Hi Freesurfer Team, When we tried to process some subjects in FS 5.0.0 through the cross-sectional step in the longitudinal processing stream, we got inaccurate surfaces generated. Also, after doing skullstripping or adding control points and re-running the cross-sectional reconstruction, inaccurate pial and white matter surfaces were generated (see attached pictures). We are not sure how to fix this problem and this has affected about 70 of our scans. Several of these subjects we also processed in FS 3 and FS 4.3.1, and the surfaces were generated fine. Are there any known solutions to fixing the surfaces in the newer FreeSurfer? If not, then could we feed the 4.3.1 cross-sectionals into FS 5 to create the base template, and then use FS 5 to create the longitudinal reconstructions?
Thank you, Jeff Sadino
