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 suggested here: 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