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Hi Sara,
If you happen to also have INV1 and INV2, one solution is to run mri_synthstrip on any of these two images (instead of on UNI) and save the brain mask using option -m. This should give you a better brain mask since the background of INV1 and INV2 are not as
noisy as UNI. Once you have the brain mask, you can just multiply the brain mask by UNI.
Best,
Kaibo
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of De Giorgi, Sara <sdegiorgi@mgh.harvard.edu>
Sent: Saturday, September 28, 2024 12:27 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Freesurfer - skull stripping error
Sent: Saturday, September 28, 2024 12:27 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Freesurfer - skull stripping error
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Dear all,
Skull stripping on Freesurfer failed due to MP2RAGE sequence. That’s the only sequence we have. This is how it looks:
Skull stripping on Freesurfer failed due to MP2RAGE sequence. That’s the only sequence we have. This is how it looks:
This is how the skull stripping appears:
Please find the log file as an attachment.
I also tried to manually adjust brainmask.mgz , but also brain.mgz is incorrect.
How can I solve this issue?
Thanks,
Sara