascii <S32> ]
write *.mesh in ASCII [default=binar]
[ --precisionmap <file name (read only): texture of FLOAT> ]
precision map texture: if provided, use this texture to determine if
vertices can be removed easily or not during decimation, instead of the
default edges angles (see --deciAngle parameter)
[ --precthreshold <vector of FLOAT> ]
precision map thresholds (see --precisionmap parameter): vertices with
precision above the threshold are not removed at a given iteration step.
Several values may be used for the successive iteration steps.
If no threshold is provided, the proportion from the decimation reduction
rate is used at step 0, then increases exponentially to asymtotically reach
the max precision within about 20 steps
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMeshDistance
-------------------------------------------------------------------------
AimsMeshDistance -i[nput] <meshfilein>
[-t[exture] <input_texture>]
[-o[utput] <output_dist_texture>]
[--tri]
[--ascii]
[-h[elp]]
-------------------------------------------------------------------------
Compute geodesic distance to object
-------------------------------------------------------------------------
meshfilein : input *.tri or *.mesh file
output_dist_texture : output *.tex file (distance)
input_texture : object definition
tri : mesh in *.tri format [default=*.mesh]
ascii : write *.tex file in ASCII [default=binar]
-------------------------------------------------------------------------
AimsMeshGenerate
AimsMeshGenerate
----------------
Generates a common-shaped mesh
Options :
-i | --input <string>
input parameter file (.minf-like)
Possible types and parameters:
type : arrow
arrow_length_factor : relative length of the head
arrow_radius : radius of the tail
facets : (optional) number of facets of the cone section (default: 4)
point1 : 3D position of the head
point2 : 3D position of the center of the bottom
radius : radius of the head
type : cone
closed : (optional) if non-zero, make polygons for the cone end (default:
0)
facets : (optional) number of facets of the cone section (default: 4)
point1 : 3D position of the sharp end
point2 : 3D position of the center of the other end
radius : radius of the 2nd end
smooth : (optional) make smooth normals and shared vertices (default: 0)
type : cube
center : 3D position of the center
radius : half-length of the edge
smooth : (optional) make smooth normals and shared vertices (default: 0)
type : cylinder
closed : (optional) if non-zero, make polygons for the cylinder ends
(default: 0)
facets : (optional) number of facets of the cylinder section (default: 4)
point1 : 3D position of the center of the 1st end
point2 : 3D position of the center of the 2nd end
radius : radius of the 1st end
radius2 : (optional) radius of the 2nd end (default: same as radius)
smooth : (optional) make smooth normals and shared vertices (default: 0)
type : ellipse
center : 3D position of the center, may also be specified as 'point1'
parameter
facets : (optional) number of facets of the sphere. May also be specified
as 'nfacets' parameter (default: 225)
radius1 : radius1
radius2 : radius2
uniquevertices : (optional) if set to 1, the pole vertices are not
duplicated( default: 0)
type : icosahedron
center : 3D position of the center
radius : radius
type : icosphere
center : 3D position of the center, may also be specified as 'point1'
parameter
facets : (optional) minimum number of facets of the sphere. (default: 30)
radius : radius
type : sphere
center : 3D position of the center, may also be specified as 'point1'
parameter
facets : (optional) number of facets of the sphere. May also be specified
as 'nfacets' parameter (default: 225)
radius : radius
uniquevertices : (optional) if set to 1, the pole vertices are not
duplicated( default: 0)
-o | --output <filename: mesh of VOID>
output mesh
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMeshGeodesicDepth
-------------------------------------------------------------------------
AimsMeshClose -i[nput] <meshfilein>
-v[volume] <mask_volume>
[-c[close] <radius_close>]
[-e[rosion] <radius_erosion>]
[-o[utput] <output_vor_texture>
[-h[elp]]
-------------------------------------------------------------------------
Compute geodesic depth on a triangulation.
-------------------------------------------------------------------------
meshfilein : input *.tri or *.mesh file
brain_envelop : object definition (binary image relative to the triangualtion )
radius_close : radius of the closing [default = 10]
radius_erode : radius of the erosion [default = 5]
output_vor_texture : output *.tex file (voronoi diagram)
-------------------------------------------------------------------------
AimsMeshIsoLine
AimsMeshIsoLine
---------------
Create an isoline mesh (tube) for a textured mesh
Options :
-i | --inputMesh <string>
input mesh
-t | --inputTex <string>
input texture (TimeTexture<float>)
-o | --output <string>
output mesh
-v | --value <S32>
value of the isoline
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMeshLineMeasurement
AimsMeshLineMeasurement
-----------------------
Measurement along a line on a mesh
Options :
-i | --input <file name (read only): mesh of VOID>
input mesh
-p1 <POINT3DF>
3D position of the starting point (x,y,z)
-p2 <POINT3DF>
3D position of the end point (x,y,z)
[ -o | --output <filename: texture of FLOAT> ]
output texture line (default: not written)
[ -m <string> ]
mode: 'shortest' line, 'plane' line (default: shortest)
[ -pe <VECTOR_OF_4_FLOAT> ]
plane equation for 'plane' mode (see -m option) (a,b,c,d) for plane
ax+by+cz+d=0
[ -r <FLOAT> ]
ratio of the length between p1 and p2 where a point has to be determined
(default: 1)
[ -pe2 <VECTOR_OF_4_FLOAT> ]
half-space (plane equation) where to look for the target point in case of
ambiguity (useful only in 'plane' mode) (default: no restriction)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMeshMatching
AimsMeshMatching
----------------
Registration of a mesh on a binary image, by affine deformation
Options :
-r | --reference <file name (read only): volume of S16>
Reference binary image
-t | --test <file name (read only): mesh of VOID>
Test mesh
[ --transfo <string> ]
Specify transformation: RIGID/SIMILARITY/AFFINE [default=AFFINE]
[ --trm <filename: AffineTransformation3d> ]
File to save optimal transformation [default=[transfo]_[ref]_TO_[test].trm]
[ --trmInv <filename: AffineTransformation3d> ]
File to save inverse transformation [default=[test]_TO_[ref].trm]
[ --mesh <filename: mesh of VOID> ]
File to save the resulting mesh [default=no saving file]
[ --gcinit <string> ]
Initialize translation with gravity centers: yes/no [default=yes]
[ --log <string> ]
Log reporting the running process [default=no log]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
terminate called after throwing an instance of 'carto::user_interruption'
what(): user interruption
AimsMeshMedianSurface
AimsMeshMedianSurface
---------------------
AimsMeshMedianSurface
Options :
-i <string>
White Hemisphere Mesh
-e <string>
Grey/CSF Hemisphere Mesh
[ -v <string> ]
Neighbours table file (from "arrival" mesh)
-d <U32>
Process direction (int -> ext || ext -> int)
[ -vout <string> ]
Output file in case the neighbours table would not be available and should
be computed (8th order by default)
[ -o <string> ]
Output mesh
[ -v2 <string> ]
[DEBUG ONLY] Neighbours table file (from "other arrival" mesh)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMeshMni2Mesh
-------------------------------------------------------------------------
siMeshMni2Mesh -i[nput] <meshfilein>
-o[utput] <meshfileout>
[-h[elp]]
-------------------------------------------------------------------------
Transform MNI mesh format (.obj) to SHFJ mesh format (.tri or .mesh)
-------------------------------------------------------------------------
AimsMeshParcellation2VolumeParcellation
AimsMeshParcellation2VolumeParcellation
---------------------------------------
Project a mesh parcellation to a volume
Options :
-t | -texture <file name (read only): texture of S16>
input label (short) texture
-m | -mesh <file name (read only): mesh of VOID>
input mesh
-o | -output <string>
output parcellation volume
-v | -volume <string>
input volume file
[ -l | -label <S16> ]
label of the object in the volume (default = 100)
[ -T | -Time | -time <U32> ]
make graph from time T of input texture
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMeshPlane
-------------------------------------------------------------------------
AimsMeshPlane -n
[-t[exture] <output_tex>
-m[mesh]
[-h[elp]]
-------------------------------------------------------------------------
Build a mesh plane with sulci
-------------------------------------------------------------------------
meshfilein : input *.tri or *.mesh file
output_vor_texture : output *.tex file (voronoi diagram)
-------------------------------------------------------------------------
AimsMeshSmoothing
--------------------------------------------------------------------------
AimsMeshSmoothing -i[nput] <filein>
[-o[utput] <fileout>]
[-n[Iteration] <niter>]
[-I[sotropic]]
[-r[ate] <rate>]
[-x[rate] <rate>]
[-y[rate] <rate>]
[-z[rate] <rate>]
[-f[eatureAngle] <angle>]
[--tri]
[--ascii]
[-h[elp]]
--------------------------------------------------------------------------
Smoothes a triangulation
--------------------------------------------------------------------------
-i[nput] : prefix name for input triangulation is <filein>
-o[utput] : prefix name for output triangulation is <fileout>
[default=filein]
-n[Iteration] : number of iterations is <nb> [default=10]
-I[sotropic] : type of smoothing is isotropic [default=anisotropic]
-r[ate] : moving factor at each iteration for isotropic
smoothing is <rate> [default=0.2]
-x[rate] : moving factor on x axis is <rate> [default=0.2]
-y[rate] : moving factor on y axis is <rate> [default=0.2]
-z[rate] : moving factor on z axis is <rate> [default=0.2]
-f[eatureAngle] : feature angle is <angle> degree, between 0 and 180
[default=180]
--tri : *.tri file format [default=*.mesh]
--ascii : write *.mesh in ASCII [default=binar]
-h[elp] : display the current help message
--------------------------------------------------------------------------
AimsMeshToAtlas
AimsMeshToAtlas
---------------
Remesh a surface to a template atlas using spherical parameterization of both.
x-coordinate is the longitude (with a period). The atlas and the resulting mesh
then have a node to node correspondance
Options :
-i | --inputMesh <string>
input mesh
-o | --outputTex <string>
output mesh
-a | --atlasMesh <string>
atlas mesh
-ix <string>
mesh x-coordinate texture
-iy <string>
mesh y-coordinate texture
-ax <string>
atlas x-coordinate texture
-ay <string>
atlas y-coordinate texture
-px <FLOAT>
x-coord period (none=0)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMeshToMeshPoint
AimsMeshToMeshPoint
-------------------
From a point on a mesh find the closest point on another mesh
Options :
-m1 | --mesh1 <string>
source mesh
-m2 | --mesh2 <string>
target mesh
-p | --point <U32>
point index on source mesh
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMeshTransform
AimsMeshTransform
-----------------
Applies a transformation to a mesh
Options :
-i | --input <file name (read only): mesh of VOID>
input mesh
[ -o | --output <filename: mesh of VOID> ]
output (transformed) mesh [default: same as input]
[ -t | --transform <string> ]
transformation file *.trm
[ -a | --ascii <boolean> ]
write in ascii format
[ --scaleX <FLOAT> ]
specify X scale factor
[ --scaleY <FLOAT> ]
specify Y scale factor
[ --scaleZ <FLOAT> ]
specify Z scale factor
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMeshWhite
--------------------------------------------------------------------------
AimsMeshWhite -i[nput] <filein>
[-o[utput] <fileout>]
[--deciMaxClearance <clearance>]
[--deciMaxError <error>]
[--minFacetNumber <fnumber>]
[--ascii]
[-h[elp]]
--------------------------------------------------------------------------
Computes the brain surface from a segmented image and saves it in a
*.mesh or *.tri format file
--------------------------------------------------------------------------
-i[nput] : input short volume label is file <filein>
(level 0 is assumed to be the back)
-o[utput] : output prefix name for *.tri or *.mesh is <fileout>
[default=filein]
--deciMaxClearance : maximum clearance expected in the resulting mesh is
<clearance> mm [default= 5 mm]
--deciMaxError : maximum error distance from the original data
expected is <error> mm , [default = 3 mm]
--minFacetNumber : minimum number of facets to allow decimation
[default=50]
--ascii : write *.mesh file in ASCII mode [default=binar]
-h[elp] : display the current help message
--------------------------------------------------------------------------
AimsMeshes2Graph
AimsMeshes2Graph
----------------
Makes a graph from a set of meshes
Options :
-o | -output <string>
output data graph
[ -n | --name <string> ]
name attribute given to the graph's nodes (default=name of corresponding
mesh file)
[ -i | -input <vector of string> ]
input meshes filenames
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMidPlaneAlign
AimsMidPlaneAlign
-----------------
Rectify the image and compute the rectified transformation (superposition of
the interhemispheric plane with the plane x=dimX/2)
Options :
-i <string>
input image to rectify
[ -o <string> ]
output rectified image (default=rectified)
[ --start <S32> ]
pyramid start level for registration
[ --stop <S32> ]
pyramid stop level for registration
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMoment
----------------------------------------------------------------
AimsMoment -i[nput] <filein>
[-l[abel] <label>]
[-o[utput] <out>]
[-m[ode] <mode>]
[-t[ype] <type>]
[-h[elp]]
----------------------------------------------------------------
Compute the moment invariant
----------------------------------------------------------------
filein : input data (in 8 or 16 bits) or triangulated mesh
label : object label in raster image [default=all label]
out : ASCII result file name [default=stdout]
mode : mode f -> full i -> invariant only [default=f]
type : type v -> volumic s -> surfacic [default=v]
(only for triangulated mesh)
----------------------------------------------------------------
AimsMorphoMath
AimsMorphoMath
--------------
Morphological operators (erosion, dilation, closing, opening)
for both binary and gray level intensity images
Options :
[ -i <file name (read only): { Volume of DOUBLE, Volume of FLOAT, Volume of S16,
Volume of S32, Volume of S8, Volume of U16, Volume of U32, Volume of U8 }>
Input image ]
[ -r <FLOAT> ]
Radius parameter (in mm)
[ -m <string> ]
Mode that can be:
ero --> erosion
dil --> dilation
clo --> closing
ope --> opening
[ -o <string> ]
Output image
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMosaic
AimsMosaic
----------
Reconstruct an image mosaic from a list of images.
Options :
-i <string>
Input list of images (add a ' *' at the end of a line in the list if the
corresponding image is empty)
-x <S32>
Number of images along X
-y <S32>
Number of images along Y
-t <S32>
Data type :
S16 : 1
U8 : 2
FLOAT : 3
RGB : 4
-o <string>
Output reconstructed image
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMultiRecal
AimsMultiRecal
--------------
Compute registrations between two 2D or 3D volumes
Options :
-r <string>
input reference data
-t <string>
input test data
[ --roi <string> ]
input roi test data (default : connex components research)
[ -o <string> ]
output data
[ -m <string> ]
initialisation motion (default = identity)
[ --start <S32> ]
starting pyramid level (default = auto)
[ --stop <S32> ]
end pyramid level (default = auto)
[ --transfo <S32> ]
transformation type : 1 for rigid, 2 for similitude, 3 for affine (default
= 1)
[ --Xsize <S16> ]
x size of the bloc in voxel (default = 4)
[ --Ysize <S16> ]
y size of the bloc in voxel (default = 4)
[ --Zsize <S16> ]
z size of the bloc in voxel (default = 4)
[ --cutVar <DOUBLE> ]
% initial de blocs de plus forte variance conserv�s (default=auto)
[ --stopVar <DOUBLE> ]
minimum de ce % de blocs conserv�s (default=auto)
[ --%kept <DOUBLE> ]
% de blocs de plus faibles r�sidus conserv�s pour l'estimation robuste
(default=0.5)
[ --radius <FLOAT> ]
rayon de l'�rosion max en nombre de voxels (default = 5)
[ --correlThresh <DOUBLE> ]
threshold on the similarity criterion norm (default=-1, no threshold)
[ --lthRef <S16> ]
low grey level threshhold on ref image (default = -100000)
[ --hthRef <S16> ]
high grey level threshhold on ref image (default = +100000)
[ --lthTest <S16> ]
low grey level threshhold on test image (default = -100000)
[ --hthTest <S16> ]
high grey level threshhold on test image (default = +100000)
[ --iter <S32> ]
maximum number of iterations per pyramid level (default=3)
[ --field <string> ]
Displacement field (sorry, not active)
[ --Info <string> ]
list all the initial parameters : y or n (default=y)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsMultiply
------------------------------------------------------------------
AimsMultiply -i <i1>
-j <i2>
-o[utput] <fileout>
[-t[ype] <datatype>]
[-h[elp]]
------------------------------------------------------------------
Multiplication I1 x I2
------------------------------------------------------------------
i1 : first factor data
i2 : second factor data
fileout : destination data
datatype: output data type (S16, U8, ...). Default = i1 type
------------------------------------------------------------------
AimsNormDiff
----------------------------------------------------------------
AimsNormDiff
-r[eference image] < ref filename >
-c[ompared image] < compared filename >
-a[ref to mri dep] <filename >
-b[com to mri dep] <filename >
-o[utput] < norm image >
[-h[elp]]
----------------------------------------------------------------
Compute ration (R - C) / R
----------------------------------------------------------------
AimsNormWithRegion
----------------------------------------------------------------
AimsNormWithRegion
-i[nput series] < dynamic series >
-v[oi] < voifile >
-m[otion] < motionfile (default is identity) >
-n[ame] < reference ROI name (from selectionlist)>
-o[utput] < norm image >
-s[elector] < user defined selector file name >
-l[ist] < list of available template selectors>
-d[ose] < injected dose >
--hierarchy < hierarchyfile >
--selection < template selector>
[-h[elp]]
----------------------------------------------------------------
dyn series : input dynamic data
motionfile : displacement file default val : Identity
voifile : file containing roi information see(--voitype)
injected dose: if injected dose is specified, ROI
activity is normalized by this dose :
(Region - Reference)/Dose.
Otherwise it is normalized by the reference
ROI name : (Region - Reference)/Reference
--selection: template selector name available
: selectors may be listed (switch -l)
: OR
: all to disable selection mode
----------------------------------------------------------------
AimsOpening
-------------------------------------------------------------------------
AimsOpening -i[nput] <filein>
-o[utput] <fileout>
-e[radius] <radius>
[-x[mask] <xxx>] [-y[mask] <yyy>] [-z[mask] <zzz>]
[-f[actor] <fff>]
[-r[ead] <reader>]
[-h[elp]]
-------------------------------------------------------------------------
Morphological opening
-------------------------------------------------------------------------
filein : source volume
fileout : destination volume
radius : radius of the structuring element
xxx : X size of the distance mask [default=3]
yyy : Y size of the distance mask [default=3]
zzz : Z size of the distance mask [default=3]
fff : chamfer multiplication factor [default=50]
-------------------------------------------------------------------------
AimsOverVolume
-------------------------------------------------------------------------
AimsOverVolume -i[nput] <filein>
-o[utput] <fileout>
[--x0 <x0> --y0 <y0> --z0 <z0> --t0 <t0> ]
--dx <dimx> --dy <dimy> --dz <dimz> --dt <dimT>
[-h[elp]]
-------------------------------------------------------------------------
Change the dimension of an image.
-------------------------------------------------------------------------
filein : source volume
fileout : destination volume
dimx, dimy, dimz, dimT : size of the output volume
x0, y0, z0, t0 : translation (int) of the input image (default = none)
-------------------------------------------------------------------------
AimsPCAfilter
AimsPCAfilter
-------------
PCAnalysis
Options :
-i <file name (read only): volume of FLOAT>
input file
[ -c <S32> ]
for mask closing (default 1)
[ -r <S32> ]
for reduction (default 0)
[ -n <S32> ]
for temporal normalisation (default 0, 1-->max, 2-->euclid)
[ --am <S32> ]
for median aggreg (default 0)
[ --fm <S32> ]
for median filt (default 0)
[ --rx <S32> ]
x resolution (default 1)
[ --ry <S32> ]
y resolution (default 1)
[ --rz <S32> ]
z resolution (default 1)
[ --vp <S32> ]
eigenvalues kept (default 6)
[ -verbose <boolean> ]
yields some more info
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsPCAloc
AimsPCAloc
----------
LocalPCAnalysis
Options :
-i <file name (read only): volume of FLOAT>
input files
[ -verbose <boolean> ]
yields some more info
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsPCAloc2
AimsPCAloc2
-----------
PCAnalysis
Options :
-i <file name (read only): volume of FLOAT>
input files
[ -verbose <boolean> ]
yields some more info
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsParamCorrectDti
-------------------------------------------------------------------------
AimsParamCorrectDTI -d[istorded] <distorded>
-o[utput] <fileout>
-p[arameter] <param>
[--memMap]
[-r[ead] <reader>]
[-h[elp]]
-------------------------------------------------------------------------
Correction of DTI distorsions from an existing parameter file
-------------------------------------------------------------------------
distorded : source S16 distorded data
fileout : destination S16 data file name
param : parameter file containing corrections
memMap : memory mapping activated (obsolete, automatic)
-------------------------------------------------------------------------
AimsParameterize2DImageDomain
AimsParameterize2DImageDomain
-----------------------------
Lissage couplé d'un couple d'images 2D avec des contraintes
Options :
[ -i1 | --input1 <string> ]
input Image1
[ -i2 | --input2 <string> ]
input Image2
-c1 | --cont1 <string>
input constraint1
-c2 | --cont2 <string>
input constraint2
-o1 | --output1 <string>
output Image1
-o2 | --output2 <string>
output Image2
-t | --scale <FLOAT>
scale
[ -dt | --deltat <FLOAT> ]
time step (diffusion only; default=0.1)
[ -a <FLOAT> ]
diffusion weight
[ -b <FLOAT> ]
constraints term
[ -g <FLOAT> ]
coupling term
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsParameterizeGyri
AimsParameterizeGyri
--------------------
Paramétrisation de la surface corticale à partir d'une parcellisation en gyri
Options :
-i | --inMesh <string>
inputMesh
-t | --inTex <string>
gyral parcellation inputTexture
-g | --gyri <string>
gyri to texture correspondance table
-m | --model <string>
text file model of the relations between gyri and the system constraints
[ -s | --spmtex <string> ]
activation texture for surface-based mapping ( default = "" )
-c | --constraint <U32>
constraint method (0 = w/o constraints, 1 = iso-extracted constraints, 2 =
mixed constraints, 3 = functional constraints iso-extracted mode, 4 =
functional constraints mixed mode, 5 = spot constraints)
[ -C | --criter <FLOAT> ]
Limit for the diffusion process ( default = 1e-4 )
[ -d | --dt <FLOAT> ]
Iterative step ( default = 0.05 )
-o | --outTex <string>
outputTexture
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsParameterizeSulcus
AimsParameterizeSulcus
----------------------
Parameterize the mesh of a sulcus
Options :
-i | --input <string>
input mesh
-b | --bottom <string>
sulcus bottom point image
-t | --top <string>
sulcus top point (junction with brain hull) image
-o | --orientation <S32>
sulcus main orientation : top->bottom = 0, back->front = 1
-ox | --outputx <string>
1st output texture (depth)
-oy | --outputy <string>
2nd output texture ('along' the sulcus)
[ -m | --method <string> ]
curvature computation method (fem/boix/barycenter, default=boix)
[ -d | --deltaT <FLOAT> ]
diffusion iteration step (default=0.05)
[ -s | --stop <FLOAT> ]
laplacian variation stopping criterion (default=0.000003)
[ -di | --dilation <S16> ]
dilation of the ridges (1=yes (default), 0=no)
-mo <FLOAT>
Morphological offset between dilation and erosion of ridges for extrem
cases (default=0, otherwise should be 1.0)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsPlotCoordinatesOnMesh
AimsPlotCoordinatesOnMesh
-------------------------
Plot a point defined by 2D coordinates by creating a texture
Options :
-i | --inputMesh <string>
input mesh
-l | --lat <string>
latitude texture
-L | --lon <string>
longitude texture
-x | --plat <FLOAT>
point latitude
-y | --plon <FLOAT>
point longitude
-o | --outT <string>
output texture
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsPlotOnSPhericalAtlas
--------------------------------------------------------------------------
AimsPlotOnSphericalAtlas -i[nput] <coordinates file>
-m <atlas mesh>
-u <longitude texture>
-v <latitude texture>
-o <output mesh>
[-h[elp]]
coordinate file (ASCII) contains one line per point, each line
contains only longitude and latitude separated by a space :
u1 v1
u2 v2
u3 v3
...
--------------------------------------------------------------------------
AimsPowerComb
------------------------------------------------------------------
AimsPowerComb -i <i1> [-a <num1>] [-b <den1>]
[-j <i2> [-c <num2>] [-d <den2>]]
[-e <cst>]
-o[utput] <fileout>
[-t[ype] <datatype>
[-h[elp]]
------------------------------------------------------------------
Power combination e * I1^(a/b) * I2^(c/d)
Note : a,b,c,d,e must be real
------------------------------------------------------------------
i1 : first data (volume or texture)
num1 : multiplicative coefficient for the first data [1.0]
den1 : divisor coefficient for the first data [1.0]
i2 : second data (volume or texture)
(if none, I1^(a/b) )
num2 : multiplicative coefficient for the second data[1.0]
den2 : divisor coefficient for the second data [1.0]
cst : constant offset value [default=1.0]
fileout : destination data
datatype: data type of the destination volume/texture (S16, U8, ...)
