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Hi Cain
If some brain was stripped I think you need to run all of autorecon2 and
autorecon3
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of DS
Sent: Sunday, August 6, 2023 8:09 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Bad skull stripping
External Email - Use Caution
Hi Bruce,
Thanks for your reply. That's awesome. I just now tried mri_synthstrip, it
works very well. I have another question. I first run recon-all and constructed
the cortical surface. But, I found an issue of skull stripping, which caused
the incorrect brainmask.mgz. Now this issue has been fixed. How can I
regenerate the FreeSurfer output based on the new brainmask.mgz. Can I use the
following command line to rerun it? Do I need to specify any other items?
recon-all \
-autorecon-pial \
-subjid <subject name>
Thanks,
Cain
At 2023-08-07 05:22:33, "Fischl, Bruce R.,PHD"
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> wrote:
External Email - Use Caution
Hi Cain
Have you tried using mri_synthstrip instead?
Cheers
Bruce
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 DS
Sent: Sunday, August 6, 2023 3:34 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Bad skull stripping
External Email - Use Caution
Hi expert,
I found an issue when I do skull stripping. I used the following command line.
recon-all \
-skullstrip \
-s fs_output \
-clean-bm \
-wsthresh 100
But, I found too much brain tissue has been removed, particularly for the
visual and motor cortex (almost the entire visual cortex has been removed).
Do you have any thoughts about this issue? Even though I tried wsthresh=100,
it's still not working. I am not sure how I can include all of the brain
tissues. Thanks.
PS. I am trying to attach a screenshot to show the skull stripping results,
however, I found the message with figure has been filtered. So, I have to post
this question without any figures. I am not sure whether I clarify my question.
Can I post any questions by showing screenshots?
Best,
Cain
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