Hi Jon

maybe, depending on the quality of the image. Did the intensity normalization fail? Looks like it might have eaten into the gray matter. Compare the brain.mgz and the orig.mgz. If cortex is intensity-normalized to look like wm try using the -gentle flag, otherwise try setting some of the mri_segment intensity thresholds with xopts

Bruce

On Tue, 15 Jul 2014, Jonathan Holt wrote:

Attached is an image of wm.mgz after a routine recon-all...