Aims tutorial
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Aims tutorial
Table of Contents
1. Foreward
2. Basic command lines
AimsFileConvert: Performs file format and data conversion
AimsSubVolume: Carve a subvolume in the input volume
AimsThreshold: Threshold on data
AimsGraphMesh: Performs graph storage conversion and sub-buckets meshing. This command is an improved version of AimsGraphConvert
AimsRoiFeatures: Compute scalar features (mean, volume ...) from regions of interest.
3. Conversion
AimsDiffusionBundleToRoi: conversion from bundles.bundles to ROI graph
AimsGraphConvert: conversion from label image to ROI graph
Table of format conversions
4. Calculation of images
AimsLinearComb: sum 2 activation maps
5. Handling meshes
Creation of a cube mesh from a point list
AimsZCat: concatenates volumes (along Z axis), meshes or buckets
6. Handling referentials and transformations
Coordinates systems in AIMS
AIMS and Anatomist
SPM
Changing between SPM and AIMS
Issues
Technical details
Compute the inverse transformation
Compose a transformation
7. Handling graphs
Copy a set of graph attributes to another graph
8. Rigid registration
AimsManualRegistration: manual registration between 2 volumes from 3 specific landmarks.
AimsMIRegister: registration based on mutual information.
9. Advanced level
Get a symmetrical ROI
10. Programming with AIMS in Python language
Using data structures
Module importation
IO: reading and writing objects
Volumes
Meshes
Textures
Buckets
Graphs
Other examples
Using algorithms
PyAIMS / PyAnatomist integration
List of Figures
2.1.
Select label
2.2.
Viewing of non-meshed and meshed ROI
4.1.
Sum of 2 activation maps
6.1.
Referentials and normalization transformations
10.1.
3D volume: value 12 at voxel (100, 100 ,60)
10.2.
Distance example
10.3.
Thresholded Audio-Video T-map
10.4.
Downsampled anatomical image
10.5.
3D volume containing a cube
10.6.
Flying saucer mesh
10.7.
Inflated mesh
10.8.
Inflated mesh with timesteps
10.9.
Computed time-texture vs 3D fusion
10.10.
Thresholded T1 MRI
10.11.
Closing of a thresholded T1 MRI
10.12.
Head mesh
10.13.
Generated icosahedron and arrow
10.14.
Interpolated vs not interpolated texture
10.15.
Aimsalgo resampling
10.16.
3D volume modified with numpy
10.17.
Modified cut mesh
List of Tables
3.1.
Table of format conversions
9.1.
Summary to preserve the ROI volume