I’ve been having trouble on a few of our subjects with getting the white matter and pial surface files to “line up” correctly with the volume files. I’ve attached a screenshot of what is happening: the pial surface is in red and the white matter surface file is in yellow. I have also attached an example of a “good” subject for comparison.

I’ve tried looking through the tutorials online but didn’t see anything that was really related to my issue and I was wondering what the best way to correct this. We have T2 weighted images for several subjects is well if that helps. Not sure if Freesurfer can use T2 images instead of T1 in the –reconall script but I thought I would mention it. Thank you very much in advance!