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 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

---

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.

thanks a lot, now it works!

On 8 June 2017 at 16:29, Harms, Michael mharms@wustl.edu wrote:

The HCP Pipeline scripts use ‘bash’. (setenv is for the csh shell). The equivalent for bash is:

export OMP_NUM_THREADS=2

-- Michael Harms, Ph.D.

---

Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 <(314)%20747-6173> St. Louis, MO 63110 Email: mharms@wustl.edu

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lisa Kramarenko lisa.kramarenko@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, June 8, 2017 at 9:26 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -openmp flag in mri_em_register

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 as suggestedhere: https://www.mail-archive.com/freesurfer@nmr.m gh.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.

---

The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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.

yes, i'm using bash and it worked with export, thanks!

On 8 June 2017 at 17:42, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

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.m

ail-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_sku

ll.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.