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