Re: [Freesurfer] mri_watershed and improvements of skullstripping

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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Michelangelo Fabbrizzi Sent: Sunday, July 30, 2023 11:34 AM To: freesurfer@nmr.mgh.harvard.edu; fsbuild fsbuild@contbay.com; freesurfer-owner@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 <michefabb@gmail.commailto:michefabb@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