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


_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you
in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.