{"id":13676381,"url":"https://github.com/bids-apps/HCPPipelines","last_synced_at":"2025-04-29T06:31:54.324Z","repository":{"id":47404542,"uuid":"67323691","full_name":"bids-apps/HCPPipelines","owner":"bids-apps","description":"A BIDS App for minimal preprocessing using the HCP Pipelines","archived":false,"fork":false,"pushed_at":"2024-11-04T08:30:15.000Z","size":152,"stargazers_count":33,"open_issues_count":21,"forks_count":30,"subscribers_count":12,"default_branch":"master","last_synced_at":"2024-11-11T18:41:10.166Z","etag":null,"topics":["anatomical-mri","bids","bidsapp","functional-mri","mri","preprocessing"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bids-apps.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2016-09-04T03:30:09.000Z","updated_at":"2024-11-04T08:30:19.000Z","dependencies_parsed_at":"2023-10-20T18:14:16.120Z","dependency_job_id":"60c3fe55-79f1-4e86-b263-91939fbbad01","html_url":"https://github.com/bids-apps/HCPPipelines","commit_stats":null,"previous_names":[],"tags_count":24,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2FHCPPipelines","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2FHCPPipelines/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2FHCPPipelines/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bids-apps%2FHCPPipelines/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bids-apps","download_url":"https://codeload.github.com/bids-apps/HCPPipelines/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":251450656,"owners_count":21591407,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["anatomical-mri","bids","bidsapp","functional-mri","mri","preprocessing"],"created_at":"2024-08-02T13:00:24.576Z","updated_at":"2025-04-29T06:31:49.311Z","avatar_url":"https://github.com/bids-apps.png","language":"Python","funding_links":[],"categories":["BIDS Apps"],"sub_categories":["others"],"readme":"## HCP Pipelines BIDS App\n\nThis a [BIDS App](https://bids-apps.neuroimaging.io) wrapper for [HCP Pipelines](https://github.com/Washington-University/Pipelines) [v4.3.0](https://github.com/Washington-University/HCPpipelines/releases/tag/v4.3.0).\nLike every BIDS App it consists of a container that includes all of the dependencies and run script that parses a [BIDS dataset](http://bids.neuroimaging.io).\nBIDS Apps run on Windows, Linux, Mac as well as HPCs/clusters.\n\nTo convert DICOMs from your HCP-Style (CMRR) acquisitions to BIDS try using [heudiconv](https://github.com/nipy/heudiconv) with this [heuristic file](https://github.com/nipy/heudiconv/blob/master/heudiconv/heuristics/cmrr_heuristic.py).\n\n### Description\n\nThe HCP Pipelines product is a set of tools (primarily, but not exclusively,\nshell scripts) for processing MRI images for the [Human Connectome Project][HCP].\nAmong other things, these tools implement the Minimal Preprocessing Pipeline\n(MPP) described in [Glasser et al. 2013][GlasserEtAl].\n\n**This BIDS App requires that each subject has at least one T1w and one T2w scan.** Lack fMRI or dMRI scans is handled robustly.  Note that while anatomicals (T1w, T2w scans) can be processed without a fieldmap, a fieldmap is mandatory for processing fMRI scans. Support for the HCP-Pipelines 'legacy' processing mode will be added in an upcoming release.\n\n\n\n### Documentation\n\n[Release Notes, Installation, and Usage][release-install-use]\n\n### How to report errors\nDiscussion of HCP Pipeline usage and improvements can be posted to the\nhcp-users discussion list. Sign up for hcp-users at\n[http://humanconnectome.org/contact/#subscribe][hcp-users-subscribe].\n\nPlease open an issue if you encounter errors building this BIDS App or believe you have encountered an error specific to the BIDS App wrapper.\n\n### Acknowledgements\n\nPlease cite [Glasser et al. 2013][GlasserEtAl] and [Smith et al. 2013][SmithEtAl].\n\n### Usage\n\nThis App has the following command line arguments:\n\n\tusage: run.py [-h]\n\t              [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]\n\t              [--session_label SESSION_LABEL [SESSION_LABEL ...]]\n\t              [--n_cpus N_CPUS]\n\t              [--stages {PreFreeSurfer,FreeSurfer,PostFreeSurfer,fMRIVolume,fMRISurface} [{PreFreeSurfer,FreeSurfer,PostFreeSurfer,fMRIVolume,fMRISurface} ...]]\n\t              [--coreg {MSMSulc,FS}] [--gdcoeffs GDCOEFFS] --license_key\n\t              LICENSE_KEY [-v] [--anat_unwarpdir {x,y,z,-x,-y,-z}]\n\t              [--skip_bids_validation]\n\t              bids_dir output_dir {participant}\n\n\tHCP Pipelines BIDS App (T1w, T2w, fMRI)\n\n\tpositional arguments:\n\t  bids_dir              The directory with the input dataset formatted\n\t                        according to the BIDS standard.