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I attached the recon-all.log file. I'm not sure what you mean by the full screen output. 
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <BFISCHL@mgh.harvard.edu>
Sent: Thursday, December 3, 2020 11:56 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all issues debugging
 

Hi Courtney

 

Can you send us the recon-all.log file and the full screen output from one job that failed?

 

Cheers

Bruce

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Courtney Haswell
Sent: Thursday, December 3, 2020 9:52 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all issues debugging

 

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I am trying to debug why all of our T1's are failing Freesurfer recon-all. It seems that most of the files are being created but it isn't getting to the stats steps to output those files. In the recon-all log it does say "recon-all -s 13265 exited with ERRORS." 

 

I looked in the recon-all.error file and the only thing in that is "CMD mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix." Would this be the step where the error is happening? 

 

I have checked the T1 thoroughly and it is good quality. What is the best way to debug why this is happening with our scans?