The file recon-all.log in the scripts dir for each subject should have any error messages. Usually we start looking at the end of them to see what happened.

 

Cheers

Bruce

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of REEM ABU BAKR BAHATHIQ
Sent: Tuesday, March 1, 2022 5:10 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] check recon-all errors

 

        External Email - Use Caution        

 

Hello Freesurfer experts

I ran the full Recon-all pipeline on my 400 .scans data.
I wanted to get the "wmparc.mgz" image of each subject.
But I couldn't find it in some of them !!

Where can I find the error file for the subject, as I think the process is not completed here?

I would also like to inquire about the way to restart Recon-all from where the pre-processing stopped. How can I determine which step stopped processing and what should I write from a command in Linux to complete the processing process?

The attached picture shows the processing output for the subject that I think something went wrong with it

Thanks in advance

 

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