I ran through autorecon1 and 2 for two subjects using the dicom images. One came out ok, but one is still missing some brain (as seen in the attached screen shots). I was wondering if there was a way to change the settings autorecon uses, because our scanner makes the inside so much brighter, or a way to batch convert rather than edit control points on all our subjects. Thanks
freesurfer@nmr.mgh.harvard.edu