diff --git a/.github/workflows/pr-preview.yml b/.github/workflows/pr-preview.yml index 68f7a95..19a5519 100644 --- a/.github/workflows/pr-preview.yml +++ b/.github/workflows/pr-preview.yml @@ -1,7 +1,7 @@ name: PR Preview on: - pull_request: + pull_request_target: types: [opened, synchronize, reopened, closed] permissions: @@ -13,8 +13,10 @@ jobs: if: github.event.action != 'closed' runs-on: ubuntu-latest steps: - - name: Checkout + - name: Checkout PR code uses: actions/checkout@v4 + with: + ref: ${{ github.event.pull_request.head.sha }} - name: Setup Node.js uses: actions/setup-node@v4 diff --git a/frontend/dist/data/reproinventory_data.json b/frontend/dist/data/reproinventory_data.json index 96c1b8a..16c015c 100644 --- a/frontend/dist/data/reproinventory_data.json +++ b/frontend/dist/data/reproinventory_data.json @@ -54,12 +54,12 @@ "Johanna Bayer", "Fellow-22" ], + "description": "A beginner-friendly course introducing Git and GitHub for version control and collaboration, covering online GitHub workflows and local machine setup with GitHub Desktop, progressing from basic concepts to managing merge conflicts.", "notes": null, "quadrants": [ "problem-oriented (how to guides)", "learning-oriented (tutorials)" - ], - "description": "A beginner-friendly course introducing Git and GitHub for version control and collaboration, covering online GitHub workflows and local machine setup with GitHub Desktop, progressing from basic concepts to managing merge conflicts." + ] }, { "id": 5, @@ -121,12 +121,12 @@ "Fellow-22", "UCSB" ], + "description": "JupyterHub no longer accessible. Need to link GitHubClassroom to GitHub (uclear if links work once you do that)", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)" - ], - "description": "JupyterHub no longer accessible. Need to link GitHubClassroom to GitHub (uclear if links work once you do that)" + ] }, { "id": 7, @@ -181,12 +181,12 @@ "Fellow-22", "Donders Institute" ], + "description": "Short slide deck, very clear", "alias_links": null, "notes": "link does not work for me (JB) can someone double check", "quadrants": [ "understanding-oriented (explanation)" - ], - "description": "Short slide deck, very clear" + ] }, { "id": 8, @@ -241,13 +241,13 @@ "Fellow-22", "Donders Institute" ], + "description": "Relatively quick overview - more just what is DataLad vs detailed how to use", "alias_links": null, "notes": null, "quadrants": [ "information-oriented (reference)", "understanding-oriented (explanation)" - ], - "description": "Relatively quick overview - more just what is DataLad vs detailed how to use" + ] }, { "id": 9, @@ -303,13 +303,13 @@ "Fellow-22", "Donders Institute" ], + "description": "Very short slide deck on GIT", "alias_links": null, "notes": null, "quadrants": [ "understanding-oriented (explanation)", "information-oriented (reference)" - ], - "description": "Very short slide deck on GIT" + ] }, { "id": 10, @@ -361,12 +361,12 @@ "Fellow-22", "Donders Institute" ], + "description": "Practical intro to bash and git", "alias_links": null, "notes": null, "quadrants": [ "understanding-oriented (explanation)" - ], - "description": "Practical intro to bash and git" + ] }, { "id": 11, @@ -431,12 +431,12 @@ "Celine Provins", "Fellow-22" ], + "description": "Focuses on QC in reference to MRIQC; has lots of big picture info about QC/QA in general", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)" - ], - "description": "Focuses on QC in reference to MRIQC; has lots of big picture info about QC/QA in general" + ] }, { "id": 16, @@ -489,12 +489,12 @@ "Avery Van De Water", "Fellow-22" ], + "description": "labeled as part 1 - unclear where part 2 is", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)" - ], - "description": "labeled as part 1 - unclear where part 2 is" + ] }, { "id": 18, @@ -508,7 +508,8 @@ "Beginner" ], "platform": [ - "NA" + "Mac", + "Linux" ], "keywords": [ "Pre-registration", @@ -528,13 +529,15 @@ "English" ], "programming_language": [ - "NA" + "Python", + "shell scripting" ], "neuroimaging_software": [ - "NA" + "FSL" ], "imaging_modality": [ - "NA" + "Functional", + "Structural" ], "open_dataset": false, "last_updated": "2021", @@ -548,13 +551,13 @@ "ReproNim", "Karolina Finc" ], + "description": "Some sections are under-developed", "alias_links": null, "notes": "Reproducible Neuroimaging, tutorial guide, for cog sci students audience", "quadrants": [ "learning-oriented (tutorials)", "information-oriented (reference)" - ], - "description": "Some sections are under-developed" + ] }, { "id": 21, @@ -567,7 +570,7 @@ "Beginner" ], "platform": [ - "NA" + "Jupyter" ], "keywords": [ "BIDS", @@ -612,13 +615,13 @@ "MIchael Joseph", "Fellow-20" ], + "description": "Basic Imaging Overview. Focus on BIDS", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "understanding-oriented (explanation)" - ], - "description": "Basic