Dear John,

you can prepare expert options file with the entry:

mri_gcut -T <threshold value>

and run recon-all -skullstrip -clean-bm -gcut -subjid <subject name> -expert expert_opts_file.txt

The mri_gcut help page reads:

-T <value> set threshold to value (%) of WM intensity, the value should be >0 and <1; larger values would correspond to cleaner skull-strip but higher chance of brain erosion. Default is set conservatively at 0.40, which provide approx. the same negligible level of brain erosion as 'mri_watershed'.

Antonin Skoch

Dear FS experts, I want to inquire if there are any threshold for the flag "gcut " in the command:recon-all -skullstrip -clean-bm -gcut -subjid <subject name>

If this not available are there any tools that can help to control how much dura will be cut out

Thanks in advance! John