{"id":23442307,"url":"https://github.com/repronim/workflowcomparison","last_synced_at":"2026-03-20T01:25:50.756Z","repository":{"id":242228904,"uuid":"809009019","full_name":"ReproNim/WorkflowComparison","owner":"ReproNim","description":"The git repo for the workflow comparison project.","archived":false,"fork":false,"pushed_at":"2024-06-21T08:57:57.000Z","size":16,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":9,"default_branch":"main","last_synced_at":"2025-09-15T08:49:14.687Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Dockerfile","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ReproNim.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2024-06-01T12:26:43.000Z","updated_at":"2024-06-21T08:58:00.000Z","dependencies_parsed_at":"2024-06-04T22:51:38.209Z","dependency_job_id":"8ddf4f81-0f60-407a-9867-d508404ea1c5","html_url":"https://github.com/ReproNim/WorkflowComparison","commit_stats":null,"previous_names":["repronim/workflowcomparison"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/ReproNim/WorkflowComparison","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ReproNim%2FWorkflowComparison","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ReproNim%2FWorkflowComparison/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ReproNim%2FWorkflowComparison/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ReproNim%2FWorkflowComparison/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ReproNim","download_url":"https://codeload.github.com/ReproNim/WorkflowComparison/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ReproNim%2FWorkflowComparison/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29451933,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-14T15:52:44.973Z","status":"ssl_error","status_checked_at":"2026-02-14T15:52:11.208Z","response_time":53,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":[],"created_at":"2024-12-23T17:29:20.826Z","updated_at":"2026-02-14T18:02:41.185Z","avatar_url":"https://github.com/ReproNim.png","language":"Dockerfile","funding_links":[],"categories":[],"sub_categories":[],"readme":"# WorkflowComparison\nThere are many ways to skin a cat. But we like cats, so let's not do that.\n\nThere are many ways to run an image analysis. There, that's a bettter start. In this project we explore, for a 'standard' \nMRI image processing analysis problem, the options, pros, cons, issues, and comlpexities of approaching a specific problem \nusing a number of the ways that arailable. At the same time, we also review how to add the 'extras' that doing image\nprocessing ***The ReproNim Way*** (adding best practice operations for version control, standards, and annotation, particularly)\ncan be acheived using each of these different workflow approaches.\n\nWelcome to the The git repo for the ReproNim Workflow Comparison Project.\n\nSome additional notes are [here](https://docs.google.com/document/d/1cuR2OGhYzKYu9fi9DoBjc3ci4kwik-brXBt6BLSNwsI/edit)\n\n# The Problem\nTake the structural imaging data of the OpenNeuro dataset [ds004215](https://openneuro.org/datasets/ds004215/versions/1.0.3) \"The National \nInstitute of Mental Health (NIMH) Intramural Healthy Volunteer Dataset\", perform a structural analysis, and test for sex effects and \ncorrelation with age for all anatomic regions.\n\nBut, there is a multiverse out there of analytical flexibiulity about how to approach the above problem statement. So, for this project, \nlet's be more specific.\n\nFor the structural imaging data in ds004215, perform a quality control assessment using the tool *mriqc*, perform structural analysis \nusing the tools *fsl_anat* and *FreeSurfer*, and from these results test each region for sex, age and sex x age interaction.\n\n## Incorporate ReproNim Best Practices\nRemember to include methods for:\n* Version control everything\n    * FreeSurfer annotation via [segstats_jsonld](https://github.com/ReproNim/segstats_jsonld)   \n* Share everything\n* Annotate everything\n* Use standards and containers for everything\n\n# The Workflow Systems\nWe are starting with the following workflow systems. But, this list is not exhaustive. If you would like another system included, feel\nfree to join up and add it!\n\n* BrainLife\n* NeuroDesk\n* BABS\n* [NIPOPPY](https://github.com/neurodatascience/nipoppy) - [docs](https://nipoppy.readthedocs.io/en/latest/) \n* DataLad Containers-run / ReproMan\n* BASH Script\n* Add other options!\n\n# More about the Data\n* Healthy Controls\n* N Subjects = 157\n* Age: 18-72\n* Male/Female: 54/103\n* Handedness (right/left/ambi): 136/7/14\n\nAvailable in BIDS representation from OpenNeuro.\n\n# The Details\nFor each of the workflow systems, we will have a separate page that document how to accomplish this task using that specific system. \nPlease be as specific as possible. Present your system's approach in a way that *someone else* can replicate the process on their own.\nThe dataset is large enough that you will probably need to address how to scale to these 155 subjects if you want the analysis to run \nin a reasonable amout of time, and not on one's own personal computer. Please be specific about the prerequsites someone needs, and any \nmodifications to the problem statement you may need to make.\n\n## BrainLife\nSee the BrainLife Approach Document [here].\n\nDNKs Status - inprogress\n\n## NIPOPPY\nSee the NIPOPPY Approach Document [here](docs/nipoppy.md).\n\nDNKs Status - stalled\n\n## DataLad\nSee the DataLad Approach Document [here].\n\nDNKs Status - stalled on Mac (could try linux environment)\n\n## NeuroDesk\nSee the BrainLife Approach Document [here].\n\nDNKs Status - not started yet\n\n## BABS\nSee the BrainLife Approach Document [here](docs/babs.md).\n\nDNKs Status - not started yet\n\n## Bash\nSee the BrainLife Approach Document [here](docs/bash.md).\n\nDNKs Status - not started yet.\n\n# Results Comparrison\nTODO once there are some results!\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frepronim%2Fworkflowcomparison","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frepronim%2Fworkflowcomparison","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frepronim%2Fworkflowcomparison/lists"}