[default=type of in1]
For texture, i1, i2 and fileout must have the same type
------------------------------------------------------------------
AimsRFdf
AimsRFdf
--------
Lit des donnees Fdf
Options :
-i <string>
input data filename
[ -o <string> ]
output label data filename
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsRTiff
AimsRTiff
---------
Lit des données Tiff
Options :
-i <string>
input data filename
[ -o <string> ]
output label data filename
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsReadDpy
AimsReadDpy
-----------
Read amyloid plaques data
Options :
-i <string>
input data filename
[ -o <string> ]
output label data filename
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsRefineMesh
AimsRefineMesh
--------------
Mesh refinement
Options :
-i <file name (read only): mesh of VOID>
input mesh
-o <filename: mesh of VOID>
output mesh
[ -a <boolean> ]
write in ascii format
-l <FLOAT>
maximum edge length in mm
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsRemoveNaN
AimsRemoveNaN
-------------
Remove NaN (Not a Number) values from an image
Options :
-i <file name (read only): { Volume of DOUBLE, Volume of FLOAT }> input file
[ -o <string> ]
output file (if ommited, only information about NaN will be showed)
[ --value <DOUBLE> ]
value used to replace NaN value (default = 0, with default -np value it
corresponds to the image minimum)
[ -np <boolean> ]
By default value is expressed in percentage of voxel value: value =
min+(max-min)*(percentage/100). If this option is used, value is used
direclty
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsReplaceLevel
AimsReplaceLevel
----------------
Replace gray levels by others
Options :
-i | --input <string>
input
-o | --output <string>
outpout
-g | --graylevel <vector of FLOAT>
gray levels to replace
-n | --new <vector of FLOAT>
new values for gray levels
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsResample
AimsResample
------------
Resampling. Applies a transformation matrix to a volume. Performs linear
resampling
Options :
-i | --input <file name (read only): { Volume of DOUBLE, Volume of FLOAT,
Volume of RGB, Volume of RGBA, Volume of S16, Volume of S32, Volume of S8,
Volume of U16, Volume of U32, Volume of U8 }> source volume
-o | --output <string>
destination volume
[ -m | --motion <string> ]
motion file [default=identity]
[ --dx <S32> ]
dimx of the resampled volume
[ --dy <S32> ]
dimy of the resampled volume
[ --dz <S32> ]
dimz of the resampled volume
[ --sx <FLOAT> ]
voxel x dimension of the resampled volume
[ --sy <FLOAT> ]
voxel y dimension of the resampled volume
[ --sz <FLOAT> ]
voxel z dimension of the resampled volume
[ -t | --type <string> ]
Resampling type: l[inear], n[earest], q[uadratic], c[cubic], quartic,
quintic, six[thorder], seven[thorder] [default=linear]. Modes may also be
specified as order number: 0=nearest, 1=linear etc.
[ -r | --reference <string> ]
Volume used to define output voxel size and volume dimension (values are
overrided by --dx, --dy, --dz, --sx, --sy and --sz)
[ -d | --defaultvalue <string> ]
Default value for borders [default=0]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsResampleFromFieldsData
AimsResampleFromFieldsData
--------------------------
Resample an image from a resampling field
Options :
-i <string>
Input image
-f <string>
Resampling field data
-t <S32>
Data type :
S16 : 1
U8 : 2
FLOAT : 3
RGB : 4
-o <string>
Output resampled image
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsRgbToHsv
AimsRgbToHsv
------------
RGB-HSV conversion
Options :
-i <string>
Input RGB image
[ -ov <string> ]
Output value image
[ -os <string> ]
Output saturation image
[ -oh <string> ]
Output hue image
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsRoiFeatures
AimsRoiFeatures
---------------
Compute simple statistics on one or more images from regions of interest.
Features computed are min, max, mean, standard deviation and median. The output
can be in minf or csv format (see -f option below). In minf format, its a
dictionary containing one sub-dictionary per ROI. Each sub-dictionary contains
one entry per feature (identified by the label of the feature). In csv format
it is a text file containing values separated by tabulation character and
compatible with main spread sheet software such as OpenOffice and Excel.
Examples:
1) To compute the statistics of region drawn in Anatomist on a single image:
AimsRoiFeature -i regionsDrawnWithAnatomist.arg -s chaos_fa.ima chaos_vr.ima
2) To compute the statistics of regions defined in an image of labels on
several images:
AimsRoiFeature -i imageOfLabels.ima -s first.ima second.ima
3) To compute statistics on several images with the same filename:
AimsRoiFeature -i imageOfLabels.ima -s first:first/image.ima
second:second/image.ima
4) Same as 3) but save the result in csv format:
AimsRoiFeature -i imageOfLabels.ima -s first:first/image.ima
second:second/image.ima -f csv
5) Same as 4) but use french locale (i.e. comma for decimal point in numbers):
AimsRoiFeature -i imageOfLabels.ima -s first:first/image.ima
second:second/image.ima -f csv -l fr
Options :
-i | --input <string>
input ROI file (either ROI graph or image)
[ -s | --imageStatistics <vector of string> ]
Compute statistics from one or more images. Each argument of this parameter
can be either an image or a graph. The file name can be prefixed with
<label>: to specify the label that will be used to identify the image in
the output (by default, the file name without extention is used).
[ -t | --transformation <file name (read only): AffineTransformation3d> ]
Transformation between ROI and images (default = identity)
[ -o | --output <string> ]
output file name (default = standard output)
[ -f | --format <string> ]
output file format. Possible formats are minf or csv. Default value:
guessed according to file name extension, if the extension is unknown, the
minf format is used.
[ -l | --locale <string> ]
Change the locale used for writing numbers in csv format. For instance, to
use a csv file in a french version of Excel, one should use a french locale
with "-l fr_FR.utf8".
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsRoiOverlap
AimsRoiOverlap
--------------
Compute overlapping criteria to compare quantitatively two segmentations
only for volumes of labels (same dim + voxel_size)
ROIs must have same label in both volumes
#############################################################################
2 * | VolTest_lab(i) - VolRef_lab(i) |
Vol_Diff_lab(i) = ----------------------------------------
VolTest_lab(i) + VolRef_lab(i)
2 * intersection ( VolTest_lab(i),VolRef_lab(i) )
Dice_lab(i) = -----------------------------------------------------
VolTest_lab(i) + VolRef_lab(i)
intersection ( VolTest_lab(i),VolRef_lab(i) )
Jaccard_lab(i) = ----------------------------------------------------
union ( VolTest_lab(i),VolRef_lab(i) )
intersection ( VolTest_lab(i),VolRef_lab(i) )
Sensitivity_lab(i) = ---------------------------------------------------
VolRef_lab(i)
#############################################################################
Options :
[ -r <file name (read only): { Volume of DOUBLE, Volume of FLOAT, Volume of S16,
Volume of S32, Volume of S8, Volume of U16, Volume of U32, Volume of U8 }>
Input reference data ]
[ -t <string> ]
Input test data
[ -o <string> ]
Output textfile
[ -matrix <string> ]
Output image
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsSNR
----------------------------------------------------------------
AimsSNR -i[nput] <filein>
[-v[oi] <voi>]
[-x <X> -y <Y> -z <Z> -R <R>]
[-o[utput] <fileout>]
[--lineFlag] <output_format>]
[-h[elp]]
----------------------------------------------------------------
SNR of a VOI in a 3D image
----------------------------------------------------------------
filein : origin 3D file
voi : U08 mask file of the V.O.I.
X,Y,Z : Point3d center of a spherical ROI
R : radius of spherical ROI
fileout : output file [default=stdout]
output_format : format of the output file [default=detailed]
detailed in two columns or just a line a values
----------------------------------------------------------------
AimsSegment2Modes
AimsSegment2Modes
-----------------
Segmentation based on adaptive thresholding
Options :
-r <file name (read only): volume of S16>
Input image RED
-g <file name (read only): volume of S16>
Input image GREEN
-s <LONG>
minimum size
[ --clo <boolean> ]
morpho math [Default=no]
[ -e <FLOAT> ]
radius
-m <filename: volume of S16>
Mask image
[ --correct <boolean> ]
Apply a correction to green component [Default=no]
-o <filename: volume of S16>
Output image GREEN
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsSegmentsToMesh
--------------------------------------------------------------------------
AimsSegmentsToMesh -i[nput] <filein>
-o[utput] <fileout>
[ -w[idth] ] <size>
[ -v[erbose] ]
[ -h[elp] ]
--------------------------------------------------------------------------
Take a list of segments (pairs of points) and build a 3D composed of
cylinders. Each cylinder joins two points of a segment.
--------------------------------------------------------------------------
-i[nput] : Serie of pair of 3D points
-o[utput] : Name of the output mesh file
-w[idth] : Width of the cylinder (default 1)
-v[erbose] : display information on standard error output
-h[elp] : display the current help message
--------------------------------------------------------------------------
AimsSelectLabel
AimsSelectLabel
---------------
Select labels from a label data and put it into a new label data into a new
label data
Options :
-i <string>
input label data filename
-l <list of S16>
selected label values
-o <string>
output label data filename
[ -b <S16> ]
background label (default=-1)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsSetMinf
AimsSetMinf
-----------
Set arbitrary tag in the minf file
Options :
-i | --input <string>
input data
[ -t | --target <vector of string> ]
target name
[ -v | --value <vector of string> ]
value for target
[ -f | --from <string> ]
from other image
[ -c | --copy <vector of string> ]
copy given attribute(s) from other image (needs -f option)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsSetTransformation.py
Usage: AimsSetTransformation.py [options]
set an affine transformation information in an object header from a
transformation file
Options:
-h, --help show this help message and exit
-i FILE, --input=FILE
object to set transformation info on (volume, mesh,
etc).
-t TRMFILE, --transformation=TRMFILE
transformation file (*.trm). If not specified and -n
option is used, then erase the n-th transformation in
list.
-n TRANSNUM, --number=TRANSNUM
set transformation information as the n-th
transformation. Default: append at end of list
-d DESTINATION, --destination=DESTINATION
set destination referential name/UUID. Default: try to
get it from the transformation file header
AimsSiemensEPI2Volume
----------------------------------------------------------------
AimsSiemensEPI2Volume -i[nput] <filein>
-o[utput] <fileout>
-f[irst] <num>
-s[lices] <nbslice>
-r[epetitions] <nbrep>
[-w[rite] <writer>]
[-h[elp]]
----------------------------------------------------------------
Concatenates all Siemens NEMA EPI images to a 4D data file
----------------------------------------------------------------
filein : origin file
fileout : output file
num : first image number in series
nbslice : number of slices
nbrep : number of repetitions
----------------------------------------------------------------
AimsSimilarComponentAnalysisSegmentation
AimsSimilarComponentAnalysisSegmentation
----------------------------------------
Similar component analysis automatic segmentation
Options :
-i <string>
dynamic series file
-o <string>
fileout segmentation image filename
[ -m <string> ]
input mask of organism of interest (example: brain mask)
[ -c <S32> ]
number of classes (default : 12)
[ -r <S32> ]
number of runs (default : 5)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsSlice2Bucket
-------------------------------------------------------------------------
AimsSlice2Bucket -i[nput] <input>
-o[utput] <output>
-d[ir] <dir>
[-m[in] <minimum>]
[-M[ax] <maximum>]
[-I[ncrement] <inc>]
[-a[scii]]
[-h[elp]]
-------------------------------------------------------------------------
Save slices of a mask to buckets
-------------------------------------------------------------------------
input : input S16 or U8 mask data file
output : output file name for *.bck file
dir : direction of the slice ('x', 'y' or 'z')
minimum : lower slice index [default=0]
maximum : upper slice index [default=dim-1]
inc : increment of slices between two slices [default=1]
ascii : save buckets in ASCII mode [default=binary]
-------------------------------------------------------------------------
AimsSmoothing
AimsSmoothing
-------------
Applies a smoothing filter to a volume.
Options :
-i | --input <string>
source volume
-o | --output <string>
destination volume
[ --dx <S32> ]
x dimension of the filter to apply
[ --dy <S32> ]
y dimension of the filter to apply
[ --dz <S32> ]
z dimension of the filter to apply
[ -t | --type <string> ]
Smoothing filter type: mea[n], med[ian], min[imum], max[imum], maj[ority]
(default = majority)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsSpaghettiModel
----------------------------------------------------------------
AimsSpaghettiModel -i[nput] <filein>
-o[utput] <fileout>
[--sx <sx> --sy <sy> --sz <sz>]
[-h[elp]]
----------------------------------------------------------------
creates tensor map with elementary geometrical objects
----------------------------------------------------------------
filein : description file
+---------------------------------------+
| number of objects |
| dimx dimy dimz |
-->| CYLINDER |
| origin 0 5 17 |
| axe 0 1 0 |
| dir 1 1 0 |
| radius 4 |
| length 10 |
| aniso 0.3 |
| lambda1 6.5 |
| deltaL 0.5 |
| deltaA 30 |
| random yes |
-->| TORUS |
| origin 5 9 17 |
| axe 0 0 1 |
| Radius 8 |
| radius 3 |
| aniso 0.8 |
| lambda1 23.5 |
| deltaL 0.4 |
| deltaA 20 |
| random no |
-->| CUBE |
| p0 0 0 0 |
| p1 10 10 10 |
| axe 1 0 0 |
| aniso 0.1 |
| lambda1 1.0 |
| deltaL 0.1 |
| deltaA 30 |
| random yes |
-->| PARALLELEPIPEDE |
| origin 0 0 0 |
| v1 1 0 0 |
| v2 0 1 0 |
| L1 4 |
| L2 8 |
| L3 6 |
| axe 1 0 0 |
| aniso 0.1 |
| lambda1 1.0 |
| deltaL 0.1 |
| deltaA 30 |
| random no |
+---------------------------------------+
fileout : output volume sequence file
sx,sy,sz: voxel size [default=1.0,1.0,1.0]
----------------------------------------------------------------
AimsSphereDistribution
--------------------------------------------------------------------------
AimsSphereTriangulation -d[irections] <direction>
[ -o[utput] <fileout> ]
[ -s[steps] <steps> ]
[ -r[adius] <radius>
[-h[elp]]
--------------------------------------------------------------------------
Output a file with coordinates of discrete spheric distribution with any
number of directions.
See also : AimsIcosaList, AimsSphereTriangulation
--------------------------------------------------------------------------
-d[direction] : number of directions
-o[utput] : output file name (default: standard output)
-s[steps] : maximum number of minimization steps (default 10000)
-r[adius] : radius of the sphere (default : 1)
-h[elp] : display the current help message
--------------------------------------------------------------------------
AimsSplitArray
AimsSplitArray
--------------
Split one array image in print-tip images
Options :
-i | --input <file name (read only): volume of U16>
array image
-o | --output <filename: volume of S16>
name of output pseudo volume
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsSplitRgb
AimsSplitRgb
------------
Split an AimsData<AimsRGB> into 3 AimsData<byte> files
Options :
-i <string>
input RGB data
[ -o <string> ]
output data
[ -t <string> ]
output data type [default: U8]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsSpmNormalizationConvert.py
Usage: AimsSpmNormalizationConvert.py [options]
Reads the affine part of a SPM normalization file (_sn.mat) and converts it to
an AIMS .trm file.
Options:
-h, --help show this help message and exit
-i FILE, --input=FILE
SPM normalization file (*_sn.mat)
-s SOUREFILE, --source=SOUREFILE
source image which has been used for normalization,
but not resampled in the template space
-o TRMFILE, --output=TRMFILE
output transformationfile *.trm
-d DESTREF, --destref=DESTREF
set destination referential name/UUID. Default: none
--srcref=SRCREF set source referential name/UUID. Default: try to
guess it from source image
AimsStereologySampling
AimsStereologySampling
----------------------
Stereology sampling estimation
Options :
-i <file name (read only): volume of S16>
Binary image (segmented)
-m <file name (read only): volume of S16>
Mask image (tissue)
[ -max <S32> ]
Max sampling value [default : 50]
[ -r <string> ]
Results file (txt format)
-o <filename: volume of S16>
Grid file
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsStereotaxy
AimsStereotaxy
--------------
Reads a graph, compute stereotaxic distances
Options :
-t <A30_c>
Text file *.txt
-g <string>
Input graph name
[ -n <S32> ]
Plane number [Default: n=1]
-m <string>
Output mesh name [Extension *.mesh
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsSubSampling
AimsSubSampling
---------------
Perform Image subsampling,using average operator
Options :
-i | --input <string>
input data
-o | --output <string>
output data
[ -n <S32> ]
number of voxels [default = 2 voxels in x and y directions]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsSubTensor
----------------------------------------------------------------
AimsSubTensor [-h[elp]]
-i[nput] <filein>
-o[utput] <fileout>
[-x <xmin> -y <ymin> -z <zmin>
-X <xmax> -Y <ymax> -Z <zmax>]
[-m<ask> <bucket>]
[-a[scii]]
----------------------------------------------------------------
Extracting a subpart from a DtiTensor bucket
----------------------------------------------------------------
filein : source tensor bucket
fileout : destination bucket of sub-dtitensor
generates fileout.bck
xmin,ymin,zmin : inferior point of the box sub-part
xmax,ymax,zmax : superior point of the box sub-part
bucket : Void bucket mask
ascii : write in ascii mode rather than binary
[default=binary]
----------------------------------------------------------------
AimsSubVolume
AimsSubVolume
-------------
Carve a subvolume in the input volume
Options :
-i | --input <string>
input data
[ -x | --firstx <vector of S32> ]
first x coordinate (default 0)
[ -y | --firsty <vector of S32> ]
first y coordinate (default 0)
[ -z | --firstz <vector of S32> ]
first z coordinate (default 0)
[ -t | --firstt <vector of S32> ]
first t coordinate (default 0)
[ -X | --lastx <vector of S32> ]
last x coordinate (default SizeX-1)
[ -Y | --lasty <vector of S32> ]
last y coordinate (default SizeY-1)
[ -Z | --lastz <vector of S32> ]
last z coordinate (default SizeZ-1)
[ -T | --lastt <vector of S32> ]
last t coordinate (default SizeT-1)
[ -l | --lap <boolean> ]
take X,Y,Z and T as dimensions instead of coordinates)
-o | --output <vector of string>
output data
[ -motion <boolean> ]
Write motions whole_TO_subvolume and inverse (default=no)
[ -mdir <string> ]
Motion name : whole_TO_subvolume
[ -minv <string> ]
Motion name : subvolume_TO_whole
[ --singleminf <boolean> ]
Only write .minf meta-header on the first sub-volume (useful when writing a
series)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsSulcalLines
AimsSulcalLines
---------------
Cortical Sulcal Lines (for cortical surface coordinate system)
Options :
-i | --inMesh <string>
input Mesh
[ -m | --inMethod <S32> ]
extraction of extremities method :
1 : projection crop by basins
2 : map of probability (embc11 method)
3 : map of density (NeuroImage method, by default)
4 : map of probability (basin user defined) :
[ -o | --inSulcalines <string> ]
output sulcal lines texture (.tex)
[ -c | --inTexCurv <string> ]
input Texture Curvature (barycenter curvature by default)
[ -d | --inTexGeoDepth <string> ]
input Texture Geodesic Depth
[ -t | --inConstraint <S32> ]
constraint type (shortest path) :
1 : on curvature map (by default)
2 : on depth map
[ -st | --strain <S32> ]
strain parameter (15 by default)
[ -b | --bottom <string> ]
sulcus bottom point volume
[ -lb | --inLabelBasins <string> ]
input label of basins (.txt)
[ -ls | --inLabelSulcalines <string> ]
input file : label-constraint correspondances of Sulcalines (.txt)
[ -ct | --curvthresh <FLOAT> ]
curvature threshold for basins segmentation (0.0 by default)
[ -s | --save <string> ]
folder path for save texture
[ -si | --side <string> ]
side of hemisphere (left, right, both)
[ -sb | --size_basins <FLOAT> ]
threshold of basins size (50 by default)
[ -cv | --constraintvalue <S32> ]
constraint value :
1 Basin (by default) :
2 LatLon value
[ -e | --max_extremities <S32> ]
max number of extremities (2 by default)
[ -p <vector of FLOAT> ]
threshold of probability (0.4 by default)
[ -lon | --inTexLon <string> ]
input Texture Longitude Constraints
[ -lat | --inTexLat <string> ]
input Texture Latitude Constraints
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsSulciVoronoi.py
Usage: AimsSulciVoronoi.py [options]
Voronoi diagram of the sulci nodes regions, in the grey matter, and extending
to the whole 3D space
Options:
-h, --help show this help message and exit
-g LGW, --greywhite=LGW
left grey/white mask
-o VORONOI, --output=VORONOI
output voronoi diagram volume
-f GRAPH, --folds=GRAPH
sulci graph file
AimsSulcusCorticalSnake
AimsSulcusCorticalSnake
-----------------------
Project an entire sulcus using multi-scale snake
Options :
-i | --input <string>
input constraint texture
-m | --mesh <string>
hemisphere mesh
-v | --value <FLOAT>
value of the constraint
-a | --alpha1 <FLOAT>
Constraint distance parameter
-b | --alpha2 <FLOAT>
curvature parameter
-c | --alpha3 <FLOAT>
elasticity parameter
-o | --output <string>
output texture
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsSulcusNormalizeDepthProfile
AimsSulcusNormalizeDepthProfile
-------------------------------
Compute depth and profile curve from SC
Options :
-m | --mesh <string>
input mesh
-x | --xcoord <string>
x coordinate texture
-y | --ycoord <string>
y coordinate texture
-d | --dist <string>
dist to plan file
-o | --out <string>
output text file
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsSulcusSPAM
-------------------------------------------------------------------------
AimsSulcusSPAM -t[exture] <input_texture>
-s[ulsi_spam]
-o[utput <output_mesh>]
-m[esh] <input_mesh>]
[-h[elp]]
-------------------------------------------------------------------------
SPAM
-------------------------------------------------------------------------
input_texture : object definition
output_texture : output *.tex file (blobs)
-------------------------------------------------------------------------
AimsSumFrame
AimsSumFrame
------------
Compute The sum of the dynamic series :for a PET file, use AimsSumPETImage
Options :
-i | --input <file name (read only): { Volume of DOUBLE, Volume of FLOAT,
Volume of S16, Volume of S32, Volume of S8, Volume of U16, Volume of U32,
Volume of U8 }> input series <dynamic series>
[ -s | --startframe <S32> ]
start frame < between 1 and maxFrame >
[ -e | --endframe <S32> ]
end frame < between 1 and maxFrame >
[ -b | --byframe <boolean> ]
(to enforce frame by frame computation)
-o | --output <string>
output average volume
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsSumPETFrame
AimsSumPETFrame
---------------
Compute The sum (average) of the dynamic PET series
Options :
-i | --input <file name (read only): { Volume of DOUBLE, Volume of FLOAT,
Volume of S16, Volume of S32, Volume of S8, Volume of U16, Volume of U32,
Volume of U8 }> input series <dynamic series>
[ -s | --startframe <S32> ]
start frame < between 1 and maxFrame >
[ -e | --endframe <S32> ]
end frame < between 1 and maxFrame >
[ -b | --byframe <boolean> ]
(to enforce frame by frame computation)
-o | --output <string>
output average volume
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsSwapEndian
----------------------------------------------------------------
AimsSwapEndian -i[nput] <filein>
-o[utput] <fileout>
-t[ype] <intype>
[-h[elp]]
----------------------------------------------------------------
convert a UNIX data to a LINUX byte ordered data
----------------------------------------------------------------
filein : origin file
fileout : output file
intype : short,ushort,int,uint,float,double
----------------------------------------------------------------
AimsT2BasedCorrectionEpi
AimsT2BasedCorrectionEpi
------------------------
T2 based correction of echoplanar distortions in DW MR image
Base on a model of geometric distortion characterized by:
- a scaling S,
- a translation T0,
- a shearing T1
Options :
-i <file name (read only): volume of S16>
T2+DW image
-d <string>
Description file
-o <filename: volume of S16>
Corrected T2+DW image
[ -divider <S32> ]
divider for subresolution calculations (default=1)
[ -levels <S32> ]
number of graylevels in MI calculations (default=64)
[ -smoothing <string> ]
pdf smoothing deriche/discrete (default=discrete)
[ -sigma <FLOAT> ]
discrete : gaussian mask size (default=3)
deriche : gaussian std dev. (default=3.0mm)
[ -deltaS <FLOAT> ]
variation of S (default=0.05)
[ -deltaT0 <FLOAT> ]
variation of T0 (default=1.00)
[ -deltaT1 <FLOAT> ]
variation of T1 (default=0.01)
[ -error <FLOAT> ]
tolerance on results (default=0.005)
[ -memMap <boolean> ]
memory mapping activated (obsolete, automatic)
[ -parameters <string> ]
(S,T0,T1) parameter text file name [default=not saved]
[ -verbose <boolean> ]
show as much information as possible
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsTCat
AimsTCat
--------
Concatenates files along time.
