Hi Cain

Have you tried using mri_synthstrip instead?

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of DS
Sent: Sunday, August 6, 2023 3:34 PM
To: 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