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I just want to add (from out of nowhere) that synthstrip is fantastic..highly
reliable and accurate.
Josh Lee
Assistant Professional Researcher
Department of Psychiatry and Behavioral Sciences
University of California, MIND Institute
jki...@ucdavis.edu
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD
<bfis...@mgh.harvard.edu>
Sent: Sunday, September 29, 2024 1:20 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer - skull stripping error
You could try synthstrip, it might work
Cheers
Bruce
On Sep 29, 2024, at 7:38 AM, William Baare <w...@drcmr.dk> wrote:
External Email - Use Caution
Hi Sara,
You need to denoise the background.
Here are some links that might be of help. Always check the quality of the
output :-)
https://secure-web.cisco.com/1dRuxSA4h9rnOhMJRNBEr790phW8LKhre1MLsJpnnS0gxWo4NbIopejW5JsJk6pcQJ8Dtu5hH1QluL-OYvspFQS55Qpq6bSp1ui7OKMeR64vXxLaG15wUZkuRJ8toxyDcNKDxrQKRIQZkIM5C2iacAsmSFXI0Ql2zzA6r7hWMMCUEQa49Fc3q8OniQrOni2VVHio9g6LZ2a9uZFvo53_cHe-Pgj2tFoeKlXaXdiT6ZI6uGKidwT5u3I8PVQRE4odXwcorRaCk-8oR2N3ROX2GFluf7WUTNwFv1UlnVo660CYWtSNhWQiSzzOcZKuofUHEZarC3mYdIUPEfemrGzJBXg/https%3A%2F%2Fgithub.com%2Fsrikash%2FMP2RAGE-utils%2Fblob%2Fmain%2Fcore%2Fmp2rage_func%2FRobustCombination.m
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https://secure-web.cisco.com/1szgS5ncRMmXYiE0It-GuxwpXSrOs91SjsE1o1Tpq4vOpTISzqXYusL_T2m4IW0CECLeiXjBeyqeH5uGj3FIUM57nTMdtVOnG2JZIibCju7ehRSUrG7PQleYX-vl6whp8UyoNIGH1TZNb5fy1OptOjAyh2UdrNRBSkygC_CxquXcwwEHA0iLoPKgtDmiAf2Eb3-DjVhyWGwyVejyDNcsiUpP_vlaws-d9hvbxKj-fzYhZZdx5hvgNnQcKmymFKyr8X3Aa_8UeY7excAm41MSL0RTtdGZZRrp4AsFq2sW2PiLp062uESvLP8OagpBeUwmcvxC2D38NUJ-SKQCWvnr0TA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fdocs%2Fsynthstrip%2F
(incorporated in freesurfer)
Cheers
William
On 28 Sep 2024, at 18.27, De Giorgi, Sara <sdegio...@mgh.harvard.edu> wrote:
Dear all,
Skull stripping on Freesurfer failed due to MP2RAGE sequence. That’s the only
sequence we have. This is how it looks:
<image.png>
This is how the skull stripping appears:
<image.png>
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
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