Hi FreeSurfers, After a months of QC'ing FreeSurfer results, my team and I are now working toward end stage analysis of our cortical thickness data. All along, we have been aiming to make improvements in the wm.mgz volume so that we can assure that the white matter and gray matter surfaces are as accurate as possible. This was under the assumption that if the white matter and gray matter surfaces are accurate, then the voxel-wise representation of the white and gray matter in the aparc+aseg.mgz file would be accurate. However, in almost all of our cases, the aparc+aseg.mgz segmentation looks very bad. The bad aparc+aseg.mgz representation of what seem to be accurate white and gray matter segmentations in the wm.mgz file is leading us to believe that the cortical correspondences created after template mapping are wrong.
Does anyone else have an explanation for such a discrepancy? Is this a common problem and if so, is there any way to remedy this situation? Thanks, Ryan
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