Hi Gunes

 

Just set it in your environment before calling mri_em_register.  For example

 

setenv OMP_NUM_THREADS 1

 

in csh/tcsh or

 

export OMP_NUM_THREADS=1

 

in bash. I think you can also give -openmp 1 to recon-all (hopefully that will also work)

 

cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of gunes
Sent: Monday, February 8, 2021 6:04 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Number of threads in mri_em_register

 

        External Email - Use Caution        

Dear freesurfer developers,

 

I'm using freesurfer v5.3.0 and having problems with the number of threads opened by `mri_em_register`. It automatically opens up as many threads as there are in the system, but I need to limit that. 

 

I have seen this post with the same problem: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41604.html

 

In the end, it seems to be solved by setting OMP_NUM_THREADS to 1 in the mri_em_register script, but it is a binary file. I don't know how to set it. 

 

Kind regards,

Gunes

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