thanks a lot, now it works!
On 8 June 2017 at 16:29, Harms, Michael mharms@wustl.edu wrote:
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 <(314)%20747-6173> 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.m gh.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
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