External Email - Use Caution
You don’t need ‘-careg’ if you just run autorecon3.
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
<yhuan...@mgh.harvard.edu<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto: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<mailto:freesurfer@nmr.mgh.harvard.edu>;
fsbuild <fsbu...@contbay.com<mailto:fsbu...@contbay.com>>;
freesurfer-ow...@nmr.mgh.harvard.edu<mailto: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<mailto: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
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