Hi, I release a new version with a bugfix: v3.17.0-14. Please give it a try,
Best, Chris On Thu, Jun 22, 2017 at 1:43 PM, Chris Gorgolewski < [email protected]> wrote: > On Thu, Jun 22, 2017 at 4:04 PM, <[email protected]> wrote: > >> Hi Chris, >> >> Thank you for your response! This worked very well and I hope it will >> help others in the future. >> I am now trying to run the entire HCP pipeline on one subject, labeled >> "Asample", using the following command: >> >> ./bids_hcppipelines_v3.17.0-13-2016-11-02-c9c1c3cc2228.img >> /tmp/BIDS_HCP_test /tmp/BIDS_HCP_test/HCP_PreProc_output participant >> --participant_label Asample --license_key CX2frM4fbVCk >> >> >> I am getting the following error: >> >> Final FOV is: >> 0.000000 176.000000 0.000000 256.000000 89.000000 150.000000 >> >> Image Exception : #22 :: ERROR: Could not open image >> /opt/HCP-Pipelines/global/templates/MNI152_T1_1.0mm >> terminate called after throwing an instance of 'RBD_COMMON::BaseException' >> /opt/HCP-Pipelines/PreFreeSurfer/scripts/ACPCAlignment.sh: line 84: >> 4731 Aborted ${FSLDIR}/bin/flirt -interp spline -in >> "$WD"/robustroi.nii.gz -ref "$Reference" -omat "$WD"/roi2std.mat -out >> "$WD"/acpc_final.nii.gz -searchrx -30 30 -searchry -30 30 -searchrz -30 30 >> >> Traceback (most recent call last): >> File "/run.py", line 340, in <module> >> stage_func() >> File "/run.py", line 69, in run_pre_freesurfer >> run(cmd, cwd=args["path"], env={"OMP_NUM_THREADS": >> str(args["n_cpus"])}) >> File "/run.py", line 28, in run >> raise Exception("Non zero return code: %d"%process.returncode) >> Exception: Non zero return code: 134 >> >> It seems like /opt/HCP-Pipelines/global/templates/ is not in my HPC but >> rather in the container, is this correct? >> > This is a bug - I'm working on a fix > <https://github.com/BIDS-Apps/HCPPipelines/pull/16>. Will get back to you. > > Best, > Chris > > >> Could you please advise on ways to debug or things to try? >> Should I be using Joke's Singularity file at all? I see the HCPPIPEDIR in >> question on there. >> >> Any advice on how to proceed/troubleshoot would be greatly appreciated! >> >> Thanks, >> Paola Odriozola >> >> >> >> >> >> On Thursday, June 15, 2017 at 4:07:53 PM UTC-4, Chris Gorgolewski wrote: >>> >>> >>> >>> 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/ms >>>> gid/bids-apps-dev/87d5389a-dc9b-4f05-8715-34f8685c5958%40goo >>>> glegroups.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. >>>> >>> >>> -- >> 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/ms >> gid/bids-apps-dev/c37be065-88cd-4559-a6e0-48cff1b29b3e%40googlegroups.com >> <https://groups.google.com/d/msgid/bids-apps-dev/c37be065-88cd-4559-a6e0-48cff1b29b3e%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
