Hi Peter,

I would suggest not to use ‘-parallel’. It is handled by recon-all to run multiple commands in parallel. It can run into collisions if they are not synchronized.

These recon-all options ‘-threads <>’, ‘-openmp <>’, ‘-nthreads <>’ tell individual program to split the tasks and run them in parallel. They are the same flags.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of P Pieperhoff
Sent: Wednesday, November 8, 2023 5:28 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] parallel processing of long-run fails

        External Email - Use Caution        

Dear FreeSurfer developers,

when I execute a long-run with parallel processing by calling

recon-all -sd <directory> -threads 64 -openmp 64 -parallel -long <imageid> <template_id> -all

it fails in step "autorecon3" at the surface registration.

But when I start it again without the option "-parallel", it finishs without errors.

I'm using FreeSurfer version 7.4.1 with Linux CentOS.

I have attached the log file to this mail.

Best regards,

Peter