Works on homogen input data (volumes of S16, ...). Currently supports:
Bucket of VOID
Mesh of VOID
Mesh2 of VOID
Mesh4 of VOID
Texture of FLOAT
Texture of POINT2D
Texture of POINT2DF
Texture of S16
Texture of U32
Volume of CDOUBLE
Volume of CFLOAT
Volume of DOUBLE
Volume of FLOAT
Volume of POINT3DF
Volume of RGB
Volume of RGBA
Volume of S16
Volume of S32
Volume of S8
Volume of U16
Volume of U32
Volume of U8
Options :
-o | --output <string>
output data
-i | --input <vector of string>
input files
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsTMSCone.py
Usage: AimsTMSCone.py [options]
Creates a cone or other mesh representing the TMS active zone at the specified
target position along the head mesh
Options:
-h, --help show this help message and exit
-i HEADMESHFILE, --input=HEADMESHFILE
input head mesh
-o CONEFILE, --output=CONEFILE
output mesh
-s STIMPOINT, --stimpoint=STIMPOINT
stimulation position in mm on head or cortex (3 float
numbers)
-r BASERADIUS, --radius=BASERADIUS
stimulation cone base radius
-d DEPTH, --depth=DEPTH
stimulation cone depth
-n NORMALRADIUS, --normalradius=NORMALRADIUS
radius around stimulation point to average normal
[optional, default=20]
-m NORMALMESH, --normalmesh=NORMALMESH
output mesh for the normal line (just for
visualization purpose) [optional]
-t TARGETLINEMESH, --targetlinemesh=TARGETLINEMESH
output mesh for the target-head projection line, which
might be slightly different from the normal. If the
target is specified on the head, this line is by
defninition the normal. [optional]
-b BRAIN, --brain=BRAIN
brain (or grey/white cortex) mask [optional, -z option
needed]
-c CORTEXVALUE, --cortex=CORTEXVALUE
cortex value in grey/white mask image, [default: all
non-zero]
-z STIMZONE, --zone=STIMZONE
stimulation zone output filename (.bck) [optional, -b
option needed]
-w WRITERESULTS, --writeresults=WRITERESULTS
output text file where to write results (points and
directions) [optional]
AimsTMStarget
AimsTMStarget
-------------
Creates texture target for TMS aiming
Options :
-i | --input <string>
input mesh file (head)
-o | --output <string>
output target texture file
[ -n <U32> ]
Neighbourhood size for the target position estimation
[default = 10]
-l | --landmarks <string>
landmarks positions file
[ --ascii <boolean> ]
write texture file in ASCII mode
[default=binary]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsTalairachTransform
AimsTalairachTransform
----------------------
Compute talairach transform from talairach base coordinates and a mask
Options :
[ -apc <string> ]
apc file transformation
[ -o <string> ]
Output transformation file
[ -m <string> ]
Mask
[ -ns <boolean> ]
No scale factor is applied, single rotation around AC, no talairach
coordinates
[ -p <string> ]
Roi graph containing points placed on the extremities of the brain
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsTensor2Bucket
----------------------------------------------------------------
AimsTensor2Bucket [-h[elp]]
-i[nput] <filein>
-o[utput] <fileout>
-m[ask] <brain>
[-a[scii]]
[-s[upplement]]
[-r[eplace]]
[-u[ncorrected]]
----------------------------------------------------------------
Transformation of 4D tensor image to tensor bucket
----------------------------------------------------------------
filein : source echo data (GIS)
fileout : destination bucket of dtitensor
generates fileout.bck
brain : U8 mask of the brain or white matter
ascii : save bucket in ASCII mode
supplement : save also files fileout_traceTC.ima
fileout_traceEV.ima
fileout_VR.ima
fileout_FA.ima
fileout_dir.ima
fileout_dirRGB.ima
replace : when a point is NOT_POSITIVE_MATRIX, replace
by an isotropic tensor which mean diffusivity
is estimated on the N26 neighborhood of the
point rather than the mean diffusivity equal
to traceTC / 3.0
uncorrected: let traceEV and traceTC not corrected
(they may become negative with noise)
----------------------------------------------------------------
AimsTensorExtract
----------------------------------------------------------------
AimsTensorExtract [-h[elp]]
-i[nput] <filein>
[-o[utput] <fileout>]
-x[dim] <dimX>
-y[dim] <dimY>
-z[dim] <dimZ>
----------------------------------------------------------------
Extract anisotropy,trace,directions from dtitensor bucket
----------------------------------------------------------------
filein : source dtitensor bucket
fileout : destination base file name
fileout_traceTC.ima
fileout_traceEV.ima
fileout_VR.ima
fileout_FA.ima
fileout_dir.ima
fileout_dirRGB.ima
[default=filein]
dimX,dimY,dimZ : dimensions of output images
----------------------------------------------------------------
AimsTensorSNR
----------------------------------------------------------------
AimsSNR -i[nput] <filein>
[-v[oi] <voi>]
[-x <X> -y <Y> -z <Z> -R <R>]
[-o[utput] <fileout>]
[-h[elp]]
----------------------------------------------------------------
SNR of a VOI in a tensor image
----------------------------------------------------------------
filein : dtitensor bucket file
voi : U8 data file of the V.O.I.
X,Y,Z : Point3d center of a spherical ROI
R : radius of spherical ROI
fileout : output file [default=stdout]
----------------------------------------------------------------
AimsTex2Graph
AimsTex2Graph
-------------
Makes a roi graph from a mesh and a texture of labels
Options :
-t | -texture <file name (read only): texture of S16>
input label (short) texture
-m | -mesh <file name (read only): mesh of VOID>
input mesh
-o | -output <string>
output graph
[ -T | -Time | -time <U32> ]
make graph from time T of input texture
[ -c | -conversion <string> ]
conversion table (short label to name)
[ --reverse <boolean> ]
flip conversion table (name to short label)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsTexture2Primal
-------------------------------------------------------------------------
AimsTexture2Primal -i[nput] <input_texture>
-v[olume] <input_volume>
-M[esh] <input mesh>
-F[lat] <input inflated_mesh>
-b[egin] <begin_scale>
-e[nd] <end_scale>
-d[t] <scalespace sample step>
--log <logarithm scale>
[-H[max] <texture_threshold> ]
[-p[primal] <output_primal>]
[-g[raph] <output_graph>]
-B[lobs] <output_blobs_texture>
-o[utputss] <output_scalespace_textur>
[-g[raph] <output_graph>]
[-s[urface] <surface_type>]
[-G[row] <grow_mode>]
[-t[ranslation] <coef_translation>]
[-m[indt] <min scalespace sample step>]
[-W[max] <Weight threshold>
[-S[moothstep] <smooth step for the edp>]
[-c[onvexity] ]
[-h[elp]]
-------------------------------------------------------------------------
Build the primal sketch of a texture using 2D geodesic diffusion
-------------------------------------------------------------------------
begin_scale : First scale in the scale space
end_scale : Last scale in the scale space
scale space sample step : Max sample step in the scale space
min scale space sample step : Min sample step in the scale space
<default = scale space sample step>
Smooth step for the edp : Time step for te edp (depending from the triangulation)
<default = automatic>
Weight threshold : (Absolute) threshold for the laplacian weight estimate
<default = 0.1>
Texture threshold : (Absolute) threshold for the textures values
<default = auto (max of the texture)>
Convexity : Grey level blob correspond to:
-local minima (convexity = -1)
-local maxima (convexity = 1)
<default = -1>
output_primal : Make also the corresponding primal sketch graph
(Scale Space Blob graph) <default = not used>
output_graph : Make also the corresponding graph
(Grey Level Blob graph) <default = not used>
surface_type : Tore (default) or surface
coef_translation : Link between the scale and the distance to the mesh
grow_mode : Mesh growing mode along scales: scale (default),
translate, or pushnormal
-------------------------------------------------------------------------
AimsTextureAverage
-------------------------------------------------------------------------
AimsTextureAverage -f[loat_texture] <input_float_texture>]
-o[utput <output_mesh>]
--binary
--max
--min
[-h[elp]]
-------------------------------------------------------------------------
Compute the average of a time-serie texture
-------------------------------------------------------------------------
input_float_texture : input time-serie texture
output_texture : output mean texture
binary : binarise the input texture
max : compute the maximum instead of the mean input texture
min : compute the minimum instead of the mean input texture
-------------------------------------------------------------------------
AimsTextureCompare
AimsTextureCompare
------------------
Compute the Hausdorff distance between two curves
Options :
-im | --inputMesh <string>
mesh
-itS | --inputTexSource <string>
input texture source
-itT | --inputTexTarget <string>
input texture target
-v | --inputValue <S32>
input texture value
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsTextureDerivative
-------------------------------------------------------------------------
AimsTextureDerivative -i[nput] <input_texture>
[-o[utput] <output_texture>]
-p[inv] <pinv_filename>
-m[esh] <mesh_file>
--curvature
--Lvv
--Lw
--laplacien
--div
[-h[elp]]
-------------------------------------------------------------------------
Compute first and second derivative of the input texture
-------------------------------------------------------------------------
input_texture : texture definition
output_texture : output *.tex file
-------------------------------------------------------------------------
AimsTextureDilation
-------------------------------------------------------------------------
AimsTextureDilation -i[nput] <meshfilein>
-t[exture] <input_texture>
-o[utput <output_dist_texture>
-s[ize] <erosion_size>
[-b[ackground] <background label>]
[-f[orbidden] <forbidden label>]
[--connexity]
[--ascii]
[-h[elp]]
-------------------------------------------------------------------------
Dilation of an image(binar or grey level ) painted on a triangulation
Input texture of 'short int' are dilated with binar structurant element
The 'background label' corresponds to the label of the background (default = 0)
The 'forbidden label' corresponds to the label out of the domain (default = -1)
Input texture of 'float' are dilated with the max function as structurant element
-------------------------------------------------------------------------
meshfilein : input *.tri or *.mesh file
output_dist_texture : output *.tex file (labelled opening)
input_texture : object definition
ascii : write *.tex file in ASCII [default=binar]
connexity : euclidean or mesh connexity distance [default=euclidean]
-------------------------------------------------------------------------
AimsTextureErosion
-------------------------------------------------------------------------
AimsTextureErosion -i[nput] <meshfilein>
-t[exture] <input_texture>
-o[utput <output_dist_texture>
-s[ize] <erosion_size>
[-b[ackground] <background label>]
[-f[orbidden] <forbidden label>]
[--connexity]
[--grey]
[--ascii]
[-h[elp]]
-------------------------------------------------------------------------
Erosion of an image(binar or grey level ) painted on a triangulation
Input texture of 'short int' are eroded with binar structurant element
The 'background label' corresponds to the label of the background (default = 0)
The 'forbidden label' corresponds to the label out of the domain (default = -1)
Input texture of 'float' are eroded with the min function as structurant element
-------------------------------------------------------------------------
meshfilein : input *.tri or *.mesh file
output_dist_texture : output *.tex file (labelled opening)
input_texture : object definition
ascii : write *.tex file in ASCII [default=binar]
connexity : euclidean or mesh connexity [default=euclidean]
-------------------------------------------------------------------------
AimsTexturePrimalSketch
AimsTexturePrimalSketch
-----------------------
ScaleSpace et grey level blobs d'une surface/texture au format float
Options :
-t | --inputT <string>
inputTexture
-o <string>
output primal sketch graph
-m | --inputM <string>
inputMesh
-os | --output-scales <string>
scale space texture filename
-ob | --output-blobs <string>
blobs texture filename
[ -t1 | --scalemin <FLOAT> ]
minimum scale (default=1.0)
-t2 | --scalemax <FLOAT>
maximum scale
[ -dt | --deltat <FLOAT> ]
time step (default=0.05)
[ -mX | --auxmesh <string> ]
auxilliary mesh (for the rendering)
[ -sj | --subject | --subject <string> ]
subject name (default : inputImage)
[ --trans <string> ]
Transformation matrix to Talairach space
[ -iP <U32> ]
Intersection condition for grey-level blobs matching across scales
[ -f <FLOAT> ]
filter out blobs whose tvalues are under (default=1.0)
[ -l <string> ]
texture latitude
[ -L <string> ]
texture longitude
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsTextureRegularization
AimsTextureRegularization
-------------------------
Regularize the texture
Options :
-t | --texture <string>
texture file
-o | --output <string>
output texture
[ -r | --ratio <FLOAT> ]
proportion (%) of point to be thresholded
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsTextureScaleSpace
AimsTextureScaleSpace
---------------------
ScaleSpace d'une surface/texture
Options :
-i1 | --input1 <string>
inputTexture
-i2 | --input2 <string>
inputMesh
-o | --output <string>
output filename pattern
-tm | --scalemax <FLOAT>
maximum scale
-dt | --deltat <FLOAT>
time step
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsTextureSmoothing
-------------------------------------------------------------------------
AimsTextureSmoothing -i[nput] <input_texture>
[-S[ource] <input_source_texture> default = none]
-o[utput <output_texture>]
[-t[imestep] <dt> default = automatic estimation]
-m[esh] <mesh_file>
[-W[max] <weight ratio threshold> default = 0.98
[-H[max] <output threshold> default = 10000]
[-s[igma] <equivalent gaussian sigma>]
[-T[ime] <time serie> default = 0]
[-d[uration] <duration>]
[-h[elp]]
-------------------------------------------------------------------------
Geodesic smoothing of the input texture (heat equation)
-------------------------------------------------------------------------
input_texture : object definition
input_source_texture: source definition
output_texture : output *.tex file (blobs)
-------------------------------------------------------------------------
AimsTextureThreshold
----------------------------------------------------------------
AimsTextureThreshold -i[nput] <filein>
-o[utput] <fileout>
-m[ode] <mm>
-t <threshold1>
[-u <threshold2>]
[-b[inary]]
[-h[elp]]
----------------------------------------------------------------
Threshold on texture (each time serie is thresholded)
----------------------------------------------------------------
filein : origin file
fileout : output file
mm : mode that can be
lt --> lower than
le --> lower or equal to
gt --> greater than
ge --> greater or equal to
eq --> equal to
di --> differ
be --> between
ou --> outside
threshold1 : first threshold
threshold2 : second threshold
binary : returns a short binary texture
(background : 0 ; object : 1)
----------------------------------------------------------------
AimsTextureToAtlas
AimsTextureToAtlas
------------------
Projet a texture from one mesh onto an atlas using spherical parameterization
of both. x-coordinate is the longitude (with a period)
Options :
-i | --inputMesh <string>
input mesh
-t | --inputTex <string>
input texture (float)
-o | --outputTex <string>
output texture
-a | --atlasMesh <string>
atlas mesh
-ix <string>
mesh x-coordinate texture
-iy <string>
mesh y-coordinate texture
-ax <string>
atlas x-coordinate texture
-ay <string>
atlas y-coordinate texture
-px <FLOAT>
x-coord period (none=0)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsTextureVoronoi
-------------------------------------------------------------------------
AimsTextureVoronoi -m[esh] <input_mesh>
-t[exture] <input_texture>
-o[utput] <output_vor_texture>
[-s[tep] <step>]
[-b[ackground] <background_value>]
[-f[orbidden] <forbidden_value>]
[-T[ime] <time serie> default = 0]
[--c[onnexity] ]
[-h[elp]]
-------------------------------------------------------------------------
Compute the Voronoi diagram of the input (short int) seed texture
-------------------------------------------------------------------------
input_mesh : input *.tri or *.mesh file
input_texture : definition of the seed (short int)
background : background value <default = 0>
forbidden : value out of the domain <default = -1>
size : step size <default = infinity>
connexity : connexity or geodesic euclidean distance
output_vor_texture : output voronoi diagram texture
-------------------------------------------------------------------------
AimsThickness2Mesh
AimsThickness2Mesh
------------------
Optical mesh processing from thickness image
Options :
[ -i <file name (read only): { Volume of DOUBLE, Volume of FLOAT, Volume of S16,
Volume of S32, Volume of S8, Volume of U16, Volume of U32, Volume of U8 }>
input files (thickness) ]
[ -min <S32> ]
minimum value
[ -sz <FLOAT> ]
Z resolution
[ -o <string> ]
output
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsThreshold
AimsThreshold
-------------
Threshold on data
Options :
-i | --input <file name (read only): { Volume of DOUBLE, Volume of FLOAT,
Volume of S16, Volume of S32, Volume of S8, Volume of U16, Volume of U32,
Volume of U8 }> input file
-o | --output <string>
output file
[ -m | --mode <string> ]
mode that can be:
lt --> lower than
le --> lower or equal to
gt --> greater than
ge --> greater or equal to
eq --> equal to
di --> differ
be --> between
beel --> between, exclude lower bound
beeh --> between, exclude higher bound
bee --> between, exclude both bounds
ou --> outside
ouil --> outside, include lower bound
ouih --> outside, include higher bound
oui --> outside, include both bounds
[default: ge]
-t | --threshold1 <FLOAT>
first threshold
[ -u | --threshold2 <FLOAT> ]
second threshold
[ -p <boolean> ]
thresholds are expressed in percentage of voxel value: threshold =
min+(max-min)*(percentage/100)
[ -b | --binary <boolean> ]
returns a short binary data [default: false]
[ --bg <FLOAT> ]
background value set on thresholded out voxels in non-binary mode [default:
0]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsTopHat
AimsTopHat
----------
Morphological operators
for both binary and gray level intensity images
Options :
[ -i <file name (read only): { Volume of DOUBLE, Volume of FLOAT, Volume of S16,
Volume of S32, Volume of S8, Volume of U16, Volume of U32, Volume of U8 }>
Input image ]
[ -r <FLOAT> ]
Radius in mm
[ -m <string> ]
Mode that can be:
ero --> erosion
dil --> dilation
clo --> closing
ope --> opening
thc --> top-hat by closing
tho --> top-hat by opening
[ -e <string> ]
Morphology of the structuring element:
iso --> isotropic
ani --> anisotropi - much slower
cub --> cubic
3pl --> along 3 orthogonal planes
pla --> along ortho & slant planes - slower
sag --> 3 planes around sagittal axis (half radius along and tangential to
axis)
[ -recons <boolean> ]
Reconstruction (cubic opening,closing,top-hat only) :
1 --> reconstruction is active (default inactive)
[ -mask <FLOAT> ]
mask value (no morphological computation for this value) :
-998 --> no mask (default)
[ -b <FLOAT> ]
Border value : -999 = automatic (default)
[ -y0 <S32> ]
sagittal axis y location for 'sag' mode only (default : dim(Y)/2)
[ -z0 <S32> ]
sagittal axis z location for 'sag' mode only (default : dim(Z)/2)
[ -o <string> ]
Output image
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsTopologicalClassification
--------------------------------------------------------------------------
AimsTopologicalClassification -i[nput] <filein>
-o[output] <fileout>
[-h[elp]]
--------------------------------------------------------------------------
Topological classification of each point of a labeled image
--------------------------------------------------------------------------
filein : input volume
fileout : prefix name for output file name
--------------------------------------------------------------------------
AimsVFilter
----------------------------------------------------------------
AimsVFilter -i[nput] <filein>
-o[utput] <fileout>
[-m[asksize] <size>]
[-t[ype] <algo>]
[-h[elp]]
----------------------------------------------------------------
apply a V-Filter to an image
----------------------------------------------------------------
filein : origin file
fileout : output file
size : mask size [default=2]
algo : o -> optimized n -> non optimized [default=o]
----------------------------------------------------------------
AimsValidateFit
AimsValidateFit
---------------
A test program I think, nothing useful
Options :
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsVectorFieldToMesh
AimsVectorFieldToMesh
---------------------
Converts a vector field volume to a mesh of arrows
Options :
-i | --input <string>
input vector field (either one RGB image or a 4D image with 3 components)
-o | --output <string>
output mesh
[ -s <FLOAT> ]
scale factor (default=normalization)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsVeinExtraction
AimsVeinExtraction
------------------
Semi-automatic vein extraction using global minimum energy path for active
contours with geodesics
Options :
-i <string>
Input image
-o <string>
Output segmented image
[ -m <string> ]
Input image modality (MRI, Other)
[ -b <vector of FLOAT> ]
First point on vein
[ -e <vector of FLOAT> ]
Last Point on vein
[ -d <FLOAT> ]
vein diameter (default : 5 mm)
[ -w <S32> ]
Border with for twisted veins (default : 15 voxels )
[ -li <boolean> ]
lowervalue of image is inaccessible (default : false)
[ -t <string> ]
Voi type : arg, image (default : arg )
[ -wi <boolean> ]
using whole image (default : no )
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsVoiStat
AimsVoiStat
-----------
Compute ordinary stat from a RoiArg and and Image (Warning:--selection all and
--voitype gtm are incompatibles) (Warning: DOUBLE images are converted to FLOAT
so there si a possible loss of information)
Options :
-i | --input <string>
input dynamic data
-v | --voi <string>
file containing roi information see (--voitype)
-o | --output <string>
output
[ -d | --displ <string> ]
displacement file from functional image to ROI. default val : Identity
[ -s | --selector <string> ]
user defined selector file name
[ -l | --list <boolean> ]
list of available template selectors
[ --hierarchy <string> ]
nomenclature file
[ --selection <string> ]
template selector name available selectors may be listed (switch -l) OR
"all" to disable selection mode
[ --voitype <string> ]
subselector for voi file type arg (for arg format), image (for image
format), gtm (for composite gtm arg file and roi arg file)
[Default: arg]
[ --byframe <boolean> ]
set frame by frame computation mode
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
AimsVoronoi
--------------------------------------------------------------------------
AimsVoronoi -i[nput] <filein>
-o[output] <fileout>
[-d[omain] <val_domain>
[-f[orbiden] <val_outside>
[-x[mask] <X>] [-y[mask] <Y>] [-z[mask] <Z>] [-F[actor] <F>]
[-h[elp]]
--------------------------------------------------------------------------
Construct a Voronoi's diagram from labelled seed
--------------------------------------------------------------------------
filein : input seed SHORT volume
fileout : prefix name for output SHORT Voronoi's diagram
val_domain : value of the domain where to propagate the diagram
[default=0]
val_outside : value of the outside of the domain [default=-1]
X : X size of the distance mask [default=3]
Y : Y size of the distance mask [default=3]
Z : Z size of the distance mask [default=3]
F : chamfer multiplication factor [default=50]
--------------------------------------------------------------------------
AimsZCat
AimsZCat
--------
concatenates volumes (along Z axis), meshes or buckets
Options :
-i <list of string>
input files (1 minimum)
-o <string>
Output file name
[ --memmap <boolean> ]
read in Memory Mapping mode (obsolete, automatic)
[ --nocheckvs <boolean> ]
Don't check if voxel sizes of all volumes to concatenate match
[ --vsx <FLOAT> ]
Force voxelsize X value
[ --vsy <FLOAT> ]
Force voxelsize Y value
[ --vsz <FLOAT> ]
Force voxelsize Z value
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
VipAlternatedSequentialFilter
------------------------------
VIP Info:
Succession of opening and closing on an object defined as all non zero points
------------------------------
The structuring element is a ball of radius size for a chamfer distance.
Usage: VipAlternatedSequentialFilter
-i[nput] {image name} : object definition
[-s[ize] {maximum opening size in mm (default:1 mm)}]
[-S[ize] {maximum closing size in mm (default:same as opening size)}]
The maximum size corresponds to the last cycle structure element size.
For each iteration, the structure element size is Iter*SizeMax/Ncycle
[-N[cycle] number of cycle {int (default:1)}]
[-f[irst] {char: o or c (default:"o")}]
o:opening first, c:closing first
[-a[lgo] {char: f or t (default:"f")}]
f:bounded thick front propagation, t: chamfer transformation
[-n[itermax] {int (default:5)}]
maximum number of iterations for Voronoi iterated chamfer transform
[-o[utput] {image name (default:"smoothed")}]
[-x[masksize] {int (default:3)}: chamfer mask xsize]
[-y[masksize] {int (default:3)}: chamfer mask ysize]
[-z[masksize] {int (default:3)}: chamfer mask zsize]
[-m[ultfactor] {float (default:VIP_USUAL_DISTMAP_MULTFACT)}]
[-c[onnectivity] {string:n/6/18/26/4/8/4s/8s/4c/8c (default:6)}]
"n" means not used. Suffixes "s" and "c" means sagittal and coronal orientations
[-r[eadformat] {char: v, s or t (default:v)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
[-w[riteformat] {char: v, s or t (default:v)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
[-h[elp]
VipAngleToDeplacement
------------------------------
VIP Info:
Creates a deplacement files from translation and rotation angles
------------------------------
Usage: VipAngleToDeplacement
-o[utput] {file name}
[-x[trans] X translation in mm {float (default:0.0)}]
[-y[trans] Y translation in mm {float (default:0.0)}]
[-z[trans] Z translation in mm {float (default:0.0)}]
[-a[lpha] rotation around X in degree {float (default:0.0)}]
[-b[eta] rotation around Y in degree {float (default:0.0)}]
[-g[amma] rotation around Z in degree {float (default:0.0)}]
[-X[center] X rotation center position in mm {float (default:0.0)}]
[-Y[center] Y rotation center position in mm {float (default:0.0)}]
[-Z[center] Z rotation center position in mm {float (default:0.0)}]
[-h[elp]
VipBiasCorrection
------------------------------
VIP Info:
Computes a smooth multiplicative field which corrects for non stationarities.
