antsCorticalThickness and antsLongitudinalCorticalThickness output

antsCorticalThickness.sh

antsCorticalThickness.sh output is to a single directory, with multiple files.

Definitions

Subject space

Template space

Some files are produced only if optional input parameters are set. The full file name will be ${outputPrefix}description${outputSuffix}, the prefix and suffix are set at run time by the user.

• BrainExtractionMask- Brain extraction mask in subject space.

• BrainNormalizedToTemplate - Extracted brain image normalized to the template space.

• BrainSegmentation0N4 - Input to the segmentation algorithm. It is not brain extracted, but is bias-corrected. If multiple images are used for segmentation, there will be BrainSegmentation1N4 and so on. The brain extracted version of this is ExtractedBrain0N4.

• BrainSegmentation - Segmentation image, one label per tissue class. The number of classes is determined by the input priors.

• BrainSegmentationPosteriors1 - Posterior probability of class 1 (usually CSF). A similar image is produced for all classes. The numbering scheme matches the input priors.

• CorticalThickness - Cortical thickness image in subject space.

• CorticalThicknessNormalizedToTemplate - Cortical thickness image in template space.

• ExtractedBrain0N4 - Brain-extracted version of BrainSegmentation0N4.

• SubjectToTemplate1Warp, SubjectToTemplate0GenericAffine.mat - Transforms to be used when warping images from the subject space to the template space (see below).

• SubjectToTemplateLogJacobian - Log of the determinant of the Jacobian, quantifies volume changes in the subject to template warp.

• TemplateToSubject0Warp, TemplateToSubject1GenericAffine.mat - Transforms to be used when warping images from the template to the subject space (see below).

Applying the warps

The warps produced by antsCorticalThickness.sh are named differently to the usual antsRegistration convention. The inverse affine transform is written to disk, so users do not need to invert the affine transform explicitly in the call to antsApplyTransforms.

To warp an image from the subject to template space:

antsApplyTransforms -d 3 -i imageInSubjectSpace.nii.gz -o imageInTemplateSpace.nii.gz \
-t outputPrefixSubjectToTemplate1Warp.nii.gz -t SubjectToTemplate0GenericAffine.mat -r template.nii.gz

To warp an image from the template to subject space:

antsApplyTransforms -d 3 -i imageInTemplateSpace.nii.gz -o imageInSubjectSpace.nii.gz \
-t outputPrefixTemplateToSubject1Affine.mat -t outputPrefixTemplateToSubject0Warp.nii.gz -r template.nii.gz

Note that the ordering of the affine and warp field are reversed, but the numbering is consistent (1 then 0, reading left to right).