Hi Cody

yes, it could be due to poor contrast. The watershed isn't the issue though, it is mri_segment and mris_make_surfaces. You can try changing the wm/gm limits, or upload the subject and we will take a look cheers Bruce On Tue, 24 Apr 2018, Barlow, Cody wrote:

External Email - Use Caution

Hi FreeSurfer Experts,

After running my subject through FS6 autorecon3 and QCing the data, I noticed that FS6 is outlining white matter as grey matter and then bumping out the grey matter segmentation accordingly. I have tried using different watershed preflood heights during various skull strips with no success as well as using the flag gcut. I’m thinking the issue has to do with atrophy due to my subject population, dementia patients, or poor contrast between GM and WM during image acquisition.

Is there a flag or tkmedit tool I can use to help solve this problem. I have attached an image showing the issue.

Thanks for the help,

Cody