Hi all, I am using mri_watershed to create skull surfaces for a cohort of subjects for whom we were unable to collect a FLASH sequence. To improve the estimation of the inner skull layer, I would like to use edited brainmasks. However whenever I supply the -mask flag, and only when I supply -mask flag to mri_watershed, the code does not run; it only brings up the help screen.
So two questions: (1) Is the -mask flag in mri_watershed doing what I think it is doing? Is it masking the T1 image to only the brain so that the inner skull layer will be estimated from the brainmask? (2) Am I using the -mask flag correctly? I get the same result if I use mri_watershed -mask and mri_watershed -mask <path to mask>. Should I be doing something differently? All the best, Sam
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