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antsCorticalThickness and antsLongitudinalCorticalThickness output

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Philip Cook edited this page Apr 19, 2016 · 8 revisions

antsCorticalThickness.sh

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

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 - these are transforms to be used when warping images from the subject space to the template space (see below).

  • TemplateToSubject0Warp, TemplateToSubject0GenericAffine.mat -

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