mvpa.atlases.transformation

Module transformation

Classes

TypeProxy
Simple class to convert from and then back to original type working with list, tuple, ndarray and having

TransformationBase
Basic class to describe a transformation. Pretty much an interface

SpaceTransformation
To perform transformation from Voxel into Real Space. Simple one -- would subtract the origin and multiply by voxelSize. if toRealSpace is True then on call/getitem converts to RealSpace

Linear
Simple linear transformation defined by a matrix

MNI2Tal_MatthewBrett
Transformation to bring MNI coordinates into MNI space

Functions

[hide private]

MNI2Tal_MeyerLindenberg98(*args, **kwargs)
Due to Andreas Meyer-Lindenberg Taken from http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach

source code

MNI2Tal_YOHflirt(*args, **kwargs)
Transformations obtained using flirt from Talairach to Standard

source code

Tal2MNI_YOHflirt(*args, **kwargs)
See MNI2Tal_YOHflirt doc

source code

MNI2Tal_Lancaster07FSL(*args, **kwargs)

source code

Tal2MNI_Lancaster07FSL(*args, **kwargs)

source code

MNI2Tal_Lancaster07pooled(*args, **kwargs)

source code

Tal2MNI_Lancaster07pooled(*args, **kwargs)

source code

Imports: N, debug

Function Details

[hide private]

MNI2Tal_YOHflirt(*args, **kwargs)

source code

Transformations obtained using flirt from Talairach to Standard

Transformations were obtained by registration of grey/white matter image from talairach atlas to FSL's standard volume. Following sequence of commands was used:

fslroi /usr/share/rumba/atlases/data/talairach_atlas.nii.gz talairach_graywhite.nii.gz 3 1 flirt -in talairach_graywhite.nii.gz -ref /usr/apps/fsl.4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out talairach2mni.nii.gz -omat talairach2mni.mat -searchrx -20 20 -searchry -20 20 -searchrz -20 20 -coarsesearch 10 -finesearch 6 -v flirt -datatype float -in talairach_graywhite.nii.gz -init talairach2mni.mat -ref /usr/apps/fsl.4.1/data/standard/MNI152_T1_1mm_brain.nii.gz -out talairach2mni_fine1.nii.gz -omat talairach2mni_fine1.mat -searchrx -10 10 -searchry -10 10 -searchrz -10 10 -coarsesearch 5 -finesearch 1 -v convert_xfm -inverse -omat mni2talairach.mat talairach2mni_fine1.mat