The HCP Pipeline scripts use ‘bash’.  (setenv is for the csh shell).

The equivalent for bash is:

export OMP_NUM_THREADS=2

-- 

Michael Harms, Ph.D.

-----------------------------------------------------------

Conte Center for the Neuroscience of Mental Disorders

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave. Tel: 314-747-6173

St. Louis, MO  63110 Email: mharms@wustl.edu

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Lisa Kramarenko <lisa.kramarenko@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, June 8, 2017 at 9:26 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] -openmp flag in mri_em_register

Hi,

thanks for the quick reply. I pasted this line in the script, yet it gives me the following error:

setenv: command not found

Then I tried to just run it in the Terminal before calling the script, yet "No command 'setenv' was found". 

Any idea on what is wrong?

Thanks,

Lisa

On 8 June 2017 at 15:26, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Lisa

the individual commands don't accept -openmp. Try doing:

setenv OMP_NUM_THREADS 2

mri_em_register ...

cheers
Bruce

On Thu, 8 Jun 2017, Lisa Kramarenko wrote:

Hello,
I am using HCP pipelines and I would like mri_em_register which is being
called from a pipeline script to run on 2 cores instead on all available
ones. I tried to just add an -openmp flag to the command as suggestedhere: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41604.
html

my command looks like this: 

mri_em_register -mask "$SubjectDIR"/"$SubjectID"/mri/brainmask.mgz
"$SubjectDIR"/"$SubjectID"/mri/nu.mgz
$FREESURFER_HOME/average/RB_all_2008-03-26.gca
"$SubjectDIR"/"$SubjectID"/mri/transforms/talairach_with_skull.lta -openmp 2


yet I get an error:

mri_em_register: could not open GCA -openmp

Do you have an idea of how to fix it?

Thanks!
Lisa

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

 

---

The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.