------------------------------
This field aims at minimizing the volume entropy (= minimizing information...).
A tradeoff is found between this entropy and the internal energy of a membrane using annealing.
Usage: VipBiasCorrection
-i[nput] {image name}
[-o[utput] {image name (default:"nobias")}]
[-f[ield] {bias field name (default:"field")}]
[-D[imfield] {type of field (2/3) (default:3)}]
2: the correction field is constant by slice, 3: constant by cubes
[-F[write] {write field: y/n (default:y)}]
[-d[umb] {y/n (default:y)}]
[-Ke[ntropy] {float (default:1.)}]
Weight of the volume entropy which will be multiplied by the field size
[-Kr[egul] {float (default:20.)}]
Weight of the membrane/spline energy (sum of the squared log of the ratio between 6-neighbors)
[-Ko[ffset] {float (default:0.5)}]
Weight of the squared difference between old and new mean
[-c[ompression] {int [0,14] (default:auto)}]
The number of bits which are discarted during the volume entropy computation (= /2^compression))
[-tl[ow] {int (default:3*2^compression)}]
[-th[igh] {int (default:not used)}]
[-e[ges] {int (default:not used, else 2/3)}]
remove 2D/3D edges for histogram estimation (discard partial volume)
[-vt[ariance] {int (default:not used, else int threshold)}]
high threshold on standard deviation in 26-neighborhood for inclusion in histogram
Values beyond this threshold are not taken into account.
In return, the field correction is applied to all values to get the final result
[-vp[ourcentage] {int (default:not used, else int threshold)}]
Pourcentage of non null points kept with a ranking stemming from local variance
[-T[emperature] {float (default:10.)}]
Initial temperature for annealing
[-G[rid] {int (default:2)}]
Number of grid for minimization (annealing on the highest only)
[-g[eometric] {float (default:0.97)}]
Geometric decreasing for annealing schedule
[-s[ampling] {float (default:16mm)}]
The sampling of the field: one value for a parallelepipedic volume of points.
In each direction, the sampling is: sampling/DirVoxelSize.
The field is a 0-order spline during optimization (piecewise constant)
3-order spline during the final bias correction (piecewise linear)
[-n[Increment] {int (default:2)}]
Minimization is performed using a Gibbs sampler or a ICM (deterministic) approach with
several multiplicative increments are tires for each field point:
1/I^n,...,1/I,I,...I^n:
[-I[ncrement] {float (default:1.03)}]
elementary multiplicative increment (see above):
[-a[mplitude] {float ]1,10] (default:1.1)}]
The field random initialization is in the range [1/amplitude, amplitude]
[-Z[regulTuning] {float (default:1)}]
Multiplicative factor for regularization in z direction (bad coil)
[-r[eadformat] {char: a, v, s or t (default:any)}]
[-w[riteformat] {char: v, s or t (default:t)}]
[-h[elp]
More information in:
Entropy minimization for automatic correction
of intensity non uniformity, J.-F. Mangin,
MMBIA (Math. Methods in Biomed. Image Analysis),
Hilton Head Island, South Carolina, IEEE Press
162-169, 2000
VipClosing
------------------------------
VIP Info:
Dilates the object defined as all non zero points
------------------------------
The structuring element is a ball of radius size for a chamfer distance.
Usage: VipClosing
-i[nput] {image name} : object definition
-s[ize] {closing size in mm.}
[-a[lgo] {char: f or t (default:"f")}]
f:bounded thick front propagation, t: chamfer transformation
[-o[utput] {image name (default:"closed")}]
[-x[masksize] {int (default:3)}: chamfer mask xsize]
[-y[masksize] {int (default:3)}: chamfer mask ysize]
[-z[masksize] {int (default:3)}: chamfer mask zsize]
[-m[ultfactor] {float (default:VIP_USUAL_DISTMAP_MULTFACT)}]
[-c[onnectivity] {string:6/18/26/4/8/4s/8s/4c/8c (default:26)}]
Suffixes "s" and "c" means sagittal and coronal orientations
[-r[eadformat] {char: a, v, s or t (default:a)}]
a = any
[-w[riteformat] {char: v, s or t (default:t)}]
[-h[elp]
VipClusterArg
------------------------------
VIP Info:
Create a SPM cluster based attributed relational graph
------------------------------
Example: VipClusterArg -i circuit_attention -s 5
Then load circuit_attention.arg in Anatomist
and put it in 2D and 3D visualization windows
Warning: put a normalized anatomical image in 2D window before clusters
Manipulate using a browser or a dedicated hierarchy
-i[nput] {image name}
You can get it from SPM during in the RESULT section from the WRITE button
[-t[ransfo] {3D rotation/translation (default:none)}
If you are not satisfied with the link between the contrast image
and the anatomical image that is computed from SPM center
you can provide your own translation (perhaps modifying
slightly the printed one...)
The transfo file format is the following:
tx ty tz
1. 0. 0.
0. 1. 0.
0. 0. 1.
If you are a wizard, you can even add a rotation matrix...
My advice relative to translation sign:
try first with large translation. Indeed according
to normalized or non normalized situation, image may be variously flipped
[-n[ormalisation] {ascii file (default:none)}
This flag is used to get Talairach coordinate when playing
with non normalized data.
This file is an ASCII/Anatomist version of SPM anatSXXXX_sn3d.mat
You get it with the command:
AnaImportSPMsn3dFile <SXXXX_002>
[-T[emplate] {volume (default:/home/Panabase/demo/talairach/nanatRa)}
Usually the T1-weighted anatomical volume on which you will visualize the clusters in 2D
This volume gives image size and resolution
[-o[utput] {arg name (default:"input")}]
[-s[ize] {int: min cluster size in 18-connectivity (default:0)}]
[-m[esh] {char: y/n (default:y)}]
Trigger the mesh generation
With large clusters, this can be very expensive
In most situation, you can work only with voxels
but Anatomist takes some time to yield the first visualization
[-r[eadformat] {char: v, s or t (default:any)}]
[-h[elp]
VipConnexFilter
------------------------------
VIP Info:
Removes connected component according to their size
------------------------------
the smallest ones can be removed or one of the biggest kept.
It is also possible to get a labelling
Usage: VipConnexFilter
-i[nput] {image name} : object definition
[-o[utput] {image name (default:"distmap")}]
[-d[ual] (work on background)]
[-s[ize] {int (default:0)} : smaller will be removed]
[-b[iggest] {int (default:1)} : you can choose first, second...]
[-m[ode] {b, g or l (default:g)} : binary, grey result or labelling (1,2,3...)]
[-c[onnectivity] {string:6/18/26/4/8/4s/8s/4c/8c (default:26)}]
Suffixes "s" and "c" means sagittal and coronal orientations
------------------------------
VIP Info:
Read and Write flag are actually configured for debugging...
------------------------------
[-r[eadformat] {char: a, s, v or t (default:any)}]
[-w[riteformat] {char: s, v or t (default:t)}]
[-h[elp]
VipConvert
------------------------------
VIP Info:
Converts any volume to another type
------------------------------
Usage: VipConvert
-i[nput] {image name}
[-t[ype] {U8/S16/F (default:S16)}]
Be aware that the default reading and writing format is vida unscaled (S16BIT)
[-o[utput] {image name (default:"converted")}]
[-s[plit] {y/n to create SPM dynamic format (default n)}]
put this flag to s to trigger conversion of a dynamic image to SPM format
[-m[ode] {r (default:r (raw))}]
with r mode, the conversion is a simple cast
[-r[eadformat] {char: v, s or t (default: scaled vida)}]
Forces the reading of VIDA, SPM or TIVOLI image file format
By default, the vida scaled reading to float volume is used
When -r v is asked, the vida reading to S16BIT is used
[-w[riteformat] {char: v, s or t (default: unscaled vida)}]
Forces the writing of VIDA, SPM or TIVOLI image file format
the v choice forces scaled writing of float volume to vida format
the default mode do not scaled the volume
[-h[elp]
Examples:
-----------------------------------------------------
Conversion d'une image d'index DTI (trace, volume ratio...)
L'image a convertir est au format TIVOLI (ima/dim) en float (verifiez dans le .dim)
-->VipConvert -i trace -o traceSPM -w s -t F
-----------------------------------------------------
Conversion d'une serie dynamique type IRMf pour SPM
L'image a convertir est au format VIDA
-->VipConvert -i raw -o frame -w s -s yn
-----------------------------------------------------
VipCovarianceMatrix
------------------------------
VIP Info:
Compute the covariance matrix from a data matrix.
------------------------------
Usage: VipCovarianceMatrix
-i[nput] {ASCII data file}
-f[eature] {number of features}
-p[opulation] {number of individuals in population}
[-o[utput] {ASCII result file without extension (default:output on stdout)}]
[-t[type] {n | i (default:n)}]
d=NORMAL, i=INVERSE
[-d[iagonal]] {only get the matrix diagonal}
[-m[ean]] {generates an additional ASCII file of means}
[-h[elp]]
VipCylinder
------------------------------
VIP Info:
Create a triangulated cylinder given by two extremities
------------------------------
If a template is specified, extremities are specified as coordinates
Otherwise, they are supposed to be in mm
Usage: VipCylinder
[-t[emplate]] {coordinates in this image }
[-o[utput] {cylinder name (default:"cylinders")}]
-x1 {float }
-x2 {float }
-y1 {float }
-y2 {float }
-z1 {float }
-z2 {float }
[-r[adius] {float (default:0.5mm)}]
[-ha[theight] {float (default:0mm)}]
[-h[elp]
VipDeriche
------------------------------
VIP Info:
Computes gradient using deriche 2D recursive filters
------------------------------
Such filters include optimal smoothing according to Canny criteria.
Usage: VipDeriche
-i[nput] {image name}
[-a[lpha] {float (default:1.) (range:[0.3,3]}]
The smoothing importance decreases when alpha increases
[-o[utput] {image name (default:"deriche")}]
[-s[ave] {y/n (default:n)}]
save a .g2D file with gradient coordinates for inflation
during surface matching
[-f[ilter] {e/n/x/y/z/s (default:e (extrema))}]
e: norm extrema in the gradient direction
n: norm
x: x gradient coordinate
y: y gradient coordinate
z: z gradient coordinate
s: smoothing
[-t[hreshold] {int (default:0)}]
No extremum detection under threshold value
Other images are thresholded according to threshold value
[-d[im] {2/3 (default:3)}]
[-r[eadformat] {char: v or t (default:t)}]
[-w[riteformat] {char: v or t (default:t)}]
[-h[elp]
VipDilation
------------------------------
VIP Info:
Dilates the object defined as all non zero points
------------------------------
The structuring element is a ball of radius size for a chamfer distance.
Usage: VipDilation
-i[nput] {image name} : object definition
-s[ize] {dilation size in mm.}
[-a[lgo] {char: f or t (default:"f")}]
f:bounded thick front propagation, t: chamfer transformation
[-o[utput] {image name (default:"dilated")}]
[-x[masksize] {int (default:3)}: chamfer mask xsize]
[-y[masksize] {int (default:3)}: chamfer mask ysize]
[-z[masksize] {int (default:3)}: chamfer mask zsize]
[-m[ultfactor] {float (default:VIP_USUAL_DISTMAP_MULTFACT)}]
[-c[onnectivity] {string:6/18/26/4/8/4s/8s/4c/8c (default:26)}]
Suffixes "s" and "c" means sagittal and coronal orientations
[-r[eadformat] {char: a, v, s or t (default:a)}]
a = any
[-w[riteformat] {char: v, s or t (default:t)}]
[-h[elp]
VipDistanceMap
------------------------------
VIP Info:
Computes a chamfer distance to the object defined as all non zero points
------------------------------
Distances either correspond to Euclidean distance multiplied by multfactor.
or correspond to the distance related to the specified connectivity.
Usage: VipDistanceMap
-i[nput] {image name} : object definition
[-o[utput] {image name (default:"distmap")}]
[-c[onnectivity] {string:6/18/26/4/8/4s/8s/4c/8c (default:not used)}]
[-g[eodesic] {string:'i' or 'f' (default:not used)}]
geodesic distance map: 'i':iterated chamfer transform
'f':thick front propagation
[-d[omain] {int (default:0)}]
this value defines propagation domain for the geodesic distance
[-f[orbiden] {int (default:-1)}]
this value defines outside of domain for the geodesic distance
[-l[imit] {int (default:not used)}]
For front propagation, the propagation is stoped beyond limit (mm or bonds)
[-lm[ode] {int ('n,'l','f','i') (default:n)}]
according to this mode, the value given to the domain beyond limit is
l:limit*MULT_FACTOR, f: forbidden value, i: infinite (large) value
[-n[itermax] {int (default:5)}]
maximum number of iterations for iterated chamfer transform
Suffixes "s" and "c" means sagittal and coronal orientations
[-x[masksize] {int (default:3)}: chamfer mask xsize]
[-y[masksize] {int (default:3)}: chamfer mask ysize]
[-z[masksize] {int (default:3)}: chamfer mask zsize]
[-m[ultfactor] {float (default:50)}]
[-r[eadformat] {char: a, v, s or t (default:any)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
[-w[riteformat] {char: v, s or t (default:t)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
[-h[elp]
VipDoubleThreshold
------------------------------
VIP Info:
Applies a double threshold to input image according to << mode >> and << type >>
------------------------------
Usage: VipDoubleThreshold
-i[nput] {image name}
-tl {int (low threshold)
-th {int (high threshold)
[-fl] {float (low threshold)}
[-fh] {float (high threshold)}
If fl and fh are given, tl and th are no more required...
[-o[utput] {image name (default:"thresholded")}]
[-m[ode] {b | be | o | oe (default:be)}]
b=BETWEEN, be=BETWEEN_OR_EQUAL_TO, o=OUTSIDE, oe=OUTSIDE_OR_EQUAL_TO
[-c[olor] {b | g (default:g)}]
Output image nature: b=BINARY_RESULT: ( 255 / 0 ), g=GREYLEVEL_RESULT
[-r[eadformat] {char: a, v, s or t (default:any)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
[-w[riteformat] {char: v, s or t (default:t)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
[-h[elp]
VipEpiCorrect
Syntax :
epi_correct [parameter_file] distorted_epi corrected_epi phasemap
phasemap : an error occured ; exiting...
VipEpiDistParam
parameter file :
------------------------------
VIP Info:
Fill in parameter file required by VipEpiCorrect
------------------------------
Usage: VipEpiDistParam
param filename (interactive mode)
-b[atch] {command line mode} with the following options:
[-dex {double echo image - size x (default 128)}]
[-dey {double echo image - size y (default 128)}]
[-dez {double echo image - size z (default 128)}]
[-epix {epi image - size x (default 64)}]
[-epiy {double echo image - size z (default 64)}]
[-epit {epi image - number of repetitions (default 22)}]
[-revz {epi - reverse z axis ? (y/n) (default y)}]
[-iet {inter_echo_time in ms: delay between successive echos (default 2.28)}]
[-dwt {dwell_time in ms: delay between successive echos in EPI image (default 0.64)}]
[-h[elp]
Example:
-----------------------------------------------------
Mode interactif: le répertoire courant contient fidNN.raw au format Brucker
-->VipEpiDistParam distparam.txt
-----------------------------------------------------
Mode batch
Mode batch: le répertoire courant contient fidNN.raw au format Brucker
Choix par défaut pour tous les paramètres:
-->VipEpiDistParam distparam.txt -b
Autres choix pour les paramètres dex dey dez epix epiy epit revz
VipEpiDistParam distparam.txt -b -dex 256 -dey 256 -dez 256 -epix 128 -epiy 128 -epit 30 -revz n
-----------------------------------------------------
VipEpiPhaseMap
Syntax :
phasemap [parameter_file] raw_grad_echo output_phasemap distorted_epi
an error occured reading the parameters; exiting...
VipErosion
------------------------------
VIP Info:
Erodes the object defined as all non zero points
------------------------------
The structuring element is a ball of radius size for a chamfer distance.
Usage: VipErosion
-i[nput] {image name} : object definition
-s[ize] {erosion size in mm.}
[-a[lgo] {char: f or t (default:"f")}]
f:bounded thick front propagation, t: chamfer transformation
[-o[utput] {image name (default:"eroded")}]
[-x[masksize] {int (default:3)}: chamfer mask xsize]
[-y[masksize] {int (default:3)}: chamfer mask ysize]
[-z[masksize] {int (default:3)}: chamfer mask zsize]
[-m[ultfactor] {float (default:VIP_USUAL_DISTMAP_MULTFACT)}]
[-c[onnectivity] {string:6/18/26/4/8/4s/8s/4c/8c (default:26)}]
Suffixes "s" and "c" means sagittal and coronal orientations
[-r[eadformat] {char: v or t (default:v)}]
[-w[riteformat] {char: v or t (default:v)}]
[-h[elp]
VipExtEdge
------------------------------
VIP Info:
Returns edges touched by rays casted from image borders
------------------------------
Then removes connected component according to their size
the smallest ones can be removed or one of the biggest kept.
Usage: VipExtEdge
-i[nput] {image name} : object definition
[-o[utput] {image name (default:"extedge")}]
[-m[ode] {3Da/3D-ztop/3D-zbot/2Da/2D-ytop/2D-ybot (default:2Da)}]
Just a way of specifying borders...
[-f[ill] {y/n (default:n)}]
[-g[radient] (2/3 (default:not used)]
[-s[ize] {int (default:0)} : smaller will be removed]
[-b[iggest] {int (default:1)} : you can choose first, second...]
[-c[onnectivity] {string:6/18/26/4/8/4s/8s/4c/8c (default:26)}]
Suffixes "s" and "c" means sagittal and coronal orientations
[-r[eadformat] {char: v, s or t (default:t)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
[-w[riteformat] {char: v, s or t (default:t)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
[-h[elp]
VipFileDump
------------------------------
VIP Info:
Binary file dump.
------------------------------
Usage: VipDumpFile
-i[nput] {binary file name}
[-h[elp]]
For large file, use: VipDumpFile -i binaryFile | more
VipFlip
------------------------------
VIP Info:
Flips volume either in a miror way or swaping coordinates
------------------------------
Usage: VipFlip
-i[nput] {image name}
-m[ode] {xx,yy,zz,xy,xz,yz,xxzz,yyzz}
[-o[utput] {image name (default:"flipped")}]
with r mode, the conversion is a simple cast
[-r[eadformat] {char: v, s or t (default: scaled vida)}]
Forces the reading of VIDA or TIVOLI image file format
By default, the vida scaled reading to float volume is used
When -r v is asked, the vida reading to S16BIT is used
[-w[riteformat] {char: v, s or t (default: unscaled vida)}]
Forces the writing of VIDA, TIVOLI or SPM image file format
the v choice forces scaled writing of float volume to vida format
the default mode do not scaled the volume
[-h[elp]
VipFoetusHomotopicSnake
Usage: VipHomotopicSnake
-i[nput] {segmented brain image name}
-h[ana] {histogram scale-space analysis (?.han)}]
[-o[utput] {image name (default:"cortex")}]
[-fc[losing] {float (mm) closing size for f mode (default: 5)}]
[-li[nside] {int:label<290 (default:0)}]
[-lo[utside] {int:label<290 (default:11)}]
[-p[ressure] {int [0:100] (default:0)}]
[-mg[ray] {float (default:?.ana)}]
[-sg[ray] {float (default:?.ana)}]
[-mw[hite] {float (default:?.ana)}]
[-sw[hite] {float (default:?.ana)}]
[-r[eadformat] {char: v or t (default:v)}]
[-w[riteformat] {char: v or t (default:t)}]
[-h[elp]
VipFoldArg
------------------------------
VIP Info:
Create a fold based attributed relational graph
------------------------------
Usage: VipFoldArg
-i[nput] {image name} : depends on the algorithm
[-o[utput] {arg name (default:"someone")}]
[-a[rg] {arg name for conversion}]
[-v[oronoi] {roots voronoi image name}]
This voronoi stem from VipSkeleton and represent watershed catchment bassins
of sulcal roots. It is used to split topologically simple surfaces
if this image name is not given, such split will not occur...
[-s[ize] {int: min ss size (default:15)}]
ss size coorresponds to (ss points + edge points)
[-li[nside] {int:label<290 (default:0)}]
[-lo[utside] {int:label<290 (default:11)}]
[-r[eadformat] {char: v or t (default:v)}]
[-w[riteformat] {char: o or g (default:o)}]
o: old Arg format
g: Generic Arg format (C++ lib)
[-h[elp]
VipFoldArgAtt
------------------------------
VIP Info:
Computes various Fold Arg semantic attributes (depth,normal...)
------------------------------
Usage: VipFoldArgAtt
-i[nput] {skeleton name}
-a[rg] {fold arg name}
[-o[utput] {arg name (default:"input arg name")}]
[-li[nside] {int:label<290 (default:0)}]
[-lo[utside] {int:label<290 (default:11)}]
[-T[alairach] {y/n (default:y)}]
[-t[riangulation] {char:yes/no/only (default:n)}]
[-lh[emi] {left hemisphere image name}]
[-rh[emi] {right hemisphere image name}]
[-P[oints] {AC,PC,IH coord filename (*.tal) (default:not used)}]
Correct format for the commissure coordinate file toto.APC:
AC: 91 88 113
PC: 91 115 109
IH: 90 109 53
[-xA[C] {(int [0-xsize[) AC X coordinate}]
[-yA[C] {(int [0-ysize[) AC Y coordinate}]
[-zA[C] {(int [0-zsize[) AC Z coordinate}]
[-xP[C] {(int [0-xsize[) PC X coordinate}]
[-yP[C] {(int [0-ysize[) PC Y coordinate}]
[-zP[C] {(int [0-zsize[) PC Z coordinate}]
[-xI[nterHem] {(int [0-xsize[) Inter-hemis. point X coord.}]
[-yI[nterHem] {(int [0-ysize[) Inter-hemis. point Y coord.}]
[-zI[nterHem] {(int [0-zsize[) Inter-hemis. point Z coord.}]
[-r[eadformat] {char: v or t (default:v)}]
[-w[riteformat] {char: o or g (default:o)}]
o: old Arg format
g: Generic Arg format (C++ lib)
[-h[elp]
VipGaussian
------------------------------
VIP Info:
Computes convolution by a 3D gaussian using Deriche recursive filters
------------------------------
Sigma is adapted to the voxel size in each direction
Usage: VipGaussian
-i[nput] {image name}
[-s[igma] {float (mm) (default:largest pixel size)}]
[-o[utput] {image name (default:"gaussian")}]
[-f[loat] {y/n (default:n)}]
if n: output keeps the type of input, y: output is in float
[-r[eadformat] {char: v or t (default:v)}]
[-w[riteformat] {char: v or t (default:v)}]
[-h[elp]
VipGeometry
------------------------------
VIP Info:
Computes a differential invariant
------------------------------
For the Gaussian filtering Sigma is adapted to the voxel size in each direction
The result is a float Tivoli/GIS format
Usage: VipGeometry
-i[nput] {image name}
[-m[ode] {mc/gc/mlvv/glvv/pc1/pc2 (default:mc)}]
mc = isophote mean curvature, gc=isophote Gaussian curvature
mlvv = isophote mean Lvv, gc=isophote Gaussian Lvv
mc = isophote principal curvature 1, gc=isophote principal curvature 2 (pc1>pc2)
la = Laplacian, nla = Normalized Laplacian
[-s[igma] {float (mm) (default:largest pixel size)}]
Apply a smoothing (scale=sigma*sigma) to compute differentials in scale-space
[-g[aussian] {y/n (default:y)}]
[-H[isto2D] {y/n (default:n)}]
[-G[radient] {y/n (default:n)}]
[-M[asked] {image name for Histo2D (default:"input")}]
[-T[hreshold] {on masked image for Histo2D (default:"1")}]
[-G[inf] {float (min of geometry for Histo2D (default: -10))}]
[-G[sup] {float (max of geometry for Histo2D (default: 10))}]
[-o[utput] {image name (default:"geometry")}]
[-r[eadformat] {char: v or t (default:v)}]
[-h[elp]
VipGetBrain
------------------------------
VIP Info:
Performs brain segmentation using T1-histogram scale space analysis and morphomath
------------------------------
Note that the goal is to get a mask of the brain to further segment hemispheresTherefore, the cerebellum may be eroded or connected to some other tissues,You may get rid of that problem with some non default values, I hope...
