| Multivariate Pattern Analysis in Python

### Navigation

- index
- next |
- previous |
- ExpPsy Project |
- NeuroDebian Project |
- PyMVPA 0.4.x Home |
- PyMVPA Home |
- Documentation »
- Module Reference »

This content refers to the previous stable release of PyMVPA. Please visit www.pymvpa.org for the most recent version of PyMVPA and its documentation.

# 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

### Navigation

- index
- next |
- previous |
- ExpPsy Project |
- NeuroDebian Project |
- PyMVPA 0.4.x Home |
- PyMVPA Home |
- Documentation »
- Module Reference »