Commands help
Cartograph Commands
AIMS Commands
VIP commands
SiGraph commands
Connectomist commands
NMR commands
Cartograph Commands
AIMS Commands
VIP commands
SiGraph commands
Connectomist commands
NMR commands
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)
[ --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)
[ --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)
[ --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)
[ --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
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 <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)
[ --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)
[ --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)
[ --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)
AimsAtlasQualityAssessment
AimsAtlasQualityAssessment
--------------------------
Atlas quality assessment
Options :
-g <string>
Input graph containing the regions
-s <string>
Segmentation graph containing the regions
[ -m <string> ]
motion from atlas to ROI
--completeAtlas <string>
Input atlas image for all regions
[ --rawLearnedAtlas <string> ]
Input atlas image only for regions estimated from the learning base
-d <S32>
maximum distance to contour (in voxels) for the drawing of profiles
(default: 15)
-o <string>
output stat 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)
[ --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
--------------------
Displays attributed objects (.minf...) in a list view. AimsAttributedViewer can
also show any file header supported by AIMS IO system, just like AimsFileInfo
Options :
[ -i <string> ]
file to display
[ --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)
[ --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)
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)
[ --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)
[ --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)
[ --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)
[ --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)
[ --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)
[ --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 <S32> ]
scan resolution (dpi) [Default: input voxelsize]
[ -ratio <FLOAT> ]
seuil = % max [default 0.15 = 15%]
[ -v <string> ]
values of interest high/low [Default=low]
-o <filename: volume of S16>
output image
[ -t <string> ]
output translations list [default=not written]
[ -m <string> ]
output motion base name [default=not written]
[ --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)
[ --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)
[ --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
----------------------
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)
[ --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)
[ --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)
[ --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)
[ --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)
[ --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 / 26 [default=26]
[ -s | --size <U32> ]
minimum size of the seeds [default=0]
[ -n <U32> ]
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)
[ --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)
[ --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
-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)
[ --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
[ --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)
[ --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
----------------------------
Create 3 textures of node coordinates
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)
[ --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)
[ --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)
[ --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 de coordonnees sur une surface contrainte
Options :
-i | --inMesh <string>
inputMesh
-p | --inTexPar <string>
input Texture Parallel Constraints
-m | --inTexMer <string>
input Texture Meridian Constraints
[ -l | --inTexCall <string> ]
input Texture Corpus Callosum Pole
-r | --inTexPoles <string>
input Texture Poles
-c | --criter <FLOAT>
Limit for the diffusion process ( default = 1e-6 )
-d | --dt <FLOAT>
Iterative step ( default = 0.2 )
-b | --bool <S32>
context
-f | --choice <S32>
choice
-t | --attache <FLOAT>
attache
-a | --tBeta <S32>
Beta Map (1=Yes, 0=No)
-x | --latitude <string>
latitude texture output
-y | --longitude <string>
longitude texture 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)
[ --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)
[ --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)
[ --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)
[ --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)
[ --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)
[ --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
------------------------------------------------------------------
AimsDynamicImageSegmentation
AimsDynamicImageSegmentation
----------------------------
Pharmacokinetic automatic segmentation
Options :
-i <string>
dynamic series file
[ -a <string> ]
attenuation file (same referential, voxel size and dimensions as dynamic
series)
-o <string>
fileout segmentation by level filename
[ --it <boolean> ]
was image reconstructed by an interative algorithm ?
[ --decreaseCorrected <boolean> ]
are images corrected from radioactive decrease ?
[ --subject <string> ]
studied subject (Rat, Mouse, Primate, Human, Default: Rat)
[ --method <string> ]
method used between KinDist, GeodesicKinDist, Watershed,
GeodesicCriterionDist, DiscriminantAnalysis (default: GeodesicKinDist)
[ --criterionMode <string> ]
criterion assessing if more that one structure kinetics are present in a
small volume (TotalVariance, RelativeVariance, MeanVariance, default:
MeanVariance)
[ -r <FLOAT> ]
ising regularization term for sample definition (0. to 10., default: 1. )
[ -b <FLOAT> ]
mean background value, if mask extraction fails (default: 0. )
[ --smooth <FLOAT> ]
smoothing (example:0.65 for FOCUS, default: 0. )
[ -n <S32> ]
max number of samples processed (default : 100)
[ --maxNumberOfFrames <S32> ]
Maximum number of frames, frames will be aggregated to match this
constraint (default : -1 (All))
[ --connexityForFusion <boolean> ]
enforce parcels to fusion to be connected (default: false )
[ --maximalNbOfClusters <boolean> ]
enforce smallest neighborhood size to get a maximal number of clusters
(default: false )
[ --linearWeightForFirstFrame <FLOAT> ]
weighting frames with linear weights : weight for first frame (default :
1.)
[ --linearWeightForLastFrame <FLOAT> ]
weighting frames with linear weights : weight for last frame (default :
1.)
[ --secondaryCostWeight <FLOAT> ]
Weight for secondary cost function for fusion (default : 0.)
[ --borderCostWeight <FLOAT> ]
Weight for gradient based cost function for fusion (default : 0.)