Usage: VipGetBrain
-i[nput] {image name}
[-b[rain] {char y/n: write segmented brain, default:y}]
[-bn[ame] {brain image name, default:brain_input}]
[-R[idge] {White ridge image name (default: not used)}]
[-V[ariance] {Variance image name (default: not used)}]
[-E[dges] {Edges image name (default: not used)}]
[-m[ode] {char: V[2010], 5[2005], S[tandard], R[obust], s[tandard], r[obust], f[ast], default:S}]
Standard: iterative approach to choose best erosion size...
standard: fixed erosion size...
Robust: try to deal with meninge, sinus, Gibbs effect + iterative erosion...
robust: try to deal with meninge, sinus, Gibbs effect + fixed erosion size...
fast: erosion/dilatation...
[-p[atho] {pathology binary mask, default:no}]
add a mask of the lesion to the binary mask before erosion to get brain seed
This can solve bad morphological process
[-n[iter] {int nb iteration of classif. regularization (def:1)}]
The binary classification is regularized using Markov random field and
ICM minimization (nb iter). This maily prevents the opening effect
of small cavities
fast: two thresholds, erosion, largest cc, dilation
normal: classification + regularisation, erosion, largest cc, dilation + recovering
patho: classification + regularisation, white matter segmentation, whole brain segm.
this mode is dedicated to pathologies leading to high signal inside the brain
[-c[olor] {char b/g: binary/graylevel, default:b}]
[-L[ast] {int (default:3)}]
[-F[irst] {int (default:1)}]
put Last last slices to zero and First first slices to zero
The aim is to get rid of MR ghost effect disturbing morphomath
BE carefull, the default is related to SHFJ ordering (the neck is in last slices)
WARNING: if your image is spm normalized, put this setting to zero!!!
[-l[ayer] {int nb of extension into partial volume (def:0, max 2)}]
Add layers of voxels (6-neighbors) if it is improving contrast at mask contour
[-lo[nly] {char y/n default:n, with yes do only layer processing (reading mask)]
This is for postprocessing of bad quality mask images
[-f[ill] {char y/n: fill white cavities ,default:y}]
fill in 6-connected cavities of mask which are mainly above white matter mean
[-C[lose] {char y/n: close the brain , default:n}]
if the 'g' color mode is active, the closing adds gray level 1
[-C[size] {float: closing size , default:10mm}]
[-Cn[ame] {closed brain image name, default:closed_input}]
[-de[bug] {char y/n: debug mode, default:n}]
Write some images, WARNING: the white matter image should not be used as segmentation
indeed, it is overregularised for robustness of the morphological processing
[-be[rosion] {float: brain erosion size (default:2.mm)}]
It should be noted that erosion size is dedicated to standard use of the best mode}]
With the other procedures, you may have to increase it a bit to get more robustness,}]
It should also be noted that with a lower erosion size, you could improve}]
the final result with atrophic brains but with a lower robustness relatively to the whole process}]
[-bd[ilation] {float: brain dilation size (fast mode) (default:be+0.5mm)}]
[-br[ecover] {float: brain recovering size (default:3.mm)}]
dilation of size (erosion+recover) followed by erosion of size (recover)
[-we[rosion] {float: white matter erosion size (default:2.1mm)}]
[-wr[ecover] {float: white matter recovering size (default:30.mm)}]
dilation of size (erosion+recover) followed by erosion of size (recover)
This parameter are stranges because they are dedicated to the robust approach
where a failure like taking extra white matter tissue) is not problematic
while missing some white matter may be more problematic (but not catastrophic)
[-a[nalyse] {char y/n/r: automatic histogram analysis, default:y}]
y: automatic, r: read input.his, n: use -gm,-gs,-wm,-ws
[-hn[ame] {histo analysis, default:input )}]
read when -a r is set, this file has the .han extension (VipHistoAnalysis)
[-gm[ean] {int : gray matter mean (default:automatic)}]
[-gs[igma] {int : gray matter standard deviation (default:automatic)}]
[-wm[ean] {int : white matter mean (default:automatic)}]
[-ws[igma] {int : white matter standard deviation (default:automatic)}]
[-Tl[ow] {int : low threshold (default:automatic)}]
[-Th[igh] {int : high threshold (default:automatic)}]
For fast segmentation, brain tissues = ]Tlow,Thigh[ range
[-d[scale] {float: (default:0.5)}]
Scale discretization (0.5 is the maximum step for stability)
[-t[rack] {int (default:5)}]
Track singularities reaching at least this scale
[-s[tat] {char y/n: write old input.stat file (default:'n')}]
This file is used by an old topologically deformable model stuff
dedicated to g/w interface detection, it should not be used by somebody else...
simple Talairach normalisation may be used to improve sinus deletion
[-P[oints] {AC,PC,IH coord filename (*.tal) (default:not used)}]
Correct format for the commissure coordinate file toto.APC:
AC: 91 88 113
PC: 91 115 109
IH: 90 109 53
[-xA[C] {(int [0-xsize[) AC X coordinate}]
[-yA[C] {(int [0-ysize[) AC Y coordinate}]
[-zA[C] {(int [0-zsize[) AC Z coordinate}]
[-xP[C] {(int [0-xsize[) PC X coordinate}]
[-yP[C] {(int [0-ysize[) PC Y coordinate}]
[-zP[C] {(int [0-zsize[) PC Z coordinate}]
[-xI[nterHem] {(int [0-xsize[) Inter-hemis. point X coord.}]
[-yI[nterHem] {(int [0-ysize[) Inter-hemis. point Y coord.}]
[-zI[nterHem] {(int [0-zsize[) Inter-hemis. point Z coord.}]
[-r[eadformat] {char: a, v, s or t (default:any)}]
Forces the reading of VIDA, SPM, TIVOLI or ANY image file format
[-w[riteformat] {char: v, s or t (default:t)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
[-h[elp]
More information in:
Robust brain segmentation using histogram
scale-space analysis and mathematical morphology
J.-F. Mangin, O. Coulon, and V. Frouin
MICCAI, MIT, LNCS-1496, Springer Verlag
1230-1241, 1998
VipGetHead
Usage: VipGetHead
-i[nput] {MRI image name}
[-h[orn]] {image to be removed}
[-t[hreshold] {algo t: int (default : not used)}]
[-o[utput] {image name (default:"head")}]
[-c[losing] {float (mm) closing size for f mode (default: 4)}]
[-n[guillotine] {int (default : 3)}]
[-hn[ame] {histo analysis, default:input )}]
[-r[eadformat] {char: v or t (default:v)}]
[-w[riteformat] {char: v or t (default:v)}]
[-h[elp]
read when -a r is set, this file has the .han extension (VipHistoAnalysis)
VipGetSlice
------------------------------
VIP Info:
Extract a slice from a volume
------------------------------
Usage: VipGetSlice
-i[nput] {image name}
-s[lice] {slice to extract}
[-o[utput] {image name (default:"slice")}]
[-t[ype] {a | c | s (default:a)}]
a=AXIAL, c=CORONAL, s=SAGITTAL
[-r[eadformat] {char: v or t (default:v)}]
[-w[riteformat] {char: v or t (default:v)}]
v=VIDA, t=TIVOLI
[-h[elp]]
VipGreyStatFromClassif
------------------------------
VIP Info:
Create grey/white statistics file from classif or input
------------------------------
Can be used in case of failure of VipHistoAnalysis because of low grey/white contrast
If you gave a classified or partly classified image, for instance a drawn slice, or the result of
a classification algorithm based on Talairach grid in one way or another
Usage: VipGreyStatFromClassif
-i[nput] {MR image (bias corrected)}
-c[lassif] {label image}
-a[na] {histogram analysis (default input)}]
[-g[label] {int (default:2)}]
[-w[label] {int (default:3)}]
[-mg[ray] {float (default:from classif)}]
[-sg[ray] {float (default:from classif)}]
[-mw[hite] {float (default:from classif)}]
[-sw[hite] {float (default:from classif)}]
[-r[eadformat] {char: a, v, s or t (default:a)}]
[-h[elp]
VipGreyWhiteClassif
Usage: VipGreyWhiteClassif
-i[nput] {MR image (bias corrected)}
-a[lgo] {char: R[egularisation], N[eighbourhood], default: N}
-m[ask] {mask or Voronoi diagram}
-h[ana] {histogram scale-space analysis (?.han)}
-ed[ges] {edges image name}
-P[oints] {AC,PC,IH coord filename (*.tal)}
-ex[ttogrey] {y/n default:y}
[-l[abel] {int (default:255)}]
[-n[iterations] {int (default:5)}]
[-K[Potts] {float (default:20.)}]
[-c[onnectivity] {string:6/18/26/4/8/4s/8s/4c/8c (default:26)}]
[-o[utput] {classif (default:"input_greywhite")}]
[-mg[ray] {float (default:?.han)}]
[-sg[ray] {float (default:?.han)}]
[-mw[hite] {float (default:?.han)}]
[-sw[hite] {float (default:?.han)}]
[-r[eadformat] {char: a, v, s or t (default:a)}]
[-w[riteformat] {char: v, s or t (default:t)}]
[-h[elp]
VipHistoAnalysis
------------------------------
VIP Info:
Performs T1-histogram scale space analysis
------------------------------
[-o[utput] {histo analysis name (default input))}]
Usage: VipHistoAnalysis
-i[nput] {image name/histo name with extension (image.his)}
NB: if the histogram already exists (file name.his or name.his_bin)
it will not be computed again (the volume is not read)analysis will get the han extension
[-S[AVE] {y/n (default:n)}]
[-R[idge] {White ridge image name (default: not used)}]
[-M[ask] {mask to compute histogram (default: not used)}]
Save histogram analysis if performed (Extension: output.han)
[-m[ode] {char: e[ntropy], v[isu], f[ree], c[ascade], C[ascade], a[nalyse], m[axima], i[teration], default:v}
e: computes some kind of entropy...
v: visu mode send histogram to gnuplot or matplotlib (see -g and --matplotlib options)
h: just writes the histogram
c: cascade mode detects D1/D2 n largest cascades
C: cascade mode detects D1/D2 n highest cascades
a: analyse mode according to contrast
i: iteration of the undersampling factor
s: surface
[-e[ges] {int (default:not used, else 2/3)}]
remove 2D/3D edges for histogram estimation (discard partial volume)
[-vt[ariance] {int (default:not used, else int threshold)}]
high threshold on standard deviation in 26-neighborhood for inclusion in histogram
Values beyond this threshold are not taken into account.
[-vp[ourcentage] {int (default:not used, else int threshold)}]
Pourcentage of non null points kept with a ranking stemming from local variance
[-u[ndersampling_factor] {int (default:auto)}]
image values are compressed through a division
by undersampling_factor before scale space computation
[-C[ontrast] {int (default:auto, else h, l or s)}]
h = high, l=low, s= segmented brain, H=Histology, trigger different heuristics for analysis
2 = 2 modes, 3 = 3 modes, 4 = 4 modes
[-x[max] {int (default:not used)}]
[-H[max] {int (default:50000)}]
maxima of axes in the visu mode
[-d[scale] {float: (default:0.5)}]
Scale discretization (0.5 is the maximum step for stability)
[-t[rack] {int (default:5)}]
Track singularities reaching at least this scale
[-O[ffset] {int (default:0)}]
Add an interval of length on the histogram left
[-s[calemax] {int (default:1000)}]
[-c[ascade] {int (default:10)}]
[-0[extrema] {y/n (default:n)}]
[-1[extrema] {y/n (default:y)}]
[-2[extrema] {y/n (default:y)}]
[-3[extrema] {y/n (default:n)}]
[-4[extrema] {y/n (default:n)}]
[-g[nuplot] {char: n[o], s[creen], f[ile], p[ostscript], default:n}]
allows you to look at scalespace and histogram using gnuplot
[--matplotlib {char: n[o], s[creen], f[ile], p[ostscript], default:n}]
same as gnuplot, but uses MatPlotlib instead of GnuPlot
[-T[itle] {char y/n (default:y)}]
put title in gnuplot drawings
[-r[eadformat] {char: v, s, t or a (default:a)}]
Forces the reading of VIDA, SPM, TIVOLI(GIS) or ANY image file format
More information in:
Robust brain segmentation using histogram
scale-space analysis and mathematical morphology
J.-F. Mangin, O. Coulon, and V. Frouin
MICCAI, MIT, LNCS-1496, Springer Verlag
1230-1241, 1998
VipHomotopic
Usage: VipHomotopic
-i[nput] {MR image (bias corrected)}
-m[ode] {char: C[ortical interface] or H[emisphere surface]}
[-o[utput] {image name (default:"cortex")}]
[-h[ana] {histogram scale-space analysis (?.han) only used by the Cortical mode}]
[-cl[assif] {grey_white classification image only used by the Cortical mode}]
[-co[rtex] {cortex image name only used by the Hemisphere mode}]
[-s[keleton] {skeleton image name only used by the Hemisphere mode}]
[-fc[losing] {float (mm) closing size for f mode (default: 10)}]
[-r[eadformat] {char: v or t (default:v)}]
[-w[riteformat] {char: v or t (default:t)}]
[-h[elp]
VipHomotopicSnake
Usage: VipHomotopicSnake
-i[nput] {segmented brain image name}
-h[ana] {histogram scale-space analysis (?.han)}]
[-o[utput] {image name (default:"cortex")}]
[-fc[losing] {float (mm) closing size for f mode (default: 5)}]
[-R[idge] {White ridge image name (default: not used)}]
[-li[nside] {int:label<290 (default:0)}]
[-lo[utside] {int:label<290 (default:11)}]
[-p[ressure] {int [0:100] (default:0)}]
[-mg[ray] {float (default:?.ana)}]
[-sg[ray] {float (default:?.ana)}]
[-mw[hite] {float (default:?.ana)}]
[-sw[hite] {float (default:?.ana)}]
[-r[eadformat] {char: v or t (default:v)}]
[-w[riteformat] {char: v or t (default:t)}]
[-h[elp]
VipHyste
------------------------------
VIP Info:
Removes connected component according to their size
------------------------------
the smallest ones can be removed or one of the biggest kept.
It is also possible to get a labelling
Usage: VipHyste
-i[nput] {image name} : object definition
-tl {float (low threshold)}
-th {float (high threshold)}
[-pl {int in [1..100] (low threshold: percent of max)}]
[-ph {int in [1..100] (high threshold: percent of max)}]
[-n[points] {int (default:1) over high threshold}]
[-q[uotient] {int (quotient=[1..100] points over high threshold)}]
[-o[utput] {image name (default:"hysteresis")}]
[-s[ize] {int (default:0)} : smaller will be removed]
[-g[radient] (2/3 (default:not used)]
read, dwindle ans save .gXD file, where X=2/3
[-b[iggest] {int (default:1)} : you can choose first, second...]
[-m[ode] {b, g or l (default:b)} : binary result or labelling (1,2,3...)]
[-c[onnectivity] {string:6/18/26/4/8/4s/8s/4c/8c (default:26)}]
Suffixes "s" and "c" means sagittal and coronal orientations
[-r[eadformat] {char: v, s or t (default:v)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
[-w[riteformat] {char: v, s or t (default:v)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
[-h[elp]
VipInfantHomotopicSnake
------------------------------
VIP Info:
Homotopic segmentation of infant cortex gray/white interface
------------------------------
The result is endowed with a sphere homotopy
Object has 26-connectivity and background has 6-connectivity
Specific parameters for single Snake :
forbidden zone : it has to be within background for snake dilation
and in
Usage: VipInfantHomotopicSnake
-i[nput] {detection image name}
-ma[sk] {object mask/potential image name}]
-ex[ternal_mask] {external mask name for coupled snakes only}]
[-o[utput] {image name (default:"WMInternalInterface")}]
[-o2 {image name for coupled propagation (default:"WMExternalInterface")}]
[-d[eformation] {enum: deformation mode (default=1:object dilation 2:object erosion 3:coupled propagation(object is outside)}]
[-object {int:label (default:255)}]
-mo[bject] {float}
-so[bject] {float}
[-ko[bject] {float potential (default:24)}]
-[background {int:snake domain label (default:0)}]
-mb[ackground] {float}]
-sb[ackground] {float}]
[-kb[ackground] {float potential (default:10)}]
[-ls[peed] {int: low speed constant (default:4)}]
[-hs[speed] {int: high speed constant (default:12)}]
[-ir[egularization] {int: inner regularization constant (default:20)}]
[-or[egularization] {int: outer regularization constant (default:16)}]
[-f[orbidden] {int:forbidden field label (default:128)}]
[-oinit {bool:1=init an object at volume border for single snake ONLY (default:0:no init)}]
[-conn[ectivity] {int:6=conn6 26=conn26 (default:26)}]
[-niter {int: number of iterations for snake (default:100)}]
[-r[eadformat] {char: v or t (default:v)}]
[-w[riteformat] {char: v or t (default:t)}]
[-h[elp]
VipLabelArg
------------------------------
VIP Info:
Create a nucleus label based attributed relational graph
------------------------------
-i[nput] {image name}
[-m[ode] {n/l (nucleus/label) default:l}]
nucleus mode supposed you use the standard label set
In that case, nucleus names will be given to the VOIs
Hence, you can use nucleus hierarchy in Anatomist
[-t[riangulation] {y/n default:y}]
[-o[utput] {arg name (default:"input")}]
[-r[eadformat] {char: v or t (default:v)}]
[-h[elp]
VipLabelContour
------------------------------
VIP Info:
Get contour(s) in a label volume from a label or a list of labels
------------------------------
Usage: VipLabelContour
-i[nput] {image name}
-l[abel {(int,...) = list of labels to extract (max:256 labels)}
example : -l 60,250,16,128
-v[alue {(int,...) = list of corresponding label filling colors (max:256 colors)}
example : -v 15,245,253,75
Caution : Number of labels must be equal to number of colors
[-c[connexity] {(int) = 6, 18 or 26 (default:6)}}
[-o[utput] {image name (default:"contour")}]
[-r[eadformat] {char: v or t (default:v)}]
[-w[riteformat] {char: v or t (default:v)}]
v=VIDA, t=TIVOLI
[-h[elp]]
The input and output are label volume file.
VipLabelMatching
------------------------------
VIP Info:
Matching from labelled MRI and statistical map image resampling
------------------------------
Usage: VipLabelMatching
-r[eference] {reference image name}
-i[nput] {image name}
[-a[ctivation] {reference statistical map name (default:not used)}]
[-f[unctionnal] {statistical map name (default:not used)}]
[-l[abel] {label to match (default:use all label found)}]
[-o[utput] {image name (default:"resampled")}]
[-w[riteformat] {char: v, s or t (default:v)}]
v=VIDA, s=SPM, t=TIVOLI
[-h[elp]]
VipLabelOverlap
------------------------------
VIP Info:
Overlap measurement between structures defined by a label
------------------------------
Usage: VipLabelOverlap
-r[eference] {reference image name}
-i[nput] {image name}
[-l[abel] {reference label (default:use all label found)}]
[-il[abel] {input image label (default:use same label as reference)}]
[-h[elp]]
VipLinComb
------------------------------
VIP Info:
Computes the linear combination a1*i1+a2*i2
------------------------------
Usage: VipLinComb
-a1 {float}
-i1 {image name}
-a2 {float}
-i2 {image name}
[-f[loat]]
The command works with float volumes (reading and writing do the same)
[-m[ean]]
for a1>0, and a2>0, computes a1*i1+a2*i2/(a1+a2)
[-o[utput] {image name (default:"lincomb")}]
[-r[eadformat] {char: v, s or t (default:v)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
[-w[riteformat] {char: v, s or t (default:v)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
[-h[elp]
VipLinearResamp
------------------------------
VIP Info:
Performs a trilinear resampling of input volume according to template geometry
------------------------------
Usage: VipLinearResamp
-i[nput] {image name}
-t[emplate] {header or image name}
[-f[loat]]
The command works with float input volume (reading and writing do the same)
-d[eplacement] {deplacement file (rotation or affine}
[-o[utput] {image name (default:"linresampled")}]
[-r[eadformat] {char: v, s or t (default:v)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
[-w[riteformat] {char: v, s or t (default:v)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
[-l[abel] {char: 0 or m (default:0)}]
Forces the value of samples of the resample image outside to be set to 0(default) or minimmum of the image to resample
[-h[elp]
VipListLabel
Usage: VipListLabel
-i[mage] {image name}
VipMask
------------------------------
VIP Info:
Simply mask an image
------------------------------
Usage: VipMask
-i[nput] {image name}
-m[ask] {mask name}
[-f[loat]]
The command works with float input volume (reading and writing do the same)
[-l[evel]] {int (defines real mask)}
[-o[utput] {image name (default:"masked")}]
[-r[eadformat] {char: a, v, s or t (default:any)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
[-w[riteformat] {char: v, s or t (default:t)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
[-h[elp]
VipMatching
Surface matching tool
(the program yields several 3D transformations)
- <refsurf>_TO_<mobsurf>: alignment of the reference image along the mobile one
- <mobsurf>_TO_<refsurf>: alignment of the mobile image along the reference one
Usage: VipMatching
-r[efsurf] {image name}
The reference edge image from which is computed the distance map
-m[obsurf] {image name}
[-nr[efsurf] {reference image name for deplacement file}]
[-nm[obilesurf] {mobile image name for deplacement file}]
The mobile surface which is moved through the distance map
[-gf[ile]] {image name} (default:same as mobile surface)
The mobile surface gradient computed from VipDeriche
[-gd[im]] <2/3> (default:2)
The gradient dimension (2D or 3D) resulting from VipDeriche
[-dil[ation]] char: y/n (default:"y")
y : The mobile surface will be inflated to correct for edge localization differences
[-dis[tmap] {image name (default:"not used")}]
A distance map computed from the reference surface
[-i[nit]] <deplacement file>
This deplacement (rotation affine) initialized the minimization
[-dir[ecttransfo]] {file name (default:"<mobsurf>_TO_<refsurf>")}
[-inv[ersetransfo]] {file name (default:"<refsurf>_TO_<mobsurf>")}
[-u[ndersampling]] <int> ([1..100] (default:100)
Undersamples (percentage) the mobile surface which speeds up the process
Angle steps:
First Minimization:
[-i1[angle]] <float> (Minimization 1, init angle step(default:5.deg)
[-f1[angle]] <float> (Minimization 1, final angle step(default:0.5deg)
Second Minimization (including optimal dilation):
[-i2[angle]] <float> (Minimization 2, init angle step(default:1.deg)
[-f2[angle]] <float> (Minimization 2, final angle step(default:0.2deg)
Third Minimization (including optimal dilation and outlier elimination):
[-i3[angle]] <float> (Minimization 3, init angle step(default:1.deg)
[-f3[angle]] <float> (Minimization 3, final angle step(default:0.05deg)
[-t[hreshold]] <float> (outlier) (default:1.7 * mean dist)
Chamfer mask sizes:
[-x[masksize]] <int> ((default:5)
[-y[masksize]] <int> ((default:5)
[-z[masksize]] <int> ((default:3)
[-2[D]] <y/n> (default:"n")
Only translations and rotation around Z axis are allowed
[-R[eadformat] {char: v, s or t (default:v)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
[-h[elp]
VipMerge
------------------------------
VIP Info:
Simply mask an image
------------------------------
Usage: VipMask
-i[nput] {image name}
-m[erged] {image name}
[-f[loat]]
The command works with float input volume (reading and writing do the same)
[-c[ustomize] {a/l/s (default:a)}]
a: all to value, l: level to value, s: all to same value
[-l[evel]] {int (level to be merged) (default: not used)}
[-v[alue]] {int (merged value) (default: input "max+1")}
[-o[utput] {image name (default:"merge")}]
[-r[eadformat] {char: v, s or t (default:v)}]
[-r[eadformat] {char: a, v, s or t (default:any)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
[-w[riteformat] {char: v, s or t (default:t)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
[-h[elp]
VipMinimizeInformation
------------------------------
VIP Info:
to be writen
------------------------------
VipMoment
------------------------------
VIP Info:
Compute moment and moment invariant of a pattern from a label image.
------------------------------
Usage: VipMoment
-i[nput] {image name}
-l[abel] {pattern label in image}
[-o[utput] {ASCII result file (default:output on stdout)}]
set the file extension to .pca to have a specific
ASCII file structure for Principal Component Analysis.
set the file extension to .inv to have a specific
ASCII file structure for Covariance matrix computation.
