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

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