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
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