Imaging Overview. Focus on BIDS" + ] }, { "id": 22, @@ -632,7 +635,7 @@ "Beginner" ], "platform": [ - "NA" + "Jupyter" ], "keywords": [ "nilearn", @@ -676,13 +679,13 @@ "MIchael Joseph", "Fellow-20" ], + "description": "Tutorial on functional neuroimaging in Python", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "problem-oriented (how to guides)" - ], - "description": "Tutorial on functional neuroimaging in Python" + ] }, { "id": 23, @@ -695,7 +698,7 @@ "Beginner" ], "platform": [ - "NA" + "Jupyter" ], "keywords": [ "dMRI", @@ -708,7 +711,9 @@ "instruction_medium": [ "Hands-on tutorial / notebooks" ], - "delivery": null, + "delivery": [ + "self-paced" + ], "language": [ "English" ], @@ -734,13 +739,13 @@ "MIchael Joseph", "Fellow-20" ], + "description": "A Carpentries Incubator lesson introducing diffusion MRI concepts and data organization using BIDS, with hands-on analysis using Python-based tools like Dipy and Nibabel.", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "problem-oriented (how to guides)" - ], - "description": "A Carpentries Incubator lesson introducing diffusion MRI concepts and data organization using BIDS, with hands-on analysis using Python-based tools like Dipy and Nibabel." + ] }, { "id": 25, @@ -768,7 +773,9 @@ "instruction_medium": [ "notes" ], - "delivery": null, + "delivery": [ + "instructor" + ], "language": [ "English" ], @@ -779,9 +786,10 @@ "Multiple" ], "imaging_modality": [ - "NA" + "Functional", + "Structural" ], - "open_dataset": null, + "open_dataset": false, "last_updated": "2020", "functionality": null, "assessment": false, @@ -794,14 +802,14 @@ "Jennifer Legault", "Fellow-20" ], + "description": "example syllabus for hackathon/course", "alias_links": null, "notes": null, "quadrants": [ "understanding-oriented (explanation)", "learning-oriented (tutorials)", "information-oriented (reference)" - ], - "description": "example syllabus for hackathon/course" + ] }, { "id": 26, @@ -814,7 +822,9 @@ "Beginner" ], "platform": [ - "NA" + "Mac", + "Windows", + "Linux" ], "keywords": [ "Rehabilitation", @@ -825,7 +835,10 @@ "instruction_medium": [ "video" ], - "delivery": null, + "delivery": [ + "self-paced", + "instructor" + ], "language": [ "English" ], @@ -853,13 +866,13 @@ "Fellow-20", "ReproRehab" ], + "description": "Entire first year bootcamp videos online", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "understanding-oriented (explanation)" - ], - "description": "Entire first year bootcamp videos online" + ] }, { "id": 28, @@ -883,7 +896,9 @@ "instruction_medium": [ "Hands-on tutorial / notebooks" ], - "delivery": null, + "delivery": [ + "self-paced" + ], "language": [ "English" ], @@ -909,13 +924,13 @@ "Fellow-20", "Princeton" ], + "description": "Jupyter tutorials from the basics to advanced machine learning analyses on fMRI data", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "problem-oriented (how to guides)" - ], - "description": "Jupyter tutorials from the basics to advanced machine learning analyses on fMRI data" + ] }, { "id": 29, @@ -928,7 +943,8 @@ "Intermediate" ], "platform": [ - "NA" + "Mac", + "Linux" ], "keywords": [ "Syllabus", @@ -939,7 +955,9 @@ "instruction_medium": [ "lecture" ], - "delivery": null, + "delivery": [ + "instructor" + ], "language": [ "English" ], @@ -966,13 +984,13 @@ "Chris Rorden", "Fellow-20" ], + "description": "Syllabus for course on fMRI, including slides, from collection to inferencing", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "understanding-oriented (explanation)" - ], - "description": "Syllabus for course on fMRI, including slides, from collection to inferencing" + ] }, { "id": 30, @@ -985,7 +1003,9 @@ "Beginner" ], "platform": [ - "NA" + "Mac", + "Windows", + "Linux" ], "keywords": [ "BIDS", @@ -996,7 +1016,9 @@ "instruction_medium": [ "lecture" ], - "delivery": null, + "delivery": [ + "instructor" + ], "language": [ "English" ], @@ -1011,7 +1033,7 @@ "imaging_modality": [ "Functional" ], - "open_dataset": null, + "open_dataset": false, "last_updated": "NA", "functionality": null, "assessment": true, @@ -1024,13 +1046,13 @@ "Julie Schneider", "Fellow-20" ], + "description": "Syllabus for reproducible neuroimaging multi-week course", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "problem-oriented (how to guides)" - ], - "description": "Syllabus for reproducible neuroimaging multi-week course" + ] }, { "id": 31, @@ -1043,7 +1065,9 @@ "Beginner" ], "platform": [ - "NA" + "Mac", + "Windows", + "Linux" ], "keywords": [ "syllabus", @@ -1055,7 +1079,9 @@ "instruction_medium": [ "notes" ], - "delivery": null, + "delivery": [ + "self-paced" + ], "language": [ "English" ], @@ -1068,7 +1094,7 @@ "imaging_modality": [ "MRI" ], - "open_dataset": null, + "open_dataset": false, "last_updated": "2020", "functionality": null, "assessment": false, @@ -1079,13 +1105,13 @@ "source": [ "ReproNim" ], + "description": "syllabus for tutorial; details unclear. Might be unfinished.", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "information-oriented (reference)" - ], - "description": "syllabus for tutorial; details unclear. Might be unfinished." + ] }, { "id": 32, @@ -1099,7 +1125,9 @@ "Intermediate" ], "platform": [ - "NA" + "Mac", + "Windows", + "Linux" ], "keywords": [ "DataLad", @@ -1126,7 +1154,7 @@ "imaging_modality": [ "NA" ], - "open_dataset": null, + "open_dataset": false, "last_updated": "2024", "functionality": "2025", "assessment": false, @@ -1137,14 +1165,14 @@ "ReproNim", "Adina Wagner" ], + "description": "very good resource for data provenance", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "information-oriented (reference)", "problem-oriented (how to guides)" - ], - "description": "very good resource for data provenance" + ] }, { "id": 33, @@ -1159,7 +1187,9 @@ "Beginner" ], "platform": [ - "NA" + "Mac", + "Windows", + "Linux" ], "keywords": [ "AI", @@ -1169,7 +1199,9 @@ "instruction_medium": [ "video" ], - "delivery": null, + "delivery": [ + "self-paced" + ], "language": [ "English", "German" @@ -1183,7 +1215,7 @@ "imaging_modality": [ "NA" ], - "open_dataset": null, + "open_dataset": false, "last_updated": "2024", "functionality": null, "assessment": false, @@ -1191,13 +1223,13 @@ "source": [ "AI campus" ], + "description": "Nice videos and course material on AI", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "understanding-oriented (explanation)" - ], - "description": "Nice videos and course material on AI" + ] }, { "id": 34, @@ -1212,7 +1244,9 @@ "Beginner" ], "platform": [ - "NA" + "Mac", + "Windows", + "Linux" ], "keywords": [ "Datalad", @@ -1223,7 +1257,9 @@ "instruction_medium": [ "video" ], - "delivery": null, + "delivery": [ + "self-paced" + ], "language": [ "English" ], @@ -1246,13 +1282,13 @@ "Lennart Wittkuhn", "Adina Wagner" ], + "description": "Good video", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "understanding-oriented (explanation)" - ], - "description": "Good video" + ] }, { "id": 35, @@ -1265,7 +1301,8 @@ "Intermediate" ], "platform": [ - "NA" + "Mac", + "Linux" ], "keywords": [ "Datalad", @@ -1299,14 +1336,16 @@ "Basic Git", "Unix" ], - "source": null, + "source": [ + "Adina Wagner", + "Max Planck Institute" + ], "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "problem-oriented (how to guides)" - ], - "description": "Course outline for Data Lad Course" + ] }, { "id": 36, @@ -1321,7 +1360,9 @@ "Beginner" ], "platform": [ - "NA" + "Mac", + "Windows", + "Linux" ], "keywords": [ "Git", @@ -1331,7 +1372,10 @@ "instruction_medium": [ "notes" ], - "delivery": null, + "delivery": [ + "self-paced", + "instructor" + ], "language": [ "English" ], @@ -1344,7 +1388,7 @@ "imaging_modality": [ "NA" ], - "open_dataset": null, + "open_dataset": false, "last_updated": "2024", "functionality": null, "assessment": false, @@ -1353,13 +1397,13 @@ "ReproNim", "Lennart Wittkuhn" ], + "description": "An open-access online book that teaches version control using Git, designed for researchers with no prior experience. It covers core Git concepts and workflows through hands-on exercises and practical examples relevant to scientific work.", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "information-oriented (reference)" - ], - "description": "An open-access online book that teaches version control using Git, designed for researchers with no prior experience. It covers core Git concepts and workflows through hands-on exercises and practical examples relevant to scientific work." + ] }, { "id": 38, @@ -1374,7 +1418,8 @@ "Beginner" ], "platform": [ - "NA" + "Jupyter", + "Linux" ], "keywords": [ "Git", @@ -1387,7 +1432,9 @@ "instruction_medium": [ "lecture" ], - "delivery": null, + "delivery": [ + "instructor" + ], "language": [ "English" ], @@ -1411,13 +1458,13 @@ "ReproNim", "Xihe Xie" ], + "description": "Review of previous materials, full course", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "understanding-oriented (explanation)" - ], - "description": "Review of previous materials, full course" + ] }, { "id": 39, @@ -1431,7 +1478,8 @@ "Beginner" ], "platform": [ - "NA" + "Mac", + "Linux" ], "keywords": [ "Syllabus", @@ -1446,7 +1494,9 @@ "instruction_medium": [ "notes" ], - "delivery": null, + "delivery": [ + "instructor" + ], "language": [ "English" ], @@ -1459,7 +1509,7 @@ "imaging_modality": [ "MRI" ], - "open_dataset": null, + "open_dataset": true, "last_updated": "2019", "functionality": null, "assessment": false, @@ -1472,13 +1522,13 @@ "Michael Dayan", "Fellow-19" ], + "description": "Syllabus for ReproNim workshop", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "information-oriented (reference)" - ], - "description": "Syllabus for ReproNim workshop" + ] }, { "id": 