Re: [Freesurfer] gcut problem

Isabelle,

If gcut fails, and you've exhausted the various threshold options (per the tutorial on brainmask fixes), then i think the only option is to manually edit the brainmask.

Nick

Good morning,

I tried to run the following command:

recon-all -skullstrip -clean-bm -gcut -subjid S01

to remove the skull and remaining dura mater. However, for some subjects, I get the following error:

** Gcutted brain is much smaller than the mask! ** Using the mask as the output instead!

I tried adjusting the wsthresh, as suggested in previous posts, but without success.

Is there something else, I can try?

Thank you in advance for your help,

Isabelle

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer