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/ > msgid/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
