Synthstrip is extremely robust, it on both
Cheers
Bruce 

On Sep 29, 2024, at 6:34 PM, De Giorgi, Sara <sdegiorgi@mgh.harvard.edu> wrote:


Thank you all for the help. I have available the T1 post contrast, could I use it alternatively? (After freesurfer analysis I have to do tracula analysis).  

Thanks,
Sara

Inviato da Outlook per iOS
Da: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> per conto di Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edu>
Inviato: Sunday, September 29, 2024 4:20:00 AM
A: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Oggetto: 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 <wimb@drcmr.dk> wrote:



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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

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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