what shell are you using? THat is a tcsh/csh command.If you are using bash you need to use the export command
cheers Bruce On Thu, 8 Jun 2017, Lisa Kramarenko wrote:
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 assuggestedhere: 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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