External Email - Use Caution
Dear Yujing,
thanks again for your help, just a last question, how can give to autorecon1 the input to use certain options at the mri_watershed step (for instance a certain preflood height (-h 5) or use of the atlas option (-atlas))?
recon-all -s sub-01_recon -i T1w.nii.gz -autorecon1 xxxx
Your help is greatly appreciated!
Michelangelo
Il giorno 31 lug 2023, alle ore 17:23, Huang, Yujing YHUANG43@mgh.harvard.edu ha scritto: External Email - Use Caution
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
External Email - Use CautionDear 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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