fsVoxelBasedSegmentationRunCrossSectionals.sh

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Used to run a voxel based cortical thickness estimation on a FreeSurfer folder.

Usage: fsVoxelBasedSegmentationRunCrossSectionals.sh [ options ] ALLFR ALLHA CCCCC DDDDD etc.

  All arguments after the options are FreeSurfer directories under the current directory.
  
  Each directory structure should already contain:
  
  <patient>/mri/orig/001.mgz
  <patient>/mri/mask.mgz
  <patient>/mri/wmmask.mgz
  
Options:

  -notalairach   : When processing the wmmask.mgz, don't add the talairach transformation.
                   This is appropriate if the mask (i.e. the segmentation) was done on an image
                   that had already been registered by FreeSurfer.  i.e. if you exported the T1.mgz
                   and then segmented that, then you wont need an additional talairach transformation.