Hello,
  I had this issue raised earlier, but may be it got lost in the pile of questions you receive everyday.
  I am very new to freeSurfer, and may be its me who is dong something wrong so please advise.
  I am getting defects in the volume output of freesurfer with respect to the pial surface and whilte-matter surface boundary. I am wanting to measure the cortical thickness after running recon_all. I was inspecting the pial and white surface using tkmedit and  I noticed (volume data view using tkmedit) that in most of my subjects the freesurfer has included non-cortical matter (ex: cerebellar regions) as cortical matter and have excluded several white matter voxels.  I use brainmask volume loaded as main volume and white matter volume loaded as aux volume to inspect the final pial and white surfaces. These defects are more clearly visible when I get the subcortical segmentation in on mode to be viewed or when I am viewing the  pial/white surface  boundaries in the images where brainmask is loaded as main volume with T1.mgz as the aux volume and subcortical segmantation in on mode.   Interestingly such defects were found in same regions across the subject  and are present in more than one section. If what I am seeing are defects, this would be require too much editing.

Please advise
 
  
Rashmi.


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