40, @@ -1503,7 +1553,9 @@ "notes", "outline" ], - "delivery": null, + "delivery": [ + "instructor" + ], "language": [ "English" ], @@ -1516,7 +1568,7 @@ "imaging_modality": [ "MRI" ], - "open_dataset": null, + "open_dataset": false, "last_updated": "2019", "functionality": null, "assessment": false, @@ -1529,13 +1581,13 @@ "Aaron Kemp", "Fellow-19" ], + "description": "Syllabus for Research Imaging Informatics course. Overview of neuroimaging methods and basic processing", "alias_links": null, "notes": null, "quadrants": [ "information-oriented (reference)", "understanding-oriented (explanation)" - ], - "description": "Syllabus for Research Imaging Informatics course. Overview of neuroimaging methods and basic processing" + ] }, { "id": 43, @@ -1550,7 +1602,7 @@ "Intermediate" ], "platform": [ - "NA" + "Linux" ], "keywords": [ "DataLad", @@ -1561,7 +1613,9 @@ "instruction_medium": [ "Hands-on tutorial / notebooks" ], - "delivery": null, + "delivery": [ + "instructor" + ], "language": [ "English" ], @@ -1586,13 +1640,13 @@ "source": [ "ReproNim" ], + "description": "Syllabus for workshop that has been given", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "problem-oriented (how to guides)" - ], - "description": "Syllabus for workshop that has been given" + ] }, { "id": 46, @@ -1607,7 +1661,8 @@ "Beginner" ], "platform": [ - "NA" + "Mac", + "Linux" ], "keywords": [ "fMRI", @@ -1617,7 +1672,9 @@ "instruction_medium": [ "lecture" ], - "delivery": null, + "delivery": [ + "self-paced" + ], "language": [ "English" ], @@ -1643,12 +1700,12 @@ "ReproNim", "Princeton" ], + "description": "Very nice overview of different fMRI topics", "alias_links": null, "notes": null, "quadrants": [ "information-oriented (reference)" - ], - "description": "Very nice overview of different fMRI topics" + ] }, { "id": 47, @@ -1663,7 +1720,8 @@ "Beginner" ], "platform": [ - "NA" + "Mac", + "Linux" ], "keywords": [ "fMRI analysis", @@ -1674,20 +1732,22 @@ "instruction_medium": [ "lecture" ], - "delivery": null, + "delivery": [ + "instructor" + ], "language": [ "English" ], "programming_language": [ - "NA" + "shell scripting" ], "neuroimaging_software": [ - "NA" + "FSL" ], "imaging_modality": [ "Functional" ], - "open_dataset": null, + "open_dataset": false, "last_updated": "2019", "functionality": null, "assessment": false, @@ -1699,14 +1759,14 @@ "ReproNim", "Etienne Roesch" ], + "description": "Pretty good if you want to teach fMRI analysis from scratch", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "understanding-oriented (explanation)", "information-oriented (reference)" - ], - "description": "Pretty good if you want to teach fMRI analysis from scratch" + ] }, { "id": 50, @@ -1732,7 +1792,9 @@ "instruction_medium": [ "lecture" ], - "delivery": null, + "delivery": [ + "instructor" + ], "language": [ "English" ], @@ -1745,7 +1807,7 @@ "imaging_modality": [ "NA" ], - "open_dataset": null, + "open_dataset": false, "last_updated": "2019", "functionality": null, "assessment": false, @@ -1756,13 +1818,13 @@ "ReproNim", "Sebastien Tourbier" ], + "description": "Single presentation, good for an intro class to data management and data version control", "alias_links": null, "notes": null, "quadrants": [ "information-oriented (reference)", "understanding-oriented (explanation)" - ], - "description": "Single presentation, good for an intro class to data management and data version control" + ] }, { "id": 51, @@ -1786,7 +1848,10 @@ "instruction_medium": [ "Hands-on tutorial / notebooks" ], - "delivery": null, + "delivery": [ + "self-paced", + "instructor" + ], "language": [ "English" ], @@ -1807,13 +1872,13 @@ "source": [ "Carpentries" ], + "description": "If you want to teach carpentries use this tool - not only shell scripting, but also intro to R, Python and HPC", "alias_links": "https://github.com/jdkent/incf-fellow-jdkent/blob/gh-pages/index.md", "notes": null, "quadrants": [ "learning-oriented (tutorials)", "problem-oriented (how to guides)" - ], - "description": "If you want to teach carpentries use this tool - not only shell scripting, but also intro to R, Python and HPC" + ] }, { "id": 52, @@ -1828,7 +1893,8 @@ "Beginner" ], "platform": [ - "NA" + "Mac", + "Linux" ], "keywords": [ "Lesson plan" @@ -1837,7 +1903,9 @@ "instruction_medium": [ "reference" ], - "delivery": null, + "delivery": [ + "self-paced" + ], "language": [ "English" ], @@ -1859,13 +1927,13 @@ "ReproNim", "David Warren" ], + "description": "For internal usage", "alias_links": null, "notes": "Link to Github Importer broken", "quadrants": [ "information-oriented (reference)", "understanding-oriented (explanation)" - ], - "description": "For internal usage" + ] }, { "id": 53, @@ -1912,22 +1980,25 @@ "MRI" ], "open_dataset": true, - "last_updated": null, + "last_updated": "2024", "functionality": null, - "assessment": null, + "assessment": true, "prerequisite": [ "Basic Python", "Introductory statistics", "Basic neuroimaging knowledge" ], - "source": null, + "source": [ + "McGill University", + "NeuroDataScience" + ], + "description": "An introduction to machine learning concepts and methods in the context of neuroimaging data, covering supervised learning, model evaluation, and practical implementation in Python. Part of the QLS612 multi-week curriculum at McGill University.", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "understanding-oriented (explanation)" - ], - "description": "An introduction to machine learning concepts and methods in the context of neuroimaging data, covering supervised learning, model evaluation, and practical implementation in Python. Part of the QLS612 multi-week curriculum at McGill University." + ] }, { "id": 54, @@ -1955,10 +2026,18 @@ "Python", "version control" ], - "course_length": "NA", - "instruction_medium": null, - "delivery": null, - "language": null, + "course_length": "1+ weeks", + "instruction_medium": [ + "lecture", + "Hands-on tutorial / notebooks", + "website" + ], + "delivery": [ + "instructor" + ], + "language": [ + "English" + ], "programming_language": [ "Python", "shell scripting", @@ -1971,24 +2050,29 @@ "Multiple" ], "imaging_modality": [ - "NA" + "Structural", + "Functional", + "EEG", + "MEG" ], "open_dataset": true, - "last_updated": null, + "last_updated": "2022", "functionality": null, - "assessment": null, + "assessment": true, "prerequisite": [ "Basic Python programming", "Familiarity with neuroimaging concepts" ], - "source": null, + "source": [ + "Brainhack School" + ], + "description": "Brainhack School is an intensive, project-based training program run by a consortium of Canadian universities that teaches open and reproducible neuroscience. Participants work on collaborative projects while learning modern data science tools applied to neuroimaging.", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "problem-oriented (how to guides)" - ], - "description": "Brainhack School is an intensive, project-based training program run by a consortium of Canadian universities that teaches open and reproducible neuroscience. Participants work on collaborative projects while learning modern data science tools applied to neuroimaging." + ] }, { "id": 55, @@ -2018,10 +2102,17 @@ "summer institute", "collaborative" ], - "course_length": "NA", - "instruction_medium": null, - "delivery": null, - "language": null, + "course_length": "1+ weeks", + "instruction_medium": [ + "lecture", + "Hands-on tutorial / notebooks" + ], + "delivery": [ + "instructor" + ], + "language": [ + "English" + ], "programming_language": [ "Python", "R", @@ -2040,22 +2131,24 @@ "Resting-State" ], "open_dataset": true, - "last_updated": null, + "last_updated": "2026", "functionality": null, - "assessment": null, + "assessment": true, "prerequisite": [ "Basic Python or programming experience", "Graduate-level neuroscience or related field" ], - "source": null, + "source": [ + "University of Washington" + ], + "description": "NeuroHackademy is a summer institute at the University of Washington focused on data science and open neuroscience, combining lectures and hands-on tutorials covering neuroimaging analysis, machine learning, and reproducible research practices.", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "understanding-oriented (explanation)", "problem-oriented (how to guides)" - ], - "description": "NeuroHackademy is a summer institute at the University of Washington focused on data science and open neuroscience, combining lectures and hands-on tutorials covering neuroimaging analysis, machine learning, and reproducible research practices." + ] }, { "id": 56, @@ -2082,37 +2175,48 @@ "open science", "tutorials" ], - "course_length": "NA", - "instruction_medium": null, - "delivery": null, - "language": null, + "course_length": "1+ weeks", + "instruction_medium": [ + "lecture", + "Hands-on tutorial / notebooks" + ], + "delivery": [ + "instructor" + ], + "language": [ + "English" + ], "programming_language": [ "Python" ], - "neuroimaging_software": null, + "neuroimaging_software": [ + "NA" + ], "imaging_modality": [ "Functional", "Resting-State", "Behavioral" ], "open_dataset": true, - "last_updated": null, + "last_updated": "2024", "functionality": null, - "assessment": null, + "assessment": true, "prerequisite": [ "Linear algebra", "Basic calculus", "Python programming", "Introductory neuroscience" ], - "source": null, + "source": [ + "Neuromatch Academy" + ], + "description": "Neuromatch Academy offers intensive online computational neuroscience and deep learning courses through lectures, tutorials, and projects designed to build skills in quantitative analysis of neural data. The curriculum covers modeling, data analysis, and machine learning