On Thu, Jun 15, 2017 at 1:00 PM, <[email protected]> wrote: > Dear Chris, > > Thank you for all your contributions to reproducible science! I've read > your documentation and watched your neurohackweek video which have been > really helpful, but I am still unclear on the specific command used to run > the HCPpipeline BIDSapp using Singularity on an HPC. I see instructions for > Docker commands here > <https://github.com/BIDS-Apps/HCPPipelines/blob/master/README.md>, but > not Singularity, > There is more information here: http://bids-apps.neuroimaging.io/tutorial/ and in the paper http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005209
> I ran the following commands on my local computer to convert the image > from docker to singularity: > > $ docker run --privileged -ti --rm -v > /var/run/docker.sock:/var/run/docker.sock > -v /Users/estee/Desktop/singularity_images:/output > filo/docker2singularity bids/example:0.0.4 > > Then I transferred this image to my HPC system (now named: > bids_example_0.0.4-2016-08-28-fba9b3e0a751.img) and installed > Singularity. Is this the correct image file I should be using? > This command will create an image for the example app. To create one for the HCP Pipelines you need to replace "bids/example:0.0.4" with "bids/hcppipelines:v3.17.0-13" What is the specific command I should be running to preprocess one subject > using Singularity? Should I be running the run.py script within > singularity? And how do I specify the subjectID or directory? > ./name_of_the_image.img <input_bids_directory> <output_directory> participant --participant_label <label> You need to replace <input_bids_directory> <output_directory> <label> with values corresponding to your dataset. Please mind that HCP pipelines only work on datasets that include T2 weighted images and fieldmaps! Best, Chris > > > Thanks, > Paola > > > On Sunday, September 11, 2016 at 1:03:32 AM UTC-4, Chris Gorgolewski wrote: >> >> Dear HCP community, >> >> Many researchers want to run HCP Pipelines on their own datasets, but run >> into problems with software dependencies and different organization of data >> and metadata. To help with this issue I have created an HCP Pipelines BIDS >> App. Like all other BIDS Apps <http://bids-apps.neuroimaging.io/> the >> HCP Pipelines one has the following features: >> >> - It's portable (meaning comes with all of the dependencies with the >> correct versions - no need to install FSL or Freesurfer). >> - Runs on Windows, Mac OS X and Linux (as well as HPCs or clusters >> via Singularity <http://bids-apps.neuroimaging.io/tutorial/>). >> - No need to specify any metadata - all you need as an input is a BIDS >> <http://bids.neuroimaging.io/>dataset . >> - The only software required (across all three platforms) is Docker >> <https://www.docker.com/>. >> - The App (which includes all dependencies) is versioned and all >> historical versions are preserved. This allows you to keep the same >> software stack intact during a longitudinal study spread over years. >> >> The App was designed to parse the input datasets, figure out which scans >> are available and run HCP pipelines with optimal parameters. I have tested >> it with the HCP example subject, but if you have data you would like to >> provide for testing purposes I would be very happy to take advantage of it. >> >> I hope this will make HCP pipelines accessible to more researchers. >> Please let me know what you think! >> >> More information how to use the HCP Pipeline App can be found here: >> https://github.com/BIDS-Apps/HCPPipelines >> >> Best, >> Chris Gorgolewski >> > -- > You received this message because you are subscribed to the Google Groups > "bids-apps-dev" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > To view this discussion on the web visit https://groups.google.com/d/ > msgid/bids-apps-dev/87d5389a-dc9b-4f05-8715-34f8685c5958% > 40googlegroups.com > <https://groups.google.com/d/msgid/bids-apps-dev/87d5389a-dc9b-4f05-8715-34f8685c5958%40googlegroups.com?utm_medium=email&utm_source=footer> > . > > For more options, visit https://groups.google.com/d/optout. > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
