Hello, 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. I am very new to freeSurfer, please advise. Rashmi.
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