applied to neuroscience.", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "understanding-oriented (explanation)" - ], - "description": "Neuromatch Academy offers intensive online computational neuroscience and deep learning courses through lectures, tutorials, and projects designed to build skills in quantitative analysis of neural data. The curriculum covers modeling, data analysis, and machine learning applied to neuroscience." + ] }, { "id": 57, @@ -2129,7 +2233,9 @@ "Advanced" ], "platform": [ - "NA" + "Mac", + "Windows", + "Linux" ], "keywords": [ "List of resources" @@ -2171,12 +2277,12 @@ "source": [ "Github Repo added by Charlotte Fraze" ], + "description": "Great resource", "alias_links": null, "notes": null, "quadrants": [ "information-oriented (reference)" - ], - "description": "Great resource" + ] }, { "id": 58, @@ -2186,39 +2292,25 @@ "course_name": "Andy's brain book", "url": "https://andysbrainbook.readthedocs.io/en/latest/", "course_length": "1+ weeks", - "level": null, - "platform": null, - "keywords": null, "instruction_medium": [ "blog post", "Hands-on tutorial / notebooks" ], - "open_dataset": true, - "last_updated": 2026, - "description": "Andy's Brain Book is a comprehensive, beginner-friendly online textbook covering neuroimaging analysis with major software packages including FSL, SPM, AFNI, and Freesurfer, using real datasets and step-by-step tutorials. It is widely used as an introductory reference for fMRI and structural MRI analysis.", - "level": [ - "Beginner", - "Intermediate" - ], - "platform": [ - "Mac", - "Windows", - "Linux" + "delivery": [ + "self-paced" ], - "keywords": [ - "fMRI", - "neuroimaging", - "FSL", - "SPM", - "AFNI", - "Freesurfer", - "tutorial", - "beginner", - "structural MRI", - "connectivity", - "tractography" + "language": [ + "English" ], + "assessment": false, + "open_dataset": true, "prerequisite": null, + "source": [ + "Andrew Jahn", + "University of Michigan" + ], + "last_updated": 2026, + "description": "Andy's Brain Book is a comprehensive, beginner-friendly online textbook covering neuroimaging analysis with major software packages including FSL, SPM, AFNI, and Freesurfer, using real datasets and step-by-step tutorials. It is widely used as an introductory reference for fMRI and structural MRI analysis.", "quadrants": [ "learning-oriented (tutorials)", "problem-oriented (how to guides)", @@ -2229,6 +2321,13 @@ "Python", "Matlab" ], + "neuroimaging_software": [ + "FSL", + "SPM", + "AFNI", + "Freesurfer", + "Multiple" + ], "imaging_modality": [ "Functional", "Structural", @@ -2236,12 +2335,27 @@ "Resting-State", "Task-based" ], - "neuroimaging_software": [ + "platform": [ + "Mac", + "Windows", + "Linux" + ], + "keywords": [ + "fMRI", + "neuroimaging", "FSL", "SPM", "AFNI", "Freesurfer", - "Multiple" + "tutorial", + "beginner", + "structural MRI", + "connectivity", + "tractography" + ], + "level": [ + "Beginner", + "Intermediate" ] }, { @@ -2269,9 +2383,16 @@ "open data" ], "course_length": "1+ weeks", - "instruction_medium": null, - "delivery": null, - "language": null, + "instruction_medium": [ + "video", + "Hands-on tutorial / notebooks" + ], + "delivery": [ + "Hybrid" + ], + "language": [ + "English" + ], "programming_language": [ "Python", "R", @@ -2287,23 +2408,26 @@ "DWI" ], "open_dataset": true, - "last_updated": null, + "last_updated": "2025", "functionality": null, - "assessment": null, + "assessment": true, "prerequisite": [ "Basic Python or R programming", "Introductory neuroimaging knowledge", "Familiarity with MRI data" ], - "source": null, + "source": [ + "ABCD-ReproNim", + "ReproNim" + ], + "description": "A comprehensive course on reproducible neuroimaging using the Adolescent Brain Cognitive Development (ABCD) dataset, covering data access, processing pipelines, and ReproNim reproducibility principles. Designed for researchers working with large-scale developmental neuroimaging data.", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "understanding-oriented (explanation)", "problem-oriented (how to guides)" - ], - "description": "A comprehensive course on reproducible neuroimaging using the Adolescent Brain Cognitive Development (ABCD) dataset, covering data access, processing pipelines, and ReproNim reproducibility principles. Designed for researchers working with large-scale developmental neuroimaging data." + ] }, { "id": 60, @@ -2326,9 +2450,16 @@ "course_length": [ "1+ weeks" ], - "instruction_medium": null, - "delivery": null, - "language": null, + "instruction_medium": [ + "video", + "website" + ], + "delivery": [ + "self-paced" + ], + "language": [ + "English" + ], "programming_language": [ "Python" ], @@ -2349,14 +2480,17 @@ "Basic Python programming", "Introductory machine learning concepts" ], - "source": null, + "source": [ + "ABCD-ReproNim", + "ReproNim" + ], + "description": "3 