Re: [Freesurfer] mri_watershed and improvements of skullstripping

External Email - Use Caution

You don’t need ‘-careg’ if you just run autorecon3.

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Michelangelo Fabbrizzi Sent: Monday, July 31, 2023 8:55 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_watershed and improvements of skullstripping

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 <YHUANG43@mgh.harvard.edumailto:YHUANG43@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Michelangelo Fabbrizzi Sent: Sunday, July 30, 2023 11:34 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu; fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com>; freesurfer-owner@nmr.mgh.harvard.edumailto: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

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