[ -m <string> ]
input mask of organism of interest (example: brain mask)
[ -c <string> ]
input multistructure criterion image file (for testing purpose only)
[ -s <string> ]
Presegmentation file (for acceleration purposes)
[ --outputMask <string> ]
segmented organism mask file name (for testing purpose only, default: non
saved)
[ --outputCriterion <string> ]
multi-structure kinetics criterion output file name (for testing purpose
only, default : not saved)
[ --outputUnfusionedLabels <string> ]
segmented organism into classes not yet merged (for testing purpose only,
default : not saved)
[ --outputMeanKin <string> ]
image of mean pharmacokinetics inside each region
[ --TumorMode <string> ]
Tumor detection mode : None, Detection, Learning, DetectionAssessment
(default: None)
None : No tumor detection action: all parameters below will be ignored
Detection: Detection of tumors : you must provide
--tumorDetectionParameterImg (input), and
--tumorDetectionParameterImg(output)
[ --detectedTumors <string> ]
output segmentation file in which tumors are ordered by likelyhood to be
non-tumors (default : detectedTumors.ima)
[ --tumorDetectionParameterImg <string> ]
input (on tumor Detection or DetectionAssessment modes) or output parameter
(in LearningMode)
containing the energy panorama relative to the tumor detection parameters
settings (default : parameterImage.ima)
[ --tumorLabelledImage <string> ]
image in which tumors are labelled, for tumor detection parameters tuning
[ --bodyLabelledImage <string> ]
image in which the organs are labelled, for tumor detection assessment mode
[ --nbOfTumors <S32> ]
Number of tumors to seek, or number of tumors in the label image
[ --scanner <string> ]
Only for PVE correction: scanner type (HR+, HRRT, FOCUS, NoPsf)
[ --noPostReconstructionSmoothing <boolean> ]
only if no post reconstruction smoothing has been applied to the image to
segment
[ --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)
[ --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)
user interruption
AimsDynamicRatPhantomComputeImage
fixme: this command doesn't follow the -h option (help) and loops endlessly while outputing the same line "-1208180296". This causes the documentation system to crash (and consume all memory). This command is disabled until it is fixed.
Denis
AimsDynamicRatPhantomOrganProba
AimsDynamicRatPhantomOrganProba
-------------------------------
Dynamic rat phantom organ proba computation
Options :
-i <string>
dynamic series of labels files moving along respiration period
-l <string>
label file associating correct name to each label
-o <string>
fileout base name
-p <string>
phantom mu map
[ -ihl <FLOAT> ]
isotope half life (default F18)
[ -mr <FLOAT> ]
medular cortex artificial radius
[ -rp <FLOAT> ]
respiration period (in second)
[ -s <FLOAT> ]
bladder initial stretch
[ -g <FLOAT> ]
bladder growth
-st <vector of S32>
frames start time vector (second)
-dt <vector of S32>
frames duration time vector (second)
[ --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)
[ --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
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)
[ --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]
-------------------------------------------------------------------------
AimsExtractRegionMasks
AimsExtractRegionMasks
----------------------
Extract region masks from graph
Options :
-i <string>
Input graph containing the regions
-o <string>
Output mask of the regions
[ -r <vector of string> ]
List of the names of the regions to select
[ --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)
[ --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)
[ --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)
[ --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
[ -o <string> ]
Output image
[ -b <string> ]
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)
[ --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)
[ --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 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
[ -a | --ascii <boolean> ]
write in ASCII mode if output format supports it (default: binary)
[ -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.
[ -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
[ --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)
[ --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)
[ --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)
[ --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
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)
[ --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: 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)
[ --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)
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)
[ --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)
[ --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> ]
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)
[ --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)
[ --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)
AimsGTM
----------------------------------------------------------------
AimsGTM -i[nput] <ROI filein>
-t[ransaxial]
-a[xial]
-m[ode] <mode>
-s <selector file>
-h[elp]
-l[ist] list available Selector files
--voitype (ROI image filein)
--selection < roi selector name >
----------------------------------------------------------------
Gtm computation with 3D Deriche's recursive smoothing filter
----------------------------------------------------------------
filein : origin Roi file (arg format)
: Create output_file origin_GTM
: trans and axial width in mm
mode : s ( threshold on smooth default) or
: c ( closing from roi model )
: f ( get from file w/o processing )
-s : selector file name exact location
--voitype: Roi format arg ou image (default : arg)
--selection: selector name (.sel)
--smoothed: arbitrary smooth file (use in conjunc -m f)
----------------------------------------------------------------
Exemple d utilisation
AimsGTM -t 2.83231 -a 3.0 -i model2 --voitype image
--selection striataAll.sel
Part d un fichier de roi de format image
lissage transaxial 2.83231mm et axial 3mm
ce sont des valeurs typiques pour les hypothèses
- HR+ et le 18F
- reconstruction FourierRebinning + FBP
--selection permet le traitement des noms de la nomenclature
neuronames.hie
----------------------------------------------------------------
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]
----------------------------------------------------------------
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)
[ --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)
[ --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)
[ --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)
[ --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 p