[-t[ype] {n | l (default:n)}]
n=NORMAL, l=LEGENDRE
[-d[imension] {2 | 3 (default:3)}]
2=2D moment, 3=3D moment
[-r[eadformat] {char: v or t (default:v)}]
v=VIDA, t=TIVOLI
[-h[elp]]
VipOpenFold
------------------------------
VIP Info:
Apply an homotopic dilation to a hard seed of the brain
------------------------------
The homotopic constraint prevent the merge of two neighboring gyri
In this way, we get better triangulation for 3D rendering
Or better cortex surface representations
Usage: VipOpenFold
-i[nput] {brain image name}
a brain segmentation usually obtained with VipGetBrain
for t algorithm, this image has to include MR gray level values
[-a[lgo] {string:e/t/i/f (default : e)}]
e: the hard seed is obtained from a simple binary erosion of the binary brain
t: the hard seed related to white matter is obtained by a simple thresholding
i: the hard seed is given by another image
f: nothing happens apart from filling if trigered
[-n[iter] {nb iter homotopic dilation (default : 5)}]
the homotopic dilation follows a 6-connectivity related front based propagation
[-e[rosion] {algo e : erosion size (default : 2mm)}]
without c flag, this parameter is in mm, with c falg, it is connectivity related
[-c[onnectivity] {(erosion) string:6/18/26/4/8/4s/8s/4c/8c (default:not used)}]
[-t[hreshold] {algo t: int (default : not used)}]
[-s[eed] {algo i: image name (default : not used)}]
[-o[utput] {image name (default:"openfold")}]
[-f[ill] {y/n, fill the fold depth (default: n)}]
This refinement consists in closing the brain, then eroding the closure,
and adding the erosion result to the segmented brain to fill in the depth.
This is done for 3D rendering optimization (less triangles)
[-fc[losing] {float (mm) closing size for f mode (default: 5)}]
[-fe[rosion] {float (mm) erosion size for f mode (default: 10)}]
[-r[eadformat] {char: v or t (default:v)}]
[-w[riteformat] {char: v or t (default:v)}]
[-h[elp]
VipOpening
------------------------------
VIP Info:
Dilates the object defined as all non zero points
------------------------------
The structuring element is a ball of radius size for a chamfer distance.
Usage: VipOpening
-i[nput] {image name} : object definition
-s[ize] {opening size in mm.}
[-a[lgo] {char: f or t (default:"f")}]
f:bounded thick front propagation, t: chamfer transformation
[-o[utput] {image name (default:"opened")}]
[-x[masksize] {int (default:3)}: chamfer mask xsize]
[-y[masksize] {int (default:3)}: chamfer mask ysize]
[-z[masksize] {int (default:3)}: chamfer mask zsize]
[-m[ultfactor] {float (default:VIP_USUAL_DISTMAP_MULTFACT)}]
[-c[onnectivity] {string:6/18/26/4/8/4s/8s/4c/8c (default:26)}]
Suffixes "s" and "c" means sagittal and coronal orientations
[-r[eadformat] {char: v, s or t (default:v)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
[-w[riteformat] {char: v, s or t (default:v)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
[-h[elp]
VipPca
------------------------------
VIP Info:
Principal Components Analysis.
------------------------------
Usage: VipPca
-i[nput] {data ASCII file}
[-p[rincipal] {principal axis data file (default:stdout output)}]
set the file extension to .plot to have a specific
ASCII file structure for IDL/Matlab plot.
[-c[ircle] {correlation circle data file (default:stdout output)}]
set the file extension to .plot to have a specific
ASCII file structure for IDL/Matlab plot.
-v[ariables] {number of variables (e.g. number of moments)}
-t[ests] {number of tests (e.g. number of objects)}
[-a[nalyse] {c | v | s (default:c)}]
c=Correlation analysis, v=Variance/covariance analysis
s=SSCP analysis
[-h[elp]]
VipPreprocessing
------------------------------
!! VIP Preprocessing Error:
Execution aborted: Incoherent generic filename: -h (.gen extension required).
------------------------------
VipSetPointValue
------------------------------
VIP Info:
Set a particular point to a specified value
------------------------------
Usage: VipSetPointValue
-i[nput] {image name}
[-x[coord] {X coordinate of point (default:0)}]
[-y[coord] {Y coordinate of point (default:0)}]
[-z[coord] {Z coordinate of point (default:0)}]
[-v[alue] {int: filling value (default:255)}]
[-o[utput] {image name (default:"filled")}]
[-r[eadformat] {char: v, s or t (default:v)}]
[-w[riteformat] {char: v, s or t (default:v)}]
v=VIDA, s=SPM, t=TIVOLI
[-h[elp]]
VipSingleThreshold
------------------------------
VIP Info:
Applies a threshold to input image according to << mode >> and << type >>
------------------------------
Usage: VipSingleThreshold
-i[nput] {image name}
-t[hreshold] {int (threshold)}
[-f[threshold]] {float (threshold)}
If flevel is given, level is no more required
[-o[utput] {image name (default:"thresholded")}]
[-m[ode] {gt | ge | eq | lt | le | ne (default:ge)}]
gt=GREATER_THAN, ge=GREATER_OR_EQUAL_TO, eq=EQUAL_TO, lt=LOWER_THAN, le=LOWER_OR_EQUAL_TO, ne=NOT_EQUAL_TO
[-c[olor] {b | g (default:g)}]
Output image nature: b=BINARY_RESULT: ( 255 / 0 ), g=GREYLEVEL_RESULT
[-r[eadformat] {char: a, v, s or t (default:any)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
[-w[riteformat] {char: v, s or t (default:t)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
[-h[elp]
VipSkeleton
------------------------------
VIP Info:
Compute a 3D skeleton of the object (usually dedicated to cortical folds)
------------------------------
Default modes are dedicated to the cortex (input comes from VipHomotopicSnake)
In that case, a voronoi related to sulcal root is also proposed.
Usage: VipSkeleton
-i[nput] {image name} : object definition
[-so[utput] {image name (default:"skeleton")}]
[-vo[utput] {image name (default:"rootsvoronoi")}]
[-sk[eleton] {w/s/0 (default:w)}]
w: the skeletonization is coupled with the watershed idea
this mode is dedicated to the cortical fold extraction
this mode requires an image to compute its mean curvature as a ridge detector
The aim is an homotopic skeleton following the ridges
s: standard homotopic skeletomization
0: no skeletonization
[-im[mortality] {string:a/s/c/n (default:s)}]
property required to be preserved during the homotopic skeletonization
a: homotopic with full preservation of points, curves and surfaces
s: homotopic with full preservation of points and surfaces
c: homotopic with full preservation of points and curves
n: homotopic with no preservation
[-v[oronoi] {y/n (default:y)}]
Computes a voronoi of the input object corresponding to a sulcal root based parcellisation
this mode requires an image to compute its Gaussian curvature as a saddle point detector
This saddle points represent the anatomical plis de passage
[-p[rune] {string:c/o/co/0 (default:co)}]
c: homotopic pruning of curves
o: homotopic pruning of outside 6-neighbors
co: c & o
0: no pruning
[-wp[rune] {int:minimum catchment bassin depth (default:3mm)}]
[-li[nside] {int:label<290 (default:0)}]
[-lo[utside] {int:label<290 (default:11)}]
[-c[lassification] {y/n (default:y)}]
this flag trigered a final topological classification of the skeleton
[-g[eometry] {image name (default:nothing)}]
--------------------------Mean curvature:-----------------------------------------
with watershed flag trigered, the watershed idea is related to the isophote mean
curvature of this image, which is usually a MR image with segmented brain
but could be the input binary image or a distance map computed from it
In this context, mean curvature is used as a ridge detector
During the first iterations, points whose mc < mcthreshold can not become immortals
This trick helps the skeletonization to get rid of small non significative simple surfaces
The skeletonization itself follows an immersion like process begining above mcthreshold
--------------------------Gaussian curvature:-----------------------------------------
with voronoi flag trigered, this image is used to compute isophote Gaussian curvature
Then points of the gray/white interface whose gc<gcthreshold are marked
The cortical folds are filled in at this location to reduce depth
[-lz[ero] {(float) lowest mean curvature for watershed (default:0.3)}]
[-lu[p] {(float) highest mean curvature for watershed(default:1)}]
[-e[rosion] {(float) wave erosion for watershed (default:0.1)}]
[-mcs[igma] {float (mm) (default:1mm)}]
the sigma of the Gaussian smoothing before mean curvature computation
[-gcs[igma] {float (mm) (default:2mm)}]
the sigma of the Gaussian smoothing before Gaussian curvature computation
[-mct[hreshold] {float (default:0.2)}]
[-gct[hreshold] {float (default:-0.05)}]
cf. geometry help
[-r[eadformat] {char: v or t (default:v)}]
[-w[riteformat] {char: v or t (default:v)}]
[-h[elp]
VipSplineResamp
------------------------------
VIP Info:
Performs a spline based resampling of input volume according to template geometry
------------------------------
Usage: VipSplineResamp
-i[nput] {image name}
-t[emplate] {image name}
-th[eader] {template header name (GIS format)}
[-sx] {float:template vox size x}
[-sy] {float:template vox size y}
[-sz] {float:template vox size z}
[-dx] {int:template dim x}
[-dy] {int:template dim y}
[-dz] {int:template dim z}
[-f[loat]]
The command works with float input volume (reading and writing do the same)
-d[eplacement] {deplacement file (rotation or affine}
-d[id] {set deplacement to identity}
Warning, in that case, if the voxel size is different a translation is used
to correct for the fact that our coordinate origin is the first voxel center
-d[write] {write the deplacement file as input_TO_template}
[-or[der] {int: [0..7] (default:3)}]
Spline interpolation order:
0 : nearest neighbor
1 : linear
2 : quadratic
3 : cubic
4 : quartic
5 : quintic
6 : galactic
7 : intergalactic
[-o[utput] {image name (default:"splineresampled")}]
[-r[eadformat] {char: a, v, s or t (default:any)}]
Forces the reading of VIDA, SPM, or TIVOLI image file format
[-w[riteformat] {char: v, s or t (default:t)}]
Forces the writing of VIDA, SPM, or TIVOLI image file format
[-h[elp]
For more information:
http://bigwww.epfl.ch/thevenaz/interpolation/index.html
M. Unser, Splines: A Perfect Fit for Signal and Image Processing
IEEE Signal Processing Magazine, vol. 16, no. 6, pp. 22-38, November 1999
VipSplit
------------------------------
VIP Info:
Split multi-frame volume
------------------------------
Usage: VipSplit
-i {image name}
[-f[loat] : the volume is splited with Perfectly scale factor
[-o[utput] {image name (default:"split")}]
[-h[elp]
VipSplitBrain
Usage: VipSplitBrain
Try to split the brain into 3 parts: hemispheres and cerebellum.
White matter is segmented first, then cleaned up to prevent cavities
from disturbing morphological processing. Then the standard
Erosion, seed selection, reconstruction skim is used.
The program tries several erosion sizes in order to find the smallest one
which minimizes morphological opening effects. When provided, a template
of the localization of the 3 parts in SPM talairach space is used to select seeds.
Otherwise, simple considerations are used.
You can improve the use of the template if you provide CA, CP, and
a third point of interhemispheric plane
-i[nput] {MRI (bias corrected) image name}
[-t[emplate] {voronoi in Talairach: (default: /home2/local/Panabase/demo/talairach/closedvoronoi)}]
a 3 color image with the usual spm bounding box
[-T[emplateUse] {(y/n), default:y}]
Without template, the result is less reliable but often correct
[-C[utUse] {(y/n), default:y}]
Delete some points in corpus callosum and stem from Talairach Coord
[-R[idge] {White ridge image name (default: not used)}]
[-b[rain] {binary brain image name (default:brain)}]
brain binary mask
[-o[utput] {splitted brain image name (default:voronoi)}]
a 3 color label image (a voronoi diagram inside brain mask
[-m[ode] {char: V[oronoi], W[atershed], default:V
Voronoi: classification using voronoi diagramme
Watershed: classification using a watershed algo during the propagation
[-wa[lgo] {algo r/b/c/t, default:r
r: regulariwed grey white classification
b: barycenter, cf -B option
c: coef, cf -wt and -Coef options
t: direct input of the threshold
[-wt[hreshold] {algo t: int (default :mW - Coef*sW)}]
The threshold providing white matter after masking by brain mask
mW: white matter mean grey level, sW: standard deviation
[-ws[eed] {write seed image (y/n), default:n}]
To get an image of seeds and seeds in the template (to understand some problems
[-Co[ef) {float (default :2)}]
multiplicative factor providing threshold for white matter
[-B[ary] {float (default :0.75)}]
Factor for barycenter between gray matter (1-Bary) mean and white matter mean (Bary)
[-e[rosion] {float (default :2mm)}]
Initial erosion size, then step by step increasing by 0.5mm
[-c[csize] {int (default :500)}]
Connected component minima lsize to enter the seed selection process
[-P[oints] {AC,PC,IH coord filename (*.tal) (default:not used)}]
Correct format for the commissure coordinate file toto.APC:
AC: 91 88 113
PC: 91 115 109
IH: 90 109 53
[-xA[C] {(int [0-xsize[) AC X coordinate}]
[-yA[C] {(int [0-ysize[) AC Y coordinate}]
[-zA[C] {(int [0-zsize[) AC Z coordinate}]
[-xP[C] {(int [0-xsize[) PC X coordinate}]
[-yP[C] {(int [0-ysize[) PC Y coordinate}]
[-zP[C] {(int [0-zsize[) PC Z coordinate}]
[-a[nalyse] {char y/n/r: automatic histogram analysis, default:y}]
y: do histogram analysis to get mw and sw, r: read input.han,
n: do simpler things
[-hn[ame] {histo analysis, default:input )}]
read when -a r is set, this file has the .han extension (VipHistoAnalysis)
[-xI[nterHem] {(int [0-xsize[) Inter-hemis. point X coord.}]
[-yI[nterHem] {(int [0-ysize[) Inter-hemis. point Y coord.}]
[-zI[nterHem] {(int [0-zsize[) Inter-hemis. point Z coord.}]
[-Z[over] {int (default :zCA+10)}]
Without template, subset of the cerebellum part above Zover are deleted
in order to modify the competion between the 3 seeds for influence
[-r[eadformat] {char: a, s, v or t (default:any)}]
[-w[riteformat] {char: s, v or t (default:t)}]
[-h[elp]
Some more information in:
Shape bottlenecks and Conservative Flow systems
J.- F. Mangin, J. Regis and V. Frouin
IEEE/SIAM MMBIA Workshop (Math. Methods in
Biomed. Image Analysis), San Francisco, IEEE Press
319-328, 1996
VipSubVolume
------------------------------
VIP Info:
Extraction of a sub-volume
------------------------------
Usage: VipSubVolume
-i[nput] {image name}
-f[loat] y/n {default:no}
Trigers perfect use of vida scale factors
[-o[utput] {image name (default:"subvolume")}]
[-x {first X coordinate}] (default:0)
[-y {first Y coordinate}] (default:0)
[-z {first Z coordinate}] (default:0)
[-t {first T coordinate}] (default:0)
[-X {last X coordinate or sub-volume X-dimension}] (default:SizeX)
[-Y {last Y coordinate or sub-volume Y-dimension}] (default:SizeY)
[-Z {last Z coordinate or sub-volume Z-dimension}] (default:SizeZ)
[-T {last T coordinate or sub-volume T-dimension}] (default:SizeT)
[-l] {take X,Y,Z and T as dimensions instead of coordinates}
[-r[eadformat] {char: v or t (default:v)}]
[-w[riteformat] {char: v or t (default:v)}]
v=VIDA, t=TIVOLI
[-h[elp]]
VipSumFrame
Usage: VipSumFrame
-i[nput] {image name}
-s[cale] y/n {default:no}
Trigers perfect use of vida scale factors
[-o[utput] {image name (default:"summed")}]
-f[rom] {first frame (default:0)}
-t[o] {last frame (default:last frame of serie)}
[-h[elp]]
-----------------------------
VipSumFrame performs for each voxel, the sum
of the activity found in volume serie
starting at 'from' ending at 'to'
.No Decay correction is performed
.Relative dynamic of the different
frames is accounted for whether -scale
switch is yes or no.
.When very different dynamics exist
between frames '-scale y' is preferable
for accuracy at a non neglictable
computing cost.
.Only FLOAT and S16BIT data can be processed.
-----------------------------
VipSwapEndian
------------------------------
VIP Info:
Swap high and low bytes of a VIDA image
------------------------------
[-h[elp]]
Usage: VipSwapEndian
-i[nput] {image name}
[-o[utput] {image name (default:"swapped")}]
[-n[bytes] number of bytes involved for swap {integer: 2 or 4 (default:2)}]
2: AB -> BA; 4, ABCD -> DCBA (only used with the '-r o' option)
[-r[eadformat] {char: v, s, t or o (default:v)}]
[-w[riteformat] {char: v, s, t or o (default:v)}]
v=VIDA, s=SPM, t=TIVOLI, o=OTHER (single binary file)
VipT1BiasCorrection
------------------------------
VIP Info:
Computes a smooth multiplicative field which corrects for non stationarities.
------------------------------
This field aims at minimizing the volume entropy (= minimizing information...).
A tradeoff is found between this entropy and the internal energy of a membrane using annealing.
Usage: VipBiasCorrection
-i[nput] {image name}
[-o[utput] {image name (default:"nobias")}]
[-m[ode] {char: s,g (default:g)}]
Switch between various terms to prevent compression of information
s: without g addition
g: minimize variance of white matter ridges
[-f[ield] {bias field name (default:"biasfield")}]
[-hW[rite] {write volume for histo estimation: y/n (default:n)}]
[-hn[ame] {volume for histo estimation image: (default:variance)}]
[-w[ridges] {white matter ridges image (default:"white_ridges")}]
[-W[write] {write ridges: y/n/r (default:n)}]
[-vW[rite] {write variance: y/n (default:n)}]
[-vn[ame] {variance image: (default:variance)}]
[-eW[rite] {write edges: y/n (default:n)}]
[-en[ame] {edge image: (default:edges)}]
[-mW[rite] {write mean curvature: y/n (default:n)}]
[-mn[ame] {mean curvature image: (default:mean_curvature)}]
[-Di[mfield] {type of field (2/3) (default:3)}]
2: the correction field is constant by slice, 3: constant by cubes
[-F[write] {write field: y/n (default:n)}]
[-d[umb] {y/n (default:y)}]
[-Ke[ntropy] {float (default:1.)}]
Weight of the volume entropy which will be multiplied by the field size
[-Kr[egul] {float (default:50.)}]
Weight of the membrane/spline energy (sum of the squared log of the ratio between 6-neighbors)
[-Ko[ffset] {float (default:0.5)}]
Weight of the squared difference between old and new mean
[-Kc[rest] {float (default:20.)}]
Weight of the voxel in the white ridge volume
[-c[ompression] {int [0,14] (default:auto)}]
The number of bits which are discarted during the volume entropy computation (= /2^compression))
[-t[auto] {char: y/n default:n}]
[-tl[ow] {int (default:3*2^compression)}]
[-th[igh] {int (default:not used)}]
[-e[dges] {int (default:not used, else n/2/3)}]
remove 2D/3D edges for histogram estimation (discard partial volume)
[-vt[ariance] {int (default:not used, else int threshold)}]
high threshold on standard deviation in 26-neighborhood for inclusion in histogram
Values beyond this threshold are not taken into account.
In return, the field correction is applied to all values to get the final result
[-vp[ourcentage] {int (default:not used, else int threshold)}]
Pourcentage of non null points kept with a ranking stemming from local variance
[-T[emperature] {float (default:10.)}]
Initial temperature for annealing
[-G[rid] {int (default:2)}]
Number of grid for minimization (annealing on the highest only)
[-g[eometric] {float (default:0.97)}]
Geometric decreasing for annealing schedule
[-s[ampling] {float (default:16mm)}]
The sampling of the field: one value for a parallelepipedic volume of points.
In each direction, the sampling is: sampling/DirVoxelSize.
The field is a 0-order spline during optimization (piecewise constant)
3-order spline during the final bias correction (piecewise linear)
[-n[Increment] {int (default:2)}]
Minimization is performed using a Gibbs sampler or a ICM (deterministic) approach with
several multiplicative increments are tires for each field point:
1/I^n,...,1/I,I,...I^n:
[-I[ncrement] {float (default:1.03)}]
elementary multiplicative increment (see above):
[-a[mplitude] {float ]1,10] (default:1.1)}]
The field random initialization is in the range [1/amplitude, amplitude]
[-Z[regulTuning] {float (default:1)}]
Multiplicative factor for regularization in z direction (bad coil)
[-L[ast] {int (default:0)}]
Mask the Last last slices in all estimation (for field of view going to the shoulder)
[-P[oints] {AC,PC,IH coord filename (*.tal) (default:not used)}]
Correct format for the commissure coordinate file toto.APC:
AC: 91 88 113
PC: 91 115 109
IH: 90 109 53
[-Dc[orrect] {Do the biais correction: y/n (default:y)}]
Write the images as hfiltered or whiteridge whithout doing the bias correction if it has been done by another software
[-r[eadformat] {char: a, v, s or t (default:any)}]
[-w[riteformat] {char: v, s or t (default:t)}]
[-h[elp]
More information in:
Entropy minimization for automatic correction
of intensity non uniformity, J.-F. Mangin,
MMBIA (Math. Methods in Biomed. Image Analysis),
Hilton Head Island, South Carolina, IEEE Press
162-169, 2000
VipTalairachCoordinates
------------------------------
VIP Info:
Provide the coordinates of a point in the Talairach frame.
------------------------------
Usage: VipTalairachCoordinates
-X {input point X}
-Y {input point Y}
-Z {input point Z}
-xa[c] {AC point X}
-ya[c] {AC point Y}
-za[c] {AC point Z}
-xp[c] {PC point X}
-yp[c] {PC point Y}
-zp[c] {PC point Z}
-xh[emi] {Hemispheric point X}
-yh[emi] {Hemispheric point Y}
-zh[emi] {Hemispheric point Z}
[-h[elp]]
VipTalairachTransform
------------------------------
VIP Info:
Computes the Talairach referential and writes a transformation matrix file from a .APC commissures file
------------------------------
Usage: VipTalairachTransform
-i[nput] {commissures file name (.APC)}
-o[utput] {transformation file name (.trm)}
-m[ask] {brain mask file name, must includes hemispheres only (no cerebellum) - if a voronoi (with cereb) is provided, use the -v option too}
[-v[oronoi]]
[-h[elp]
in voronoi mode, the mask in thresholded to exclude label 3 (cerebellum) from a standard Vip voronoi image
VipTopoClassifMeaning
------------------------------
VIP Info:
Gives the meaning of a topological classification value
------------------------------
Usage: VipTopoClassifMeaning
-v[alue] {int value}
-a[ll]
[-h[elp]
------------------------------
!! VIP Error:
value arg is required by VipTopoClassifMeaning
------------------------------
Usage: VipTopoClassifMeaning
-v[alue] {int value}
-a[ll]
[-h[elp]
VipTopoClassification
------------------------------
VIP Info:
Topological classification of a given label
------------------------------
Usage: VipTopoClassification
-i[nput] {image name}
[-o[utput] {image name (default:"classified")}]
[-l[abel] {label to classify (default:255)}]
[-r[eadformat] {char: v, s or t (default:v)}]
[-w[riteformat] {char: v, s or t (default:v)}]
v=VIDA, s=SPM, t=TIVOLI
[-h[elp]]
VipTransform
------------------------------
VIP Info:
Translation, scale, and rotation volume transformation.
