Hello Freesurfer community,
1. I am using watershed to perform more aggressive skull stripping but it seems to be not working for me.
Command I am using: recon-all -subjid 1203 -skullstrip -wsthresh 10 -clean-bm -no-wsgcaatlas -no-isrunning
Please see attachments for before and after watershed images.
After watershed, skull stripping seems almost worse and it is not respecting the manual edits that I have done either. You can see the manual edits in the Before_Watershed.png file if you zoom in.
2. Which version of FreeSurfer do I need to have to use gcut as it is giving me the following error-
recon-all -skullstrip -clean-bm -gcut -subjid 10
ERROR: Flag -gcut unrecognized.
This is the FreeSurfer version that I am using: freesurfer-Darwin-leopard-i686-stable-pub-v4.4.0
Thank you very much for your help.
Regards,
Sourav