week machone learning course", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "problem-oriented (how to guides)" - ], - "description": "3 week machone learning course" + ] }, { "id": 61, @@ -2378,7 +2512,14 @@ "Best Practices", "Data Visualization" ], - "delivery": null, + "course_length": "1-4 hrs", + "instruction_medium": [ + "website", + "Hands-on tutorial / notebooks" + ], + "delivery": [ + "instructor" + ], "language": [ "English" ], @@ -2395,20 +2536,39 @@ "open_dataset": true, "last_updated": 2025, "functionality": null, - "assessment": null, + "assessment": false, "prerequisite": [ "Basic neuroimaging experience", "Familiarity with command-line tools", "Basic Python or shell scripting" ], - "source": null, + "source": [ + "Sina Mansour L.", + "OHBM 2025" + ], + "description": "Comprehensive website describing the necessity of reproducible research and how to achieve it (notebooks, visualisation)", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "problem-oriented (how to guides)", "understanding-oriented (explanation)" + ] + }, + { + "id": 62, + "course_name": "test course", + "platform": [ + "Mac" + ], + "instruction_medium": [ + "blog post" ], - "description": "Comprehensive website describing the necessity of reproducible research and how to achieve it (notebooks, visualisation)" + "delivery": [ + "instructor" + ], + "imaging_modality": [ + "Behavioral" + ] } ] \ No newline at end of file diff --git a/frontend/public/data/reproinventory_data.json b/frontend/public/data/reproinventory_data.json index 96c1b8a..58daf93 100644 --- a/frontend/public/data/reproinventory_data.json +++ b/frontend/public/data/reproinventory_data.json @@ -54,12 +54,12 @@ "Johanna Bayer", "Fellow-22" ], + "description": "A beginner-friendly course introducing Git and GitHub for version control and collaboration, covering online GitHub workflows and local machine setup with GitHub Desktop, progressing from basic concepts to managing merge conflicts.", "notes": null, "quadrants": [ "problem-oriented (how to guides)", "learning-oriented (tutorials)" - ], - "description": "A beginner-friendly course introducing Git and GitHub for version control and collaboration, covering online GitHub workflows and local machine setup with GitHub Desktop, progressing from basic concepts to managing merge conflicts." + ] }, { "id": 5, @@ -121,12 +121,12 @@ "Fellow-22", "UCSB" ], + "description": "JupyterHub no longer accessible. Need to link GitHubClassroom to GitHub (uclear if links work once you do that)", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)" - ], - "description": "JupyterHub no longer accessible. Need to link GitHubClassroom to GitHub (uclear if links work once you do that)" + ] }, { "id": 7, @@ -181,12 +181,12 @@ "Fellow-22", "Donders Institute" ], + "description": "Short slide deck, very clear", "alias_links": null, "notes": "link does not work for me (JB) can someone double check", "quadrants": [ "understanding-oriented (explanation)" - ], - "description": "Short slide deck, very clear" + ] }, { "id": 8, @@ -226,7 +226,8 @@ "NA" ], "imaging_modality": [ - "NA" + "EEG", + "MEG" ], "open_dataset": false, "last_updated": "2022", @@ -241,13 +242,13 @@ "Fellow-22", "Donders Institute" ], + "description": "Relatively quick overview - more just what is DataLad vs detailed how to use", "alias_links": null, "notes": null, "quadrants": [ "information-oriented (reference)", "understanding-oriented (explanation)" - ], - "description": "Relatively quick overview - more just what is DataLad vs detailed how to use" + ] }, { "id": 9, @@ -303,13 +304,13 @@ "Fellow-22", "Donders Institute" ], + "description": "Very short slide deck on GIT", "alias_links": null, "notes": null, "quadrants": [ "understanding-oriented (explanation)", "information-oriented (reference)" - ], - "description": "Very short slide deck on GIT" + ] }, { "id": 10, @@ -361,12 +362,12 @@ "Fellow-22", "Donders Institute" ], + "description": "Practical intro to bash and git", "alias_links": null, "notes": null, "quadrants": [ "understanding-oriented (explanation)" - ], - "description": "Practical intro to bash and git" + ] }, { "id": 11, @@ -431,12 +432,12 @@ "Celine Provins", "Fellow-22" ], + "description": "Focuses on QC in reference to MRIQC; has lots of big picture info about QC/QA in general", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)" - ], - "description": "Focuses on QC in reference to MRIQC; has lots of big picture info about QC/QA in general" + ] }, { "id": 16, @@ -489,12 +490,12 @@ "Avery Van De Water", "Fellow-22" ], + "description": "labeled as part 1 - unclear where part 2 is", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)" - ], - "description": "labeled as part 1 - unclear where part 2 is" + ] }, { "id": 18, @@ -508,7 +509,8 @@ "Beginner" ], "platform": [ - "NA" + "Mac", + "Linux" ], "keywords": [ "Pre-registration", @@ -528,13 +530,15 @@ "English" ], "programming_language": [ - "NA" + "Python", + "shell scripting" ], "neuroimaging_software": [ - "NA" + "FSL" ], "imaging_modality": [ - "NA" + "Functional", + "Structural" ], "open_dataset": false, "last_updated": "2021", @@ -548,13 +552,13 @@ "ReproNim", "Karolina Finc" ], + "description": "Some sections are under-developed", "alias_links": null, "notes": "Reproducible Neuroimaging, tutorial guide, for cog sci students audience", "quadrants": [ "learning-oriented (tutorials)", "information-oriented (reference)" - ], - "description": "Some sections are under-developed" + ] }, { "id": 21, @@ -567,7 +571,7 @@ "Beginner" ], "platform": [ - "NA" + "Jupyter" ], "keywords": [ "BIDS", @@ -612,13 +616,13 @@ "MIchael Joseph", "Fellow-20" ], + "description": "Basic Imaging Overview. Focus on BIDS", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "understanding-oriented (explanation)" - ], - "description": "Basic Imaging Overview. Focus on BIDS" + ] }, { "id": 22, @@ -632,7 +636,7 @@ "Beginner" ], "platform": [ - "NA" + "Jupyter" ], "keywords": [ "nilearn", @@ -676,13 +680,13 @@ "MIchael Joseph", "Fellow-20" ], + "description": "Tutorial on functional neuroimaging in Python", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "problem-oriented (how to guides)" - ], - "description": "Tutorial on functional neuroimaging in Python" + ] }, { "id": 23, @@ -695,7 +699,7 @@ "Beginner" ], "platform": [ - "NA" + "Jupyter" ], "keywords": [ "dMRI", @@ -708,7 +712,9 @@ "instruction_medium": [ "Hands-on tutorial / notebooks" ], - "delivery": null, + "delivery": [ + "self-paced" + ], "language": [ "English" ], @@ -734,13 +740,13 @@ "MIchael Joseph", "Fellow-20" ], + "description": "A Carpentries Incubator lesson introducing diffusion MRI concepts and data organization using BIDS, with hands-on analysis using Python-based tools like Dipy and Nibabel.", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "problem-oriented (how to guides)" - ], - "description": "A Carpentries Incubator lesson introducing diffusion MRI concepts and data organization using BIDS, with hands-on analysis using Python-based tools like Dipy and Nibabel." + ] }, { "id": 25, @@ -768,7 +774,9 @@ "instruction_medium": [ "notes" ], - "delivery": null, + "delivery": [ + "instructor" + ], "language": [ "English" ], @@ -779,9 +787,10 @@ "Multiple" ], "imaging_modality": [ - "NA" + "Functional", + "Structural" ], - "open_dataset": null, + "open_dataset": false, "last_updated": "2020", "functionality": null, "assessment": false, @@ -794,14 +803,14 @@ "Jennifer Legault", "Fellow-20" ], + "description": "example syllabus for hackathon/course", "alias_links": null, "notes": null, "quadrants": [ "understanding-oriented (explanation)", "learning-oriented (tutorials)", "information-oriented (reference)" - ], - "description": "example syllabus for hackathon/course" + ] }, { "id": 26, @@ -814,7 +823,9 @@ "Beginner" ], "platform": [ - "NA" + "Mac", + "Windows", + "Linux" ], "keywords": [ "Rehabilitation", @@ -825,7 +836,10 @@ "instruction_medium": [ "video" ], - "delivery": null, + "delivery": [ + "self-paced", + "instructor" + ], "language": [ "English" ], @@ -853,13 +867,13 @@ "Fellow-20", "ReproRehab" ], + "description": "Entire first year bootcamp videos online", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "understanding-oriented (explanation)" - ], - "description": "Entire first year bootcamp videos online" + ] }, { "id": 28, @@ -883,7 +897,9 @@ "instruction_medium": [ "Hands-on tutorial / notebooks" ], - "delivery": null, + "delivery": [ + "self-paced" + ], "language": [ "English" ], @@ -909,13 +925,13 @@ "Fellow-20", "Princeton" ], + "description": "Jupyter tutorials from the basics to advanced machine learning analyses on fMRI data", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "problem-oriented (how to guides)" - ], - "description": "Jupyter tutorials from the basics to advanced machine learning analyses on fMRI data" + ] }, { "id": 29, @@ -928,7 +944,8 @@ "Intermediate" ], "platform": [ - "NA" + "Mac", + "Linux" ], "keywords": [ "Syllabus", @@ -939,7 +956,9 @@ "instruction_medium": [ "lecture" ], - "delivery": null, + "delivery": [ + "instructor" + ], "language": [ "English" ], @@ -966,13 +985,13 @@ "Chris Rorden", "Fellow-20" ], + "description": "Syllabus for course on fMRI, including slides, from collection to inferencing", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "understanding-oriented (explanation)" - ], - "description": "Syllabus for course on fMRI, including slides, from collection to inferencing" + ] }, { "id": 30, @@ -985,7 +1004,9 @@ "Beginner" ], "platform": [ - "NA" + "Mac", + "Windows", + "Linux" ], "keywords": [ "BIDS", @@ -996,7 +1017,9 @@ "instruction_medium": [ "lecture" ], - "delivery": null, + "delivery": [ + "