Version 3.4.0 Hi,
The Pipelines-3.4.0//FreeSurfer/FreeSurferPipeline.sh script has a hard-coded value of 8 for the -openmp argument in the call to recon-all. This doesn't seem like a good idea. Seems it should be an option and default to 1. We've modified it to work with NSLOTS for SGE on our cluster. Here's the diff if you're interested: < cp "$SubjectDIR"/"$SubjectID"/mri/brainmask.auto.mgz "$SubjectDIR"/"$SubjectID"/mri/brainmask.mgz < < # CFN mod - use $NSLOTS to define multithreading < if [[ -z "$NSLOTS" ]]; then < NSLOTS=1 < fi < < recon-all -subjid $SubjectID -sd $SubjectDIR -autorecon2 -nosmooth2 -noinflate2 -nocurvstats -nosegstats -openmp $NSLOTS --- > cp "$SubjectDIR"/"$SubjectID"/mri/brainmask.auto.mgz "$SubjectDIR"/"$SubjectID"/mri/brainmask.mgz > recon-all -subjid $SubjectID -sd $SubjectDIR -autorecon2 -nosmooth2 -noinflate2 -nocurvstats -nosegstats -openmp 8 _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
