Talairach Transformation From Normalization
Talairach Transformation From NormalizationCompute the subject T1 MRI to Talairach-AC/PC transformation, using a normalization matrix.
Compute the subject T1 MRI to Talairach-AC/PC transformation, using a normalization matrix. The classical T1 pipeline in BrainVISA generates it only from a manual determination of AC and PC positions (see Prepare Subject), and from the brain bounding box, which is far from perfect in the cortex (see the Talairach Transformation process).
Using this alternative, normalization information may replace the manual AC/PC procedure, and should be more accurate. Normalization matrices, as their name states it, are affine transformations: elastic deformation information cannot be used. But an affine part in a non-linear normalization might be OK, like the affine part of SPM normalization.
SPM *_sn.mat normalization matrices may be converted using the SPM normalization to AIMS converter process, then given as input to this one.
The input normalization matrix is going from the subject space (its T1 image) to a common referential. The common referential should be known within BrainVISA so that BrainVISA knows how to go from this common referential to the Talairach AC/PC space. It will generally be the MNI template referential, but could be any referential with a known transformation to Talairach-AC/PC.
Optionally, AC/PC information may be retreived from the normalized space, and the commissure coordinates file (normally written by the Prepare Subject process) may be written (or replaced) with the new information.
If this process is run after a full T1 pipeline has already run, some information within the cortical folds graphs should be updated and recalculates. So users should run the Cortical Folds Graph Upgrade process. Morphometric measurements may change also since they are not measured in the same space anymore.
normalization_transformation: Transform Raw T1 MRI to Talairach-MNI template-SPM ( input )Input normalization matrix (subject T1 to a common space, the MNI template typically)
Talairach_transform: Transform Raw T1 MRI to Talairach-AC/PC-Anatomist ( output )Output transformation, going from the subject T1 space to the Talairach-AC/PC space
commissure_coordinates: Commissure coordinates ( optional, output )
t1mri: Raw T1 MRI ( optional, input )Raw T1 MRI, needed only if writing the commissure coordinates file.
source_referential: Referential ( input )Normally, the referential of the subject T1 MRI image
normalized_referential: Referential ( input )This is the destination referential of the input normalization matrix
transform_chain_ACPC_to_Normalized: ListOf ( input )
acpc_referential: Referential ( optional, input )
Toolbox : Morphologist
User level : 2
Identifier :
TalairachTransformationFromNormalizationSupported file formats :
normalization_transformation :Transformation matrixTalairach_transform :Transformation matrixcommissure_coordinates :Commissure coordinatest1mri :GIS image, VIDA image, NIFTI-1 image, MINC image, gz compressed MINC image, DICOM image, TIFF image, XBM image, PBM image, PGM image, BMP image, XPM image, PPM image, gz compressed NIFTI-1 image, TIFF(.tif) image, ECAT i image, PNG image, JPEG image, MNG image, GIF image, SPM image, ECAT v imagesource_referential :Referentialnormalized_referential :Referentialacpc_referential :Referential