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atlases.transformation

Module: atlases.transformation

Inheritance diagram for mvpa.atlases.transformation:

Coordinate transformations

Classes

Linear

Linear(transf=array([[ 1., 0., 0., 0.],

[ 0., 1., 0., 0.],

[ 0., 0., 1., 0.],

[ 0., 0., 0., 1.]]), **kwargs)

Bases: mvpa.atlases.transformation.TransformationBase

Simple linear transformation defined by a matrix

Linear.apply(coord)

MNI2Tal_MatthewBrett

class mvpa.atlases.transformation.MNI2Tal_MatthewBrett(*args, **kwargs)

Bases: mvpa.atlases.transformation.TransformationBase

Transformation to bring MNI coordinates into MNI space

Apparently it is due to Matthew Brett http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach

apply(coord)

SpaceTransformation

class mvpa.atlases.transformation.SpaceTransformation(voxelSize=None, origin=None, toRealSpace=True, *args, **kwargs)

Bases: mvpa.atlases.transformation.TransformationBase

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

toRealSpace(coord)

toVoxelSpace(coord)

TransformationBase

class mvpa.atlases.transformation.TransformationBase(previous=None)

Basic class to describe a transformation. Pretty much an interface

apply(coord)

TypeProxy

class mvpa.atlases.transformation.TypeProxy(value, toType=<built-in function array>)

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

XXX Obsolete functionality ??

Functions

mvpa.atlases.transformation.MNI2Tal_Lancaster07FSL(*args, **kwargs)

mvpa.atlases.transformation.MNI2Tal_Lancaster07pooled(*args, **kwargs)

mvpa.atlases.transformation.MNI2Tal_MeyerLindenberg98(*args, **kwargs)

Due to Andreas Meyer-Lindenberg Taken from http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach

mvpa.atlases.transformation.MNI2Tal_YOHflirt(*args, **kwargs)

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

mvpa.atlases.transformation.Tal2MNI_Lancaster07FSL(*args, **kwargs)

mvpa.atlases.transformation.Tal2MNI_Lancaster07pooled(*args, **kwargs)

mvpa.atlases.transformation.Tal2MNI_YOHflirt(*args, **kwargs)

See MNI2Tal_YOHflirt doc