Josh Lee

Assistant Professional Researcher

Department of Psychiatry and Behavioral Sciences

University of California, MIND Institute

jkilee@ucdavis.edu



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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://github.com/srikash/MP2RAGE-utils/blob/main/core/mp2rage_func/RobustCombination.m

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https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/   (incorporated in freesurfer)

Cheers

William 

On 28 Sep 2024, at 18.27, De Giorgi, Sara <sdegiorgi@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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