Hi, recon-all stage1 overstrips some of my images during the skull-stripping stage. I've played with the different options, but they don't seem to make any difference at all. Any suggestions? I've tried feeding in a pre-stripped brain (stripped using BET), but the intensity normalization doesn't seem to do to well (ie., although it finishes without error, the wm values are not very uniform, and the segmentation misses large portions of wm). Thanks, Alex
freesurfer@nmr.mgh.harvard.edu