8 Jun
2017
8 Jun
'17
9:02 a.m.
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