From the log file it got to the surface stuff and died there. You should be able to run recon-all with the -hemi [lr]h switch to just run one hemi

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Alina Rojas
Sent: Monday, July 6, 2020 11:23 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Lesioned hemisphere

        External Email - Use Caution        

Hello Bruce,

Thanks for the quick answer! I attached the recon-all.log file and a visualization of the subjects problem.

How can I run only one hemisphere? 

Thanks,

Alina

Am 06.07.2020 um 16:32 schrieb Fischl, Bruce <BFISCHL@mgh.harvard.edu>:

What is the error? You should be able to run through to the surface generation, then only run the hemi you want

Cheers
Bruce

-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Alina Rojas
Sent: Monday, July 6, 2020 10:22 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Lesioned hemisphere

       External Email - Use Caution        

Hello Freesurfer experts,

I’m analyzing subjects with a stroke in one hemisphere. Problem: recon-all breaks and gives an error at the white matter segmentation, what I understand. I don’t need the data from the lesioned hemisphere, I need the cortical thickness from the healthy one. Is there a possibility to only run one hemisphere through freesurfer? Or to project the healthy one on to the lesioned to have an intact brain and run recon-all succesfully?

Thanks,

Alina

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