The fMRIVolume pipeline also takes advantage of SGE through fslsub, and we
hacked it to use condor as well--that allows for significant time savings on
our end
_
gaurav patel
gauravpa...@gmail.com
www.neurofreak.net
> On Apr 27, 2017, at 2:29 PM, Glasser, Matthew
Hi Mike,
The only thing that is parallelized in the minimal preprocessing pipelines
aside from specific FreeSurfer binaries is wb_command. wb_command
defaults to using as many cores as the system has. More advanced
pipelines that use matlab will adhere to matlab¹s parallelization
behaviors.
Matt, Tim,
What is parallelized in the fMRI pipelines?
I would be good if we created a FAQ entry on the HCP Wiki detailing:
(1) Which aspects of the pipelines are parallelized and the default number
of cores used for each.
(2) Which wb_commands are parallelized and the default number of cores
For what its worth, on our workstations we run each subject's anatomy pipeline
as a separate thread, which takes 8-12 hours, then use the parallelization to
speed up the fMRI pipelines with either SGE/OGE or ht_condor, with a thread
devoted to each bold run being processed
The number of windows you use to launch the processing is irrelevant. But if
you only have 8 cores on your machine, and only want to use 7 of them, you
can’t run 50 subjects at once.
In this case, where you have a bunch of subjects to process, I would run 7
subjects at a time, while limiting
