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I'm not sure how to force mri_watershed command to use the brainmask.mgz already created.

Recon-all '-gcut' is achieved by running mri_gcut after mri_watershed.

-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Michelangelo Fabbrizzi
Sent: Sunday, July 30, 2023 9:32 AM
To: freesurfer@nmr.mgh.harvard.edu; fsbuild <fsbuild@contbay.com>; freesurfer-owner@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_watershed and improvements of skullstripping

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Dear Freesurfer experts,

I am new to FS, and I would have couple of questions.
I used in sequence:
A- recon-all -i sub-01_T1w.nii.gz -s sub-01_recon -autorecon1    
B- recon-all -skullstrip -wsthresh 5 -clean-bm -s sub-01_recon    
C- recon-all -skullstrip -clean-bm -gcut -subjid sub-01_recon

The brainmask.mgz obtained is good (no skull, brain is okay), however if I now use mri_watershed to obtain the bem surfaces, it looks the brainmask.mgz is not used and it is created a new one called ws.mgz that still contain some piece of skull that generate wrong BEM surfaces; even using -h 5 the result is not optimal:
mri_watershed -h 5 -useSRAS -surf /Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/sub-01_recon /Users/michelangelo/Test_skullstripping/sub-01_recon/mri/T1.mgz /Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/ws.mgz

I am wondering:
- how can I force the mri_watershed command to use the brainmask.mgz already created after step C above, instead of creating a new one?
- is it possible to use the -gcut command also for mri_watershed?

Thanks, appreciated,

Miche




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