\n\t  output_dir            The directory where the output files should be stored.\n\t                        If you are running group level analysis this folder\n\t                        should be prepopulated with the results of\n\t                        theparticipant level analysis.\n\t  {participant}         Level of the analysis that will be performed. Multiple\n\t                        participant level analyses can be run independently\n\t                        (in parallel) using the same output_dir.\n\n\toptional arguments:\n\t-h, --help            show this help message and exit\n\t--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]\n\t\t\t\t\t\t\tThe label of the participant that should be analyzed.\n\t\t\t\t\t\t\tThe label corresponds to sub-\u003cparticipant_label\u003e from\n\t\t\t\t\t\t\tthe BIDS spec (so it does not include \"sub-\"). If this\n\t\t\t\t\t\t\tparameter is not provided all subjects should be\n\t\t\t\t\t\t\tanalyzed. Multiple participants can be specified with\n\t\t\t\t\t\t\ta space separated list.\n\t--session_label SESSION_LABEL [SESSION_LABEL ...]\n\t\t\t\t\t\t\tThe label of the session that should be analyzed. The\n\t\t\t\t\t\t\tlabel corresponds to ses-\u003csession_label\u003e from the BIDS\n\t\t\t\t\t\t\tspec (so it does not include \"ses-\"). If this\n\t\t\t\t\t\t\tparameter is not provided, all sessions should be\n\t\t\t\t\t\t\tanalyzed. Multiple sessions can be specified with a\n\t\t\t\t\t\t\tspace separated list.\n\t--n_cpus N_CPUS       Number of CPUs/cores available to use.\n\t--stages {PreFreeSurfer,FreeSurfer,PostFreeSurfer,fMRIVolume,fMRISurface} [{PreFreeSurfer,FreeSurfer,PostFreeSurfer,fMRIVolume,fMRISurface} ...]\n\t\t\t\t\t\t\tWhich stages to run. Space separated list.\n\t--coreg {MSMSulc,FS}  Coregistration method to use\n\t--gdcoeffs GDCOEFFS   Path to gradients coefficients file\n\t--license_key LICENSE_KEY\n\t\t\t\t\t\t\tFreeSurfer license key - letters and numbers after \"*\"\n\t\t\t\t\t\t\tin the email you received after registration. To\n\t\t\t\t\t\t\tregister (for free) visit\n\t\t\t\t\t\t\thttps://surfer.nmr.mgh.harvard.edu/registration.html\n\t-v, --version         show program's version number and exit\n\t--anat_unwarpdir {x,y,z,x-,y-,z-}\n\t\t\t\t\t\t\tUnwarp direction for 3D volumes\n\t--skip_bids_validation, --skip-bids-validation\n\t\t\t\t\t\t\tassume the input dataset is BIDS compliant and skip\n\t\t\t\t\t\t\tthe validation\n\t--processing_mode {hcp,legacy,auto}, --processing-mode {hcp,legacy,auto}\n\t\t\t\t\t\t\tControl HCP-Pipeline modehcp (HCPStyleData): require\n\t\t\t\t\t\t\tT2w and fieldmap modalitieslegacy (LegacyStyleData):\n\t\t\t\t\t\t\talways ignore T2w and fieldmapsauto: use T2w and/or\n\t\t\t\t\t\t\tfieldmaps if available\n\t--doslicetime         Apply slice timing correction as part of fMRIVolume.\n\nTo run it in participant level mode (for one participant):\n\n    docker run -i --rm \\\n    -v /Users/filo/data/ds005:/bids_dataset:ro \\\n    -v /Users/filo/outputs:/outputs \\\n    bids/hcppipelines \\\n    /bids_dataset /outputs participant --participant_label 01 --license_key \"XXXXXX\"\n\n### Commercial use\n\nThis BIDS App incorporates several **non-free** packages required for the HCP Pipeline, including:\n\n- [MSM](https://github.com/ecr05/MSM_HOCR)\n- [FreeSurfer](https://surfer.nmr.mgh.harvard.edu/)\n- [FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence)\n- [MATLAB Runtime](https://www.mathworks.com/products/compiler/matlab-runtime.html)\n\n\nIf you are considering commercial use of this App please consult the relevant licenses.\n\n### TODO\n\n   - [ ] Add DiffusionProcessing stage\n   - [ ] More testing for fMRI with different resolution\n   - [ ] Run fMRI runs in parallel (when n_cpus present)\n   - [ ] Add support for TOPUP and GE fieldmaps for structural scans (please get in touch if you can provide sample data)\n   - [ ] Add support for GE fieldmaps for fMRI scans (please get in touch if you can provide sample data)\n   - [ ] Avoid copying fsaverage folder for every participant\n   - [ ] Add ICA FIX stage\n   - [ ] Add group level analysis\n   - [ ] Add task fMRI model fitting\n\n[HCP]: http://www.humanconnectome.org\n[GlasserEtAl]: http://www.ncbi.nlm.nih.gov/pubmed/23668970\n[SmithEtAl]: http://www.ncbi.nlm.nih.gov/pubmed/23702415\n[release-install-use]: hhttps://github.com/Washington-University/HCPpipelines/wiki/Installation-and-Usage-Instructions\n[hcp-users-subscribe]: http://humanconnectome.org/contact/#subscribe\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbids-apps%2FHCPPipelines","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbids-apps%2FHCPPipelines","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbids-apps%2FHCPPipelines/lists"}