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, TemplateToSubject0GenericAffine.mat - Transforms to be used when warping images from the template to the subject space (see below).

Applying the warps

To warp an image from the subject to template space:

To warp an image from the template to subject space: