Re: [HCP-Users] HCP Pipelines BIDS App

[Harms, Michael]

Hi Chris, This indeed looks very interesting.  Following up on Dan’s question, it will be important for users to have a transparent way to know if any changes have been made to the HCP Pipeline scripts.   Along those lines, your github page says: This BIDS App requires that each subject has at least one T1w and one T2w scan. Lack of fieldmaps, or fMRI scans is handled robustly. Is the part above that “lack of fieldmaps” is handled “robustly” only in reference to the T1/T2 scans?  Because the HCP Pipelines have always considered fieldmaps to be a mandatory acquisition for the fMRI processing (given their importance in correcting for distortions). cheers, -MH --  Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO  63110 Email: mha...@wustl.edu From: <hcp-users-boun...@humanconnectome.org> on behalf of Daniel Marcus <dmar...@wustl.edu> Date: Monday, September 12, 2016 at 2:27 PM To: Chris Gorgolewski <krzysztof.gorgolew...@gmail.com>, Hcp Users <hcp-users@humanconnectome.org>, "bids-apps-...@googlegroups.com" <bids-apps-...@googlegroups.com> Subject: Re: [HCP-Users] HCP Pipelines BIDS App Hi Chris, This is great work and I think will be a serious asset to those looking to run HCP pipelines on their data.  Can you explain what steps you’ve taken to adapt the pipelines to work with the BIDS format?  Conversely, have you taken any steps to adapt the existing HCP packages to work with these containers? -Dan From: <hcp-users-boun...@humanconnectome.org> on behalf of Chris Gorgolewski <krzysztof.gorgolew...@gmail.com> Date: Sunday, September 11, 2016 at 12:03 AM To: Hcp Users <hcp-users@humanconnectome.org>, "bids-apps-...@googlegroups.com" <bids-apps-...@googlegroups.com> Subject: [HCP-Users] HCP Pipelines BIDS App 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 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). No need to specify any metadata - all you need as an input is a BIDS dataset . The only software required (across all three platforms) is Docker. 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 _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users   The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users   The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users