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there are not options to autorecon1 specifically. You can pass some
watershed args on the command line, but it is probably easier to use an
expert options file, eg, create a text file (eg, xopts.txt) with
something like
mri_watershed -less
then run recon-all with -expert xopts.txt (and the rest of your args)
You can add as many options as you want to that line
On 7/31/2023 1:22 PM, Michelangelo Fabbrizzi wrote:
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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
<yhuan...@mgh.harvard.edu> ha scritto:
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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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Michelangelo
Fabbrizzi
Sent: Sunday, July 30, 2023 9:32 AM
To: freesurfer@nmr.mgh.harvard.edu; fsbuild <fsbu...@contbay.com>;
freesurfer-ow...@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_watershed and improvements of skullstripping
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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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