------------------------------
Usage: VipTransform
-i[nput] {volume name}
[-o[utput] {transformed volume file (default:"transfo")}]
[-xs[cale] {X scale factor (default=1.0)}]
[-ys[cale] {Y scale factor (default=1.0)}]
[-zs[cale] {Z scale factor (default=1.0)}]
[-xt[ranslate] {X translation value (default=0.0)}]
[-yt[ranslate] {Y translation value (default=0.0)}]
[-zt[ranslate] {Z translation value (default=0.0)}]
[-xr[otate] {X rotation angle in degree (default=0.0)}]
[-yr[otate] {Y rotation angle in degree (default=0.0)}]
[-zr[otate] {Z rotation angle in degree (default=0.0)}]
[-xg[ravity] {X rotation center position (default=dimx/2)}]
[-yg[ravity] {Y rotation center position (default=dimy/2)}]
[-zg[raviy] {Z rotation center position (default=dimz/2)}]
[-h[elp]]
VipTriangle
------------------------------
VIP Info:
to be writen
------------------------------
VipVFilter
------------------------------
VIP Info:
Apply a V-Filter to an image
------------------------------
Usage: VipVFilter
-i[nput] {image name}
[-o[utput] {image name (default:"vfilter")}]
[-m[masksize] {int (default:2)}]
[-t[ype] {char: o or n (default:o)}]
o=OPTIMIZED, n=NON OPTIMIZED
[-r[eadformat] {char: v, s or t (default:v)}]
[-w[riteformat] {char: v, s or t (default:v)}]
v=VIDA, s=SPM, t=TIVOLI
[-h[elp]]
VipVoiStat
----------------------------------------------
VipVoiStat performs statistics computation
given a VOI file (label) a serie file
a displacement file (and
possibly a movment compensations)
Flag --pvec_matrix triggers pvec correction
in that case the voi file must contain the
background region (default label is 200 or
given by --pvec_bkg_label
the -v[oi] parmater is the -l[abelout] file
output by the VipStriataGTM command
----------------------------------------------
Usage : VipVoiStat
-s[serie] {dynamic serie}
-v[oi] {voi volume}
-d[epla] {deplacement file (rotation/ affine}
[-c[urve] {ASCII result file (def: stdout)}]
[--dmc {file with movement compensation}]
[--pvec_matrix (pv cor y/n, default:y)]
[--pvec_bkg_label (label of bkg, default:200)]
[-h[elp]]
VipVoronoi
------------------------------
VIP Info:
Computes a (generalized) Voronoi diagram for the different seeds in input
------------------------------
Underlying distance either corresponds to a Euclidean-like chamfer distance .
or corresponds to the distance related to the specified connectivity.
Usage: VipVoronoi
-i[nput] {image name} : object definition
[-o[utput] {image name (default:"distmap")}]
[-di[stmap] {image name (default:"distmap")}]
[-wd[istmap] {'y' or 'n' (default:'n')}]
write the underlying distance map
[-c[onnectivity] {string:6/18/26/4/8/4s/8s/4c/8c (default:not used)}]
[-g[eodesic] {string:'i' or 'f' (default:not used)}]
geodesic distance map: 'i':iterated chamfer transform
'f':thick front propagation
[-d[omain] {int (default:0)}]
this value defines propagation domain for the geodesic distance
[-f[orbiden] {int (default:-1)}]
this value defines outside of domain for the geodesic distance
[-n[itermax] {int (default:5)}]
maximum number of iterations for iterated chamfer transform
Suffixes "s" and "c" means sagittal and coronal orientations
[-x[masksize] {int (default:3)}: chamfer mask xsize]
[-y[masksize] {int (default:3)}: chamfer mask ysize]
[-z[masksize] {int (default:3)}: chamfer mask zsize]
[-m[ultfactor] {float (default:50)}]
------------------------------
VIP Info:
Read and Write flag are actually configured for debugging...
------------------------------
[-r[eadformat] {char: v or t (default:v)}]
[-w[riteformat] {char: v or t (default:v)}]
[-h[elp]
siChangeModels
siChangeModels
--------------
Replaces models in some model elements according to a matching criterion on a
specific attribute
Options :
[ -p <string> ]
input parameters file (tree format) (richer than other parameter given on
the commandline)
Parameter file attributes:
mgraph string !
attribute string
pattern string !
model string !
[ -g <string> ]
model graph file
[ -a <string> ]
model attribute to discriminate on
[ -e <string> ]
regular expression to match model elements for changes
[ -m <string> ]
model file to replace matched models (.mod)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
siCopyModelDescriptors.py
Usage: Get all descriptors from a model and set it into an other model.
Options:
-h, --help show this help message and exit
-f FILTER, --labelsfilter=FILTER
only models matching this filter are covered.ex :
'label1,label2' or 'label' or 'regexp1,regexp2' (here
order is important)
--filtermode=FILTER strict, flexible or regexp
-s MODEL, --src=MODEL
model file name (default : model.arg)
-d MODEL, --dst=MODEL
model file name (default : model.arg)
siCopyNames
usage :
siCopyNames namedGraphFile unnamedGraphFile [newFile=unnamedGraphFile]
copies names / labels from an old or incomplete graph file
to a new one without names / labels
siCsvMapGraph.py
disable fff
disable fff
Usage: Map csv values onto sulci.
Options:
-h, --help show this help message and exit
-g FILE, --graph=FILE
data graph
--label-attribute=STR
'name' or 'label' (default: name)
-m FILE, --mesh=FILE grey/white mesh in the same space of the input graph
--csv=FILE csv file
--summary-csv=FILE summary csv file (one line per sulci)
-f, --format print csv format
-t FILE, --translation=FILE
translation file (.trl), or nomenclature file (.hie),
or selection file (.sel) (default : /neurospin/brainvi
sa/build/Mandriva-2008.0-x86_64/bug_fix/share
/brainvisa-share-4.2/nomenclature/translation/sulci_mo
del_2008.trl)
--log add log (neperian) of mean values read in the input
csv
--log10 add log10 of mean values read in the input csv
-c COLUMNS, --column=COLUMNS
column number to be used in the csv file
-o OPERATOR, --operator=OPERATOR
operator to apply to summarize multiple values on the
same sulcus. The default is "mean", but could be "min"
or "max"
siDiffModels.py
Usage: Compare two sigraph models.
Options:
-h, --help show this help message and exit
-f FILTER, --labelsfilter=FILTER
only models matching this filter are covered.ex :
'label1,label2' or 'label' or 'regexp1,regexp2' (here
order is important)
--filtermode=FILTER strict, flexible or regexp
-1 MODEL, --model1=MODEL
model file name (default : model.arg)
-2 MODEL, --model2=MODEL
model file name (default : none)
-g FILE, --graph=FILE
data graph file name
--hist=HIST make histogram from classifiation/regression ratesof
models. HIST should be a format supported by pylab
-p PCT, --pct=PCT percentage of the biggest differences between models
ex : 5.6%, 5.6, 5 (default : 10)
-c CMP, --cmp=CMP compared data : a list of compared elements taken in
raw, mean, good, bad (default : raw,mean,good,bad)
-m MODE, --mode=MODE return biggest or smallest values (default : biggest)
-a, --abs compare absolute differences (default : disabled)
--anatomist Display first compared value on a graph under
anatomist software (default : disabled)
siDisplayGraph.py
warning: can't load grid module 'grid.py'
warning, fff is not here or does not work. GMM will not be usable
disable fff
disable fff
Usage: Display graphs with usefull representations.
Usage : siDisplayGraph.py [Options] graph1.arg graph2.arg ...
Options:
-h, --help show this help message and exit
-t FILE, --translation=FILE
translation file (default : /neurospin/brainvisa/build
/Mandriva-2008.0-x86_64/bug_fix/share/brainvisa-share-
4.2/nomenclature/translation/sulci_model_noroots.trl)
-m FILE, --mode=FILE wireframe, gravity_centers, sulci_gravity_centers,
hull_line, bivariate_spline,extremity1, extremity2,
hull_intersection, pure_cortical,
diff_gravity_centers, centerdist_cortical,
markov_relations
-d DIR, --dir=DIR directory with siMorpho output files (used by
extremities mode).
-s LIST, --sulci=LIST
display only specified sulci.
-w, --write Write meshes
--rewrite-graphs if specified, input graphs may be modified
siDisplayGrid.py
disable fff
disable fff
Usage: Generate diagrams based on grid optimization.
Options:
-h, --help show this help message and exit
-f FILTER, --labelsfilter=FILTER
only models matching this filter are covered.ex :
'label1,label2' or 'label' or 'regexp1,regexp2' (here
order is important)
--filtermode=FILTER strict, flexible or regexp
-m MODEL, --model=MODEL
model file name (default : model.arg)
--max best value is the maximum one (default : min)
--svg generate svg diagrams (default : eps)
-a, --all generate all optimization grids
-v VERBOSE, --verbose=VERBOSE
level of verbosity
siDivNameList
usage :
siDivNameList [-p prefix] n directory savefile
siDivNameList [-p prefix] -c directory savefile n1 n2...
Divise une liste de modèles (fichiers .mod dans le directory
donné) en n expressions régulières. Les expressions crées sont
sauvées dans les fichiers savefile.0, savefile.1 ...
savefile.(n-1)
-p enlève le préfixe donné aux noms de fichiers avant
de construire les expressions régulières
-c mode cpu, donne une liste d'indices correspondant chacun
à la puissance CPU de la machine concernée
siDomTrain
usage :
siDomTrain paramFile
siDomTrain [-uncb] modelFile.arg graphFile1.arg ... graphFileN.arg
Learning of validity domains of a model graph.
-u : (uninitialized) don't initialize domains before learning
-n : (nosave) don't save results
-c : (clean) eliminates afterwards unused model elements
-b : (no buckets) don't load buckets (by default, they are loaded)
siEnergy
siEnergy
--------
Energy of a labelled graph
In verbose mode, potentials of each individual clique is displayed
Options :
-m <string>
model graph
-i <string>
data graph
[ -w <FLOAT> ]
weight factor (0: keep as is (default), <0: remove existing weights
according to neighbours number)
[ -t <string> ]
labels translation file
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
siError
siError
-------
Count labelling differences on auto/manual recognitions on a cortical folds
graph. Graph must be labelled manually ("name" attribute) and automatically
("label" attribute)
Options :
[ -i <string> ]
data fold graph
-l <string>
labels translation file
[ -r <string> ]
reference graph name to compare labels with (default: same as input data
graph)
[ -a <string> ]
automtic labeling attribute (default: "label")
[ -m <string> ]
manual (reference) labeling attribute (default: "name")
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
siError.py
warning: can't load grid module 'grid.py'
Usage: Count labelling differences on auto/manual recognitions on a cortical folds graph..
Options:
-h, --help show this help message and exit
-l FILE, --labeled_graph=FILE
labeled graph file (evaluated one)
-t FILE, --labels_translation=FILE
labels translation file
-b FILE, --base_graph=FILE
base graph file (reference). If not specified,
labeled_graph is taken
-s NAME, --subject=NAME
subject name (ex : amon, zeus, subject01, ...)
--csv=FILE save sulcuswise errors. If FILE already exists,
results are appened at the end. Multiple writting by
several instances of this scrip is safe.
-f FILE, --labels-filter=FILE
list of labels (one per line) fixed during recognition
based on true labels 'name' field.
-a, --append append errors at the end of an existing files instead
of erasing it
siErrorLightWrapper.py
warning: can't load grid module 'grid.py'
Usage: Call siError on graph inputs and store resulting error rate in a new entry of a CSV file.
Options:
-h, --help show this help message and exit
-m FILE, --model=FILE
graph model
-l FILE, --labeled_graph=FILE
labeled graph file (evaluated one)
-t FILE, --labels_translation=FILE
labels translation file
-b FILE, --base_graph=FILE
base graph file (reference) If not specified,
labeled_graph is taken
-c CSV, --csv=CSV file storing error rate
-n NAME, --graph_name=NAME
graph name to be stored in CSV
-a, --append append errors at the end of an existing files instead
of erasing it
siErrorStats
siErrorStats
------------
Counts differences between 'label' and 'name' attributes (automatic and manual
sulci identifications), sulcus by sulcus, and saves a tree with stats in
'resultfile.tre'
Options :
[ -c <string> ]
parameters file (if you don't provide other parameters on the commandline
options). You have to provide either this parameters file, or the other
arguments (result tree file, input graphs)
[ -o <string> ]
result tree which will contain the difference stats
[ -i <vector of string> ]
Graphs to count differences from
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
siFlip
siFlip
------
Flips coordinates attributes to appear as the other hemisphere in cortical
folds graphs
Options :
-i <string>
input graph file
[ -o <string> ]
output (flipped) graph file
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
siFoldGraph2vrml.py
warning: can't load grid module 'grid.py'
warning, fff is not here or does not work. GMM will not be usable
disable fff
disable fff
Usage: Convert Aims data fold graph to vrml1 format.
siFoldGraph2vrml.py -i input.arg -o output.vrml [OPTIONS]
Options:
-h, --help show this help message and exit
-t FILE, --translation=FILE
translation file (default : /neurospin/brainvisa/build
/Mandriva-2008.0-x86_64/bug_fix/share/brainvisa-share-
4.2/nomenclature/translation/sulci_model_noroots.trl)
-i FILE, --input=FILE
data fold graph
-o FILE, --output=FILE
vrml file
--label-mode=STR 'name': manual label, 'label': automatic label
(default: name)
--hierarchy=FILE hierarchy (links between names and colors), default : /
neurospin/brainvisa/build/Mandriva-2008.0-x86_64/bug_f
ix/share/brainvisa-share-4.2/nomenclature/hierarchy/su
lcal_root_colors.hie
siFunctionalGraphs
siFunctionalGraphs
------------------
Analyse les resultats d'un protocole fonctionnel a partir du fichier de config
utilise pour etiqueter les graphes
Options :
-i | --input <string>
config.tree
-o | --output <string>
test.hie
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
siGenerateLearningTasks.py
Usage: Generate a file of learning tasks. Each line represents a call to siLearn command on a particular model.
Options:
-h, --help show this help message and exit
-f FILTER, --labelsfilter=FILTER
only models matching this filter are covered.ex :
'label1,label2' or 'label' or 'regexp1,regexp2' (here
order is important)
--filtermode=FILTER strict, flexible or regexp
-m MODEL, --model=MODEL
model file name (default : model.arg)
-e MAIL, --email=MAIL
(default : )
-p MODE, --parallelism-mode=MODE
['cath', 'duch', 'LSF', 'grid', 'somaworkflow']
(default : duch)
-o FILE, --output=FILE
output file name storing tasks (default :
learningtasks) or pattern when several files are
generated (LSF, cath) : output files are named
$pattern1, $pattern2...
-c FILE, --config=FILE
silearn config file (default : siLearn-read.cfg)
-t TIME, --time=TIME format : hh:mm (default : 00:30 (30 min))
-b FILE, --bin=FILE siLearn binary (default : siLearn.py)
siGraph2Label
siGraph2Label
-------------
Create a volume of label from a graph and a file translation.txt (bucket:
aims_bottom, aims_ss, or aims_junction + syntax hull_junction)
Options :
-g | -graph | --graph <string>
input graph
[ -tr | -translation | --translation <string> ]
tranlslation file, labels are translated according to this dictionary if it
is provided
[ -tv | -template | --template <string> ]
template volume:
-o | -output | --output <string>
output volume
[ -b | -bucket | --bucket <vector of string> ]
bucket name[s]
[ -s | -syntax | --syntax <vector of string> ]
syntax[es] of bucket
[ -a | --attribute <vector of string> ]
attributes list that contain a label [default: 'label', 'name' ]
[ -l | --label <vector of string> ]
label values to be kept (filter) [default: all]
[ -it | --intrans <string> ]
input int/label translation file. If provided, it will be used for the
label mapping, and completed if needed
[ -ot | --outtrans <string> ]
output int/label translation file [default: not saved]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
siGraphSwithNameLabel.py
Usage: Switch label and names values
Options:
-h, --help show this help message and exit
-i FILE, --ingraph=FILE
input data graph
-o FILE, --outgraph=FILE
output data graph (default : input)
siLearn
usage :
siLearn paramFile
siLearn [-l labelsMapFile] [-n] [-u] [-s] [-c cycles] modelFile trainschemeFile graphFile1.arg ... graphFileN.arg
Learns a model graph
paramFile : parameters file for inputs for the command
(Tree file)
-l labelsMapFile : correspondance map from labels of the
graph to learn to those used by the model
(default: sillons_modele.def)
-n : (nosave) do not save the model after learning
-u : (uninitialized) do not reinitialize the model
before learning
-s : (stats) initializes learning of stats
-a attr : label attribute used to get labels from:
usually 'label' or 'name', 'auto' means try
first label, and if no label is present, take
name [default:auto]'
-c cycles : number of learning and testing cycles over the
graph set while database generation
(default: 1)
modelFile.arg : model graph file to train
trainschemeFile : learning sequence description file
graphFile1.arg .. graphFileN.arg : graphs to learn
Signal handlers:
SIGINT (kill -2) (Ctrl-C) : prompt for save, then exits
SIGSEGV, SIGBUS, SIGILL (kill -9,10,11) (error) : save and exit
SIGUSR1 (kill -16) : save and continues learning
WARNING -- Commandline-options are not being maintained any
longer. Use config file for new params.
siLearn.py
Usage: siLearn.py [Options] [silearn.cfg]
Options:
-h, --help show this help message and exit
-f FILTER, --labelsfilter=FILTER
only models matching this filter are covered.ex :
'label1,label2' or 'label' or 'regexp1,regexp2' (here
order is important)
--filtermode=FILTER strict, flexible or regexp
--label_attribute=ATTR
label attribute used to get labels from: usually
"label" or "name", "auto" means try first label, and
if no label is present, take name
[default:auto]
--debug enable debug [default: disable]
siLyxErrors
usage :
siLyxErrors resultfile.lyx resultfile.tre [dir]
dir: directory où seront écrites les images .eps
Ecrit les tableaux d'erreurs dans un fichier au format LyX
Ces erreurs doivent avoir été calculées avec siErrorStats
siMakeColoredHierarchy
siMakeColoredHierarchy
----------------------
Build colored hierarchy from p-value table.
Options :
-p | --palette <string>
Input RGV palette image.
-i | --input <string>
Input statistic file.
-o | --output <string>
Output hierarchy
[ -s | --suffix <string> ]
Suffix (eg. _left or _right) (default = none)
[ -t | --transparancy <S32> ]
Transparancy for values less than min (default = none)
[ -T | --Transparancy <S32> ]
Transparancy for values greater than max (default = none)
[ -b | --biggest <boolean> ]
Choose the biggest value (instead of the smallest value) in case of
multiple possibility (default: false)
[ -k | --keepline <boolean> ]
Keep the first line (i.e. header) of the file (default: false)
[ -inv | --invert <boolean> ]
Invert label/name (default: false)
[ -g | --graph <string> ]
Hierarchy graph syntax (default = CorticalFoldArg)
[ -M | --Max <FLOAT> ]
Maximum palette value (default = auto).
[ -m | --min <FLOAT> ]
Minimum palette value (default = auto).
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
siMakeModel
siMakeModel
-----------
Creates a sulcal model graph
Options :
-o <string>
output model filename (.arg)
-l <string>
labels translation filename
-m <string>
template node model filename (.mod)
-d <string>
template domain filename (.dom)
[ -f <string> ]
fallback node model filename (.mod) used for unknown situations ('-' can be
specified for none for compatibility with older sigraph releases)
[ -r <string> ]
fallback relation model filename (.mod)
[ --mversion <string> ]
model version [default: 4.2]
[ --dversion <string> ]
data graphs compatibility version [default: 3.1]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
siMakeParcellationHierarchy
-------------------------------------------------------------------------
siMakeParcellationHierarchy -g[yrus] <output gyrus hierarchy>
-s[ulcus]<output sulcus hierarchy >
-m[odel] <intput gyri model >
-l[evel] <level model>
[-h[elp]]
-------------------------------------------------------------------------
Make sulci and gyri hierarchy for parcellation
-------------------------------------------------------------------------
gyri model : Choice of the sulcus/sulcus relations ('*.gyr')
level model : Choice of the level of description file ('*.trl')
-------------------------------------------------------------------------
siMergeModels
siMergeModels
-------------
Merges two model graphss by taking the best elements of each
Options :
-i <string>
1st model graph
-j <string>
2nd model graph
-o <string>
output model graph
[ -f <DOUBLE> ]
comparison factor: a model from the 2nd graph will replace the one in the
1st one if conf1 < conf2 * factor, conf1 and conf2 being the confidence
factors of both models [default: 1]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
siMeshSulciOperture
-------------------------------------------------------------------------
siMeshSulciOperture -G[rey] <grey/white meshfilein>
-L[CR] <LCR/white meshfilein>
-m[odel] <gyri model>
-l[evel] <level model>
-s <sulci names>
[-n[bcc] <nb connected component> default=5]
[--de <distance threshold default=10 mm]
[--dp <distance threshold default=10 mm]
-g[raph] <sulcus graph>
-[input] <mri volume>
-v[olume] <output thickness volume>
[-t[raduction] <traduction_file> default = traduction.txt]
[-h[elp]]
-------------------------------------------------------------------------
Give different measures related to the sulci operture and cortex thickness
-------------------------------------------------------------------------
meshfilein : input *.tri or *.mesh file
gyri model : Choice of the sulcus/sulcus relations
level model : Choice of the level of description file *.def
sulci name : Attribute for the name of the sulci in the graph (name or label)
sulcus graph : Graph of the sulci *.arg
traduction_file : correspondance label string->short_label
required by siParcellation.
dmin : max distance between the voxel and its projection
-------------------------------------------------------------------------
siMeshSulciProjection
-------------------------------------------------------------------------
siMeshSulciProjection -i[nput] <meshfilein>
-m[odel] <gyri model>
-l[evel] <level model>
-s <sulci names>
-g[raph] <sulcus graph>
[-t[raduction] <traduction_file> default = traduction.txt]
[-n[umbercc] <number_connex_components> default = 4]
[-a[lpha_reg] <estimation_ratio > default = 1]
[-e[min] <euclidean distance threshold> default = 5 mm]
[-p[min] <plane distance threshold> default = 2 mm]
[-V[olume_radius] <closing volume radius> default = 1.5 mm ]
[-M[esh_radius] <closing radius for mesh > default = 1.5*r ]
[-o[utput] <output_sulc_texture>]
[--connexity <metric> default =mesh connexity
[-c[urvature] <curvature map>]
[-K <curvature coef.> default = 2]
[-h[elp]]
-------------------------------------------------------------------------
Project sulcus bottom points (voxels) on mesh texture (nodes).
Only sulci present in the <gyri model> file are projected.
Their label correspond to the hierarchy defined in the <level model> file
There are two alternative approach for the projection.
The first one uses a metric combining an euclidean distance and map (curvature or depth,..) information.
The second one uses tangent plane.
-------------------------------------------------------------------------
meshfilein : input *.tri or *.mesh file
gyri model : Choice of the sulcus/sulcus relations
level model : Choice of the level of description file *.def
sulci name : Attribute for the name of the sulci in the graph (name or label)
sulcus graph : Graph of the sulci *.arg
traduction_file : correspondance label string->short_label
required by siParcellation.
number_connex_components : minimal number of point in each connected component
estimation_ration : Distance threshold for detecting outliers for affine projection estimation.
Only points closer than (estimation_ration * dmin) are used for the estimation
dmin : max distance between a voxel and its projection
input_curvature : input *.tex curvature
curvature coef.: influence of the curvature
closing radius : Radius for the sulci closing in mm
output_sulc_texture : Projected sulci texture *.tex
connexity : Underlying mesh metric : euclidean/mesh connexity
-------------------------------------------------------------------------
siMkModelEdges
usage :
siMkModelEdges [-o num] modelGraph.arg labelsFile adapFile.mod foldgraphlist
siMkModelEdges paramFile
-o num : removes edges whose occurence frequency in the data is
less or equal to num
siModelsErrorRateInfo.py
Usage: Compute mean/std/min/max of model errors (good, bad, mean) and could make an histogram.
Options:
-h, --help show this help message and exit
-f FILTER, --labelsfilter=FILTER
only models matching this filter are covered.ex :
'label1,label2' or 'label' or 'regexp1,regexp2' (here
order is important)
--filtermode=FILTER strict, flexible or regexp
--filter-fifty-percent
filter values equal to 0.5
-m MODEL, --model=MODEL
model file name (default : model.arg)
--hist=HIST make histogram from classifiation/regression ratesof
models. HIST should be a format supported by pylab
siMonitor.py
Usage: Monitor sigraph learning process.
Options:
-h, --help show this help message and exit
-f FILTER, --labelsfilter=FILTER
only models matching this filter are covered.ex :
'label1,label2' or 'label' or 'regexp1,regexp2' (here
order is important)
--filtermode=FILTER strict, flexible or regexp
-m MODEL, --model=MODEL
model file name (default : model.arg)
-n FILE, --newer=FILE
generated files must be newer than this file
-t TASK, --task=TASK monitoring task : models, log (default : models)
--mode=MODE monitoring mode : learning, generation, models
(default : learning)
-o FILE, --outputbatch=FILE
batch file
-r, --remote enable remote control (default : disable)
-l LOGFILENAME, --log=LOGFILENAME
analyzed log
-i INPUTBATCH, --inputbatch=INPUTBATCH
input batch file
siMorpho
siMorpho
--------
Writes morphometry figures to disk files according to a model graph.
Each data graph is one single line on each file, and each file is a table for a
single element (sulcus or relation).
