Re: [Freesurfer] mri_watershed and improvements of skullstripping

[Michelangelo Fabbrizzi]

External Email - Use Caution         Dear Yujing, yes, I am using FS 7.3.2, so thanks I will try with recon-all -s sub-01_recon -autorecon2 -careg should I add the -careg also for the -autorecon3 step? Can you eventually have a look also at the questions in my first email below (at the very bottom of this email trail)? Greatly appreciated! Il giorno 31 lug 2023, alle ore 14:51, Huang, Yujing <yhuan...@mgh.harvard.edu> ha scritto:          External Email - Use Caution         Hi Michelangelo,   I’m wondering if you are using FS 7.3.2?   ‘DOCAREG’ was accidentally dropped for autonrecon2. You can fix it by adding ‘-careg’ at the end of command line.   Best,   Yujing     From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Michelangelo Fabbrizzi Sent: Sunday, July 30, 2023 11:34 AM To: freesurfer@nmr.mgh.harvard.edu; fsbuild <fsbu...@contbay.com>; freesurfer-ow...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_watershed and improvements of skullstripping           External Email - Use Caution         Dear All,   another question: after the below if I use the command to run autorecon2: recon-all -s sub-01_recon -autorecon2   I get the following error: ERROR: cannot find or read transforms/talairach.m3z   Can you help me please?   Thanks, regards,   Michelangelo Il giorno 30 lug 2023, alle ore 15:32, Michelangelo Fabbrizzi <michef...@gmail.com> ha scritto:   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   _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed.  If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> .

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