Dear Freesurfer Experts,
My apologies for what might be a very simple question, but I have been unable to locate an answer in the archives/wiki. Our group is trying to cut down on our mri_glmfit-sim time (as we are hoping to run mri_glmfit-sim -sim mc-full, rather than -sim mc-z). I know that --bg will split up the larger number of simulations into n background jobs, but I also noted the warning that this option is not to be used on the Martinos launchpad computational cluster. As we are hoping to find a way to use launchpad, I was wondering if mri_glmfit-sim is multi-threaded (or can be multi-threaded similar to -parallel flag in recon-all)?
We are currently running Freesurfer 5.3, but can move up to 6.0 if needed. (Our specific command is: mri_glmfit-sim --glmdir $SUBJECTS_DIR/.../glmdir --sim mc-full 2.3 1000 mcfull1000_2.3 --sim-sign abs --cwpvalthresh .05)
Thank you in advance for your help!
Kind regards,
Kevin
Kevin F. Dowling Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA, 02129 (p) 617.643.3215
sorry, just seeing this. If you want to use it on launchpad, you can use the secret --pbsubmit flag. Use in the same way as --bg. No need to pbsubmit mri_glmfit-sim, it will do all the pbsubmitting.
On 11/16/17 7:04 PM, Dowling, Kevin Francis wrote:
Dear Freesurfer Experts,
My apologies for what might be a very simple question, but I have been unable to locate an answer in the archives/wiki. Our group is trying to cut down on our mri_glmfit-sim time (as we are hoping to run mri_glmfit-sim -sim mc-full, rather than -sim mc-z). I know that --bg will split up the larger number of simulations into n background jobs, but I also noted the warning that this option is not to be used on the Martinos launchpad computational cluster. As we are hoping to find a way to use launchpad, I was wondering if mri_glmfit-sim is multi-threaded (or can be multi-threaded similar to -parallel flag in recon-all)?
We are currently running Freesurfer 5.3, but can move up to 6.0 if needed. (Our specific command is: mri_glmfit-sim --glmdir $SUBJECTS_DIR/.../glmdir --sim mc-full 2.3 1000 mcfull1000_2.3 --sim-sign abs --cwpvalthresh .05)
Thank you in advance for your help!
Kind regards,
Kevin
*Kevin F. Dowling * Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA, 02129 (p) 617.643.3215
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Dowling, Kevin Francis