Elements to get figures on can be filtered by providing regular expressions or
a selection (newer mechanism)
Options :
[ -p <string> ]
input parameters file (tree format) (richer than other parameter given on
the commandline)
Parameter file attributes:
modelFile string !
graphFiles string !
labelsMapFile string
filter_attributes string
filter_pattern string
output_prefix string
verbose int
name_descriptors int
label_attribute string
descriptor_aliases string
print_labels int
subjects string
subject_regex string
selection string
[ -m <string> ]
model file
[ -g <vector of string> ]
graphs to get morphometry figures on
[ -l <string> ]
correspondance map from labels of the graph to learn to those used by the
model
[ -o <string> ]
append prefix to output data file names (followed with region models names)
default: siMorpho_
[ --label_attribute <string> ]
label attribute used to get labels from: usually "label" or "name", "auto"
means try first label, and if no label is present, take name [default:auto]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
siMultilabelCompare
siMultilabelCompare
-------------------
Evaluation of different labelings.This command is a bit similar to siErrorStats
but allows to compare an arbitrary number of different labelings for the same
graph, and an arbitrary number of subjects
Options :
-o <string>
output filename for stats
[ -i <vector of string> ]
input graphs filenames and params. They should have the form
filename.arg|subjectname|label_attribute|id_attribute, with:
subjectname: identifier for the subject
label_attribute: label or name
id_attribute: attribute (int type) used to identify the same node on
different copies of the same graph.
If you are using a BrainVisa-like database, you can either use the -b
option, or build the parameters list using a sed command of the form:
ls */graphe/*.arg | sed -e \
's%.*/\([^/]*\)/graphe/[^/]*\.arg%"\0|\1|label|index"%' \
| awk '{ printf( "%s ", $0 )}'
[ -c <string> ]
config file providing the list of graphs to compare. This file only
contains a concatenation of the -i arguments equivaments.
If you are using a BrainVisa-like database, you can either use the -b
option, or build the config file using a sed command of the form:
ls */graphe/*.arg | sed -e \
's%.*/\([^/]*\)/graphe/[^/]*\.arg%\0|\1|label|index%' > configfile
[ -t <boolean> ]
output as table (default is pyhton-like dictionary object)
[ -b <boolean> ]
BrainVisa style: input parameters are only graph filenames which are
organized as a BrainVisa database: <basepath>/subjectname/graphe/*.arg
in this case, the label attribute is 'label' and the identifier attribute
is 'index'.
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
siPIDcommand
usage : siPIDcommand PIDfile command [params...]
execs command 'command' with given parameters and writes the process ID to file PIDfile
siParcellation
siParcellation
--------------
Compute parcellation in sulci regions and gyri. The input sulci texture must be
defined by siMeshSulciProjection
Options :
-i | --input <file name (read only): mesh of VOID>
grey/white mesh
-s | --sulci <file name (read only): texture of S16>
input_texture: definition of the sulci texture (given by
siMeshSulciProjection
-g | --graph <filename: Graph>
output gyri graph
-m | --model <string>
gyri model: Choice of the sulcus/sulcus relations ('gyri.gyr')
-o | --output <filename: texture of S16>
output timetexture file (sulci and gyri texture): 0: sulci, 1 : sulci
regions, 2: gyri, 3: gyri & sulci
[ -b | --brain <file name (read only): mesh of VOID> ]
brain mesh [used and required in 3D mode only]
[ -p | --parcelvol <filename: volume of S16> ]
output gyri volume [used in 3D mode only]
[ -v | --value <S32> ]
grey value in input_grey_white vol [default: 100]
[ -V | --Volume <file name (read only): volume of S16> ]
input grey white volume [used and required in 3D mode only]
[ -T | --Time <U32> ]
input sulci texture time [default: 0]
[ --sulcitranslation | --sulcitraduction <string> ]
sulci translation file: correspondance label string->short_label
[default:"sulcitraduction.txt"]
[ --gyritranslation | --gyritraduction <string> ]
output gyri translation file: correspondance label string->short_label.
This file will be written or completed if it already exists
[default:"gyritraduction.txt"]
[ --connectivity | --connexity <boolean> ]
use connectivity (true) or geodesic euclidean distance (false) [default:
false]
[ --3D <boolean> ]
compute 3D cortical ribbon gyrus graph [default: false]
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
siPotentialSummary.py
Usage: Stores potential summary information into data graph nodes
Options:
-h, --help show this help message and exit
-m MGRAPH, --model=MGRAPH
model graph filename
-d DGRAPH, --data=DGRAPH
data graph filename
siPutTextureInModel
siPutTextureInModel
-------------------
no doc at the moment...
Options :
-m <string>
model file
-v <string>
value file
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
siRelax
siRelax
usage :
siRelax paramFile
siRelax [-l labelsMapFile] [-n] [-u] [-t temp] [-m mode]
[-d rate] [-i tempICM] [-s stopRate] [-g gibbschange] [-v]
[-N nodesGrouping] [-p plotfile] [-u] [-L label] modelFile graphFile.arg
Labels a folds graph according to a model graph
by simulated annealing
Arguments :
paramFile : parameters file for inputs for the command
(Tree file)
-l labelsMapFile : correspondance map from labels of the
graph to learn to those used by the model
(default: sillons_modele.def)
-n : (nosave) do not save the graph after relaxation
-u : (uninitialized) do not initialize the fold
graph labels before annealing
-t temp : initial temperature of the relaxation
(default: 1.)
-m mode : annealing mode: metro, icm, gibbs
(default: gibbs)
-d rate : temperature decrease rate factor
(default: 0.95)
-i temp : temperature below which annealing switches
to ICM (default: 0., no ICM)
-s rate : stop rate: proportion of allowed changes
below which relaxation stops (default: 0.01)
-g gibbschange : number of synchronous changes allowed in
Gibbs and ICM modes (default: 2)
-N nodesGrouping : nodes grouping while iterating on the graph:
VERTEX, CLIQUE (default: VERTEX)
-v : verbose mode
-p plotfile : saves the energies of each timestep in a
file (useful for plotting)
-U : use 'unknown' label for initialization. The
'unknown' label is set with the -L option
-L label : sets the default unknown label.
(default: 'unknown')
modelFile.arg : model graph file to train
graphFile.arg : graph to label
siRelax.py
Usage: Annealing to label sulci.
Options:
-h, --help show this help message and exit
-c FILE, --config=FILE
siRelax config file
-w MODE, --weight=MODE
mode to weight models (sulci and relations) : volume,
size, neighbours, volumeT, sizeT, neighboursT, ratio
(0 : only sulci, 1 : only relations, 0.5 : classical
model), treshold (w < l => w = 0)
-l FILE, --lambda=FILE
lambda parameter for ratio weights modifier :
(1-lambda) for sulci, (lambda) for relations. For
threshold modifier : truncate threshold.
siRevert
siRevert
--------
Reverts an overlearned model graph to its optimal state (saved during learning)
Options :
-m <string>
model graph
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
siSulcalParcellation
-------------------------------------------------------------------------
siSulcalParcellation -i[nput] <grey/white mesh>
-s[sulci] <input_texture>
-g[raph] <output_gyri_graph>
-m[odel] <gyri model >
-b[rain] <brain mesh >
-o[utput] <output_gyri_texture>
-p[arcelfile] <output_gyri_volume>
[-v[alue] <grey value in input_grey_white vol>]
[-V[olume] <input_grey_white volume>]
[-T[ime] <input sulci texture time> default = 0]
[-t[raduction] <traduction_file> ]
[--connexity ]
[--3D ]
[-h[elp]]
-------------------------------------------------------------------------
Compute parcellation in sulcal regions
The input sulci texture must be defined by siMeshSulciProjection
-------------------------------------------------------------------------
meshfilein : input *.tri or *.mesh file
input_texture : definition of the sulci texture (given by siMeshSulciProjection
gyri model : Choice of the sulcus/sulcus relations ('gyri.gyr')
traduction_file : correspondance label string->short_label
required by siParcellation.
connexity : connexity or geodesic euclidean distance
3D : compute 3D cortical ribbon gyrus graph
output_vor_texture : output timetexture file (sulci and gyri texture)
0: sulci, 1 : sulcal regions
-------------------------------------------------------------------------
siSynthRelaxResult.py
Usage: Synthetize error rates results (default : if no option is passed : --mean is activated
siSynthRelaxResult.py [OPTIONS] file1.csv file2.csv...
Options:
-h, --help show this help message and exit
-d TYPE, --database=TYPE
one among 2000, 2005, 2008 (default : 2008)
--csv=FILE store computed data in csv
-m, --mean Show mean values. Take the mean value of each subject
and then compute the mean over subjects
-c, --correlation Show correlations between errors and energy
-b, --best Show best values. Take the best value of each subject
and then compute the mean over subjects
-s, --std Show standard deviation mesures. Take the best/mean
(see -m option) value of each subject and then compute
the std over subjects
-o, --old old behaviour of siSynthRelaxResult.py
siTestModels
siTestModels
------------
Tests some model configurations
Options :
-p <string>
input parameters file (tree format) (richer than other parameter given on
the commandline)
Parameter file attributes:
netFiles string !
learnCfgFiles string !
learnerFiles string !
netTarget string !
outputDir string !
plotFields string !
outPlotField string !
errPlotField string !
plotCmd string
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
siTestModels.py
disable fff
disable fff
Usage: Test models on databases.
Options:
-h, --help show this help message and exit
-f FILTER, --labelsfilter=FILTER
only models matching this filter are covered.ex :
'label1,label2' or 'label' or 'regexp1,regexp2' (here
order is important)
--filtermode=FILTER strict, flexible or regexp
-m MODEL, --model=MODEL
model file name (default : model.arg)
-t TEST, --test=TEST model file name (default : model.arg). Only test
part of models databases(vectors shaped) is used by
default.
--train use train part of models databases
instead of test one.
--hist=HIST make histogram from classifiation/regression rates of
models. HIST should be a format supported by pylab
siTriangModel
usage : siTriangModelmodel.arg folds.arg directory
siTryGauss
usage : siTryGauss model.mod ncycles [c(ont)]
comistBundleAnalysis_old
comistBundleAnalysis_old
------------------------
This command can be used for several purposes :
* Get quantitative information about bundles. This information is written in a
text file containing a table (one column per information, one row per bundle).
See -o and --imageStatistics options.
* Transform a bundle in another bundle according to several filters. See -t,
--split and -o options.
* Convert a bundles file to an Anatomist graph. See -g option.
Options :
-i <string>
Bundles input file
[ -t <string> ]
Transformation matrix to apply to input file (default: no transformation).
The transformation is applyed before any other processing.
[ --selectionROI <string> ]
ROI graph that will be used to select fibers and put them in bundles
according to the rule file from --selectionRules parameter.
[ --selectionROITransformation <string> ]
Transformation matrix to apply to selection ROI graph (option
--selectionROI). Default: no transformation.
[ --selectionRules <string> ]
Name of file containing selection rules. This option must be used if and
only if --selectionROI is used.
[ --selectionOverlap <FLOAT> ]
Percentage of point of a fascicle that have to be in a ROI to consider that
the ROI is touched by the fascicle. 0 (the default) means that only one
point in the ROI is engough, and 100 mean that all the fascicle points must
be inside a ROI. This option is used only with --selectionROI.
[ --split <string> ]
ROI graph that will be used to split the input bundle curves according to
the ROI boundaries. This option transform the input bundle in another
splitted bundle. The splitted bundle is used for processing that generate
output.
[ --splitTransformation <string> ]
Transformation matrix to apply to split ROI graph (option --split).
Default: no transformation.
[ --splitKeepBundle <boolean> ]
Keeps each fascicle original bundle name in output bundle (default =
false).
[ --minimumLength <DOUBLE> ]
If greater than 0, all curves whose length is below minimumLength are
ignored. This curve filtering is applied after all bundle transformation
(-t and --split options) and before any other processing. Default value is
0 (i.e. no filtering).
[ --imageStatistics <vector of string> ]
Compute statistics from a 3D image. All bundle points are projected in the
image to get a voxel value (with trilinear interpolation). For each bundle,
the mean, standard deviation, minimum and maximum of voxel values are
stored in the result file. Each argument of this parameter must have the
syntax <label>:<filename> where <label> is a label and <filename> is a 3D
image file name. For each argument, three columns are added in the result
file: <label>_mean, <label>_stddev, <label>_min and <label>_max.
[ --slices <ULONG> ]
number of slices in which each bundle is cut
[ --slicesMesh <filename: Segments of VOID> ]
Generate a mesh allowing to check the shape of the slices.
[ -o <string> ]
Generate a text file containing quantitative information about the bundles.
The file contains the following fields (in addition to the fields coming
from --imageStatistics option):
curves_count: the number of curves in a bundle
points_count: the total number of curves points in a bundle
length_mean: the mean curves length in a bundle.
length_stddev: the standard deviation of curves length in a bundle.
length_min: the minimum of curves length in a bundle.
length_max: the maximum of curves length in a bundle.
[ -g <string> ]
Create and save an ROI graph containing one node per bundle and meshes to
visualize curves in Anatomist.
[ -b <string> ]
Save the bundles resulting from all requeted transformation applied to
input bundles (options -t and --split)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
comistBundles2Ima_old
comistBundles2Ima_old
---------------------
Make an image of the bundles density
All bundles in the same volume
Options :
-i <string>
bundles input
-r <file name (read only): volume of S16>
input image template
-o <filename: volume of S32>
bundles ima output
[ -m <S32> ]
mode=1->mask,
mode=2->count(NN)
mode=3->count(LinearInterpol)
default=2
mode 3 doesn't work!!!
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
comistBundlesFusion_old
comistBundlesFusion_old
-----------------------
Bundles fusion
Options :
[ -i <list of string> ]
bundles input
-o <string>
bundles output
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
comistConcatenation
comistConcatenation
-------------------
Generic concatenation and split of T2 and DW images from acquired data
Options :
-i <vector of string>
Acquisition short images
[ -m <vector of string> ]
Header file names. If provided, there must be as many header as input image
[ -z <boolean> ]
Z concatenation instead of T concatenation
[ -nex <S32> ]
number of excitations NEX (default=ignored)
-t2 <string>
T2 output file name
-dw <string>
DW output file name
[ -verbose <boolean> ]
Show as much information as possible
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
comistDiffusionToMesh
comistDiffusionToMesh
---------------------
Build a spin graph from a diffusion MRI Q Ball Model (under developpement)
Options :
[ -t2 <file name (read only): volume of S16> ]
T2 image
[ -dw <file name (read only): volume of S16> ]
Diffusion-weighted image
[ -f <string> ]
diffusion field file
-m <string>
Mask of brain or white matter
[ -noInt <boolean> ]
don't interpolate data in tracking algorithm
[ -dInt <boolean> ]
interpolate with directions
[ -DTI <boolean> ]
DTI data else QBall data
[ -ori <string> ]
Orientation file (default = symmetric gradient orientations)
-s <file name (read only): mesh of VOID>
Discrete sphere triangulation(see AimsConvexHull from AimsDiffusionQBall
orientations)
[ -o <filename: mesh of VOID> ]
Mesh output file
-on <filename: mesh of VOID>
per Voxel Normalized Mesh output file
[ -on2 <filename: mesh of VOID> ]
per ROI Normalized Mesh output file with sdev
[ -on3 <filename: mesh of VOID> ]
per ROI Normalized Mesh output file with (80%Max - 20%Min)
[ -on4 <filename: mesh of VOID> ]
Normalized Mesh output with input map coefficient
[ --map <file name (read only): volume of FLOAT> ]
input map coefficient
[ --textureRed <filename: texture of FLOAT> ]
Red Texture output file default name _red
[ --textureBlue <filename: texture of FLOAT> ]
Blue Texture output file default name _blue
[ --textureGreen <filename: texture of FLOAT> ]
Green Texture output file default name _green
[ --decimate <boolean> ]
mesh decimation
[ --smooth <boolean> ]
smoothes the mesh for decimation
[ --smoothIt <S32> ]
smoothing number of iterations is <nb iterations> [default=10]
[ --smoothRate <FLOAT> ]
smoothing moving factor at each iteration is <smoothing rate> [default=0.2]
[ --deciReductionRate <FLOAT> ]
decimation reduction rate expected is <reduction rate> % [default=90%]
[ --deciMaxClearance <FLOAT> ]
maximum clearance of the decimated mesh expected is <clearance> mm
[default=10]
[ --deciMaxError <FLOAT> ]
maximum error distance from the original mesh expected is <error> mm ,
[default=10]
[ --deciAngle <FLOAT> ]
feature angle is <angle> degree, between 0 and 180 degree, [default=180]
[ --minFacetNumber <S32> ]
minimum number of facets to allow decimation [default=50]
-roi <string>
input ROI
[ --sdevMap <filename: volume of FLOAT> ]
write sdev Map
[ --minMaxMap <filename: volume of FLOAT> ]
write sdev Map
[ --DTIscaling <DOUBLE> ]
scaling factor for DTI mesh (default = 4e8)
[ --sdevScaling <DOUBLE> ]
scaling factor for sdev mesh (default = 1)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
comistFiberGraph
comistFiberGraph
----------------
Test command. Do not use it !
Options :
[ -t2 <file name (read only): volume of S16> ]
T2 image
[ -dw <file name (read only): volume of S16> ]
Diffusion-weighted image
[ -f <string> ]
diffusion field file
-m <string>
Mask of brain or white matter
[ -noInt <boolean> ]
don't interpolate data in tracking algorithm
[ -dInt <boolean> ]
interpolate with directions
[ -DTI <boolean> ]
DTI data else QBall data
[ -ori <string> ]
Orientation file (default = symmetric gradient orientations)
[ -n <S32> ]
Number of graph node per voxel (default = 1).
[ -p <string> ]
Potential log file name.
[ -t <string> ]
Transition log file name.
[ -s <filename: Segments of VOID> ]
Segments mesh output files.
[ -sn <S32> ]
Create an animated mesh file by saving one mesh every "sn" iterations.
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
comistFixedDTModel
comistFixedDTModel
------------------
Estimation of the Fixed DT Model from a diffusion MR image
Options :
[ -t2 <file name (read only): volume of S16> ]
T2 image
[ -dw <file name (read only): volume of S16> ]
Diffusion-weighted image
-o <filename: bucket of FIXEDDTMODEL>
Fixed DT model output file name
[ -m <string> ]
Mask of brain or white matter
[ -e <filename: volume of U8> ]
Binary mask of bad voxels (default = not saved)
[ -ascii <boolean> ]
Save bucket in ASCII (default = false)
[ -lnS0Si <file name (read only): volume of FLOAT> ]
Image of ln(S0/Si)
[ -verbose <boolean> ]
Show as much information as possible
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
comistOrientationMap
comistOrientationMap
--------------------
Estimation of orientation maps from a diffusion model bucket
The following maps are available:
- maxeigenvector
- rgb
Options :
-i <string>
Diffusion bucket data file name
-o <list of string>
Orientation output map file name list
-m <list of string>
Orientation diffusion map list
-x <S32>
forces output volume X dimension
-y <S32>
forces output volume Y dimension
-z <S32>
forces output volume Z dimension
[ -f <string> ]
force a specific output format (GIS, VIDA, ...)
(default: guessed by the output filename extension)
[ -s <FLOAT> ]
Anisotropy scale factor on RGB map
[ -ascii <boolean> ]
Save map in ASCII (default = false)
[ -verbose <boolean> ]
Show as much information as possible
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
comistQBallField
comistQBallField
----------------
Estimation of the Q-Ball Model from a diffusion MR image
Options :
-t2 <file name (read only): volume of S16>
T2 image
-dw <file name (read only): volume of S16>
Diffusion-weighted image
-o <string>
qball field file out
[ -ascii <boolean> ]
write field file out in ascii
[ -m <string> ]
Mask of brain or white matter
[ -ori <string> ]
Orientation file (default = symmetric gradient orientations)
[ -c <S32> ]
Circle point count (default = 36)
[ -a <FLOAT> ]
Maximum alpha in degrees for gaussian smoothing (default = 20.0)
[ -s <FLOAT> ]
Alpha standard deviation in degrees (default = 10.0)
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
comistQBallModelSmoothing
comistQBallModelSmoothing
-------------------------
QBall diffusion Model smoother
Options :
[ -f <string> ]
diffusion field file
-m <string>
Mask of brain or white matter
--ori <string>
directions file used for qball field
[ -a <FLOAT> ]
Maximum alpha in degrees for gaussian smoothing (default = 20.0)
[ -s <FLOAT> ]
Maximum alpha in degrees for gaussian smoothing (default = 20.0)
[ -n <S32> ]
Number of smoothing for probabilities (default = 1.0)
-o <string>
output bucket file
[ -ascii <boolean> ]
Save bucket in ASCII (default = false)
[ -verbose <boolean> ]
show as much information as possible
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
comistScalarMap
comistScalarMap
---------------
Estimation of ADC, VR, FA, STDDEV maps from a diffusion model bucket
Options :
-i <string>
Diffusion bucket data file name
-o <list of string>
Scalar output map file name list
-m <list of string>
Scalar diffusion map list (a sublist of: fa, adc, vr, stddev, dxx, dxy, dxz,
dyy, dyz, dzz, lambdamin, lambdamid, lambdamax, lambdaparallel,
lambdatransverse, prolateness, oblateness, maxevx, maxevy, maxevz)
-x <S32>
forces output volume X dimension
-y <S32>
forces output volume Y dimension
-z <S32>
forces output volume Z dimension
[ -f <string> ]
force a specific output format (GIS, VIDA, ...)
(default: guessed by the output filename extension)
[ -ascii <boolean> ]
Save map in ASCII (default = false)
[ -verbose <boolean> ]
Show as much information as possible
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
comistSelectFiberFromMask_old
comistSelectFiberFromMask_old
-----------------------------
Select fibers as a percentage in mask
Options :
-i <string>
Bundle File input
-o <string>
Bundle File output
-m <string>
mask ROI
-percent <FLOAT>
percent in mask
-min <S32>
min fiber length
-max <S32>
max fiber length
[ -verbose <boolean> ]
show as much information as possible
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
comistTConcatenation
comistTracking
comistTracking
--------------
Fiber tracking from diffusion data and a set of region of interest.
Options :
[ -t2 <file name (read only): volume of S16> ]
T2 image
[ -dw <file name (read only): volume of S16> ]
Diffusion-weighted image
[ -f <string> ]
diffusion field file
-m <string>
Mask of brain or white matter
[ -noInt <boolean> ]
don't interpolate data in tracking algorithm
[ -dInt <boolean> ]
interpolate with directions
[ -DTI <boolean> ]
DTI data else QBall data
[ -ori <string> ]
Orientation file (default = symmetric gradient orientations)
-cm <string>
Mask for trajectories computation
-b <string>
Bundles output file
[ -step <FLOAT> ]
sampling of the trajectories
-d <filename: volume of S16>
density map output file
[ -s <S32> ]
storing step in bundles (default = 1)
[ -dimT <S32> ]
dim T of density map
[ -sizeT <FLOAT> ]
size T of density map
[ -maxl <S32> ]
maximum trajectory size
[ -g <string> ]
Create and save an ROI graph containing onenode per bundle and meshes to
visualize fibers.
-roi_in <string>
starting input ROI
[ -rt <string> ]
Transformation matrix to apply to starting points (default: no
transformation)
-n <S32>
number of particle per Voxel
[ -a <FLOAT> ]
Max angle (in radian) between two consecutive directions (default = 30°)
[ --map_in <file name (read only): volume of FLOAT> ]
coeff map input
[ --map_out <filename: volume of FLOAT> ]
coeff map output
-roi <file name (read only): volume of S16>
drawing output ROI
[ -proba <boolean> ]
probabilistic tracking algorithm
[ -bc <boolean> ]
probabilistic tracking algorithm with best choice
[ -mt <boolean> ]
more times starting points (default 5)
[ -mtpercent <S32> ]
percent for more times starting point
[ -mback <boolean> ]
children fibers go back too
[ -T <FLOAT> ]
temperature to discriminate probability
[ -likely <boolean> ]
most Likely tracking algorithm
[ --minimumLength <DOUBLE> ]
If greater than 0, all fibers whose length is below minimumLength are
ignored. This fiber filtering is applied after all bundles transformation
(-t and --split options) and before any other processing. Default value is
0 (i.e. no filtering).
[ -verbose <boolean> ]
show as much information as possible
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)
comistWeightedT2
comistWeightedT2
----------------
Build a DW-T2 image from a diffusion-weighted image
Options :
-dw <file name (read only): volume of S16>
Diffusion-weighted image
-o <filename: volume of S16>
Diffusion-weighted T2 output image
[ -verbose <boolean> ]
show as much information as possible
[ --output_4d_volumes <S32> ]
Write 4D images as several 3D files (0 = series of 3D volumes, 1 = one 4D
volume, no value = use .aimsrc configuration files)
[ --debugLevel <S32> ]
Set debug information level (default = 0)
[ --verbose [ <S32> ] ]
Set verbosity level (default = 0, without value = 1)
[ -h | --help <boolean> ]
show help message
[ --version <boolean> ]
show Cartograph version
[ --info <boolean> ]
show libraries information (install, plugins, paths, etc.)
[ --optionsfile <string> ]
Read additional commandline options from the specified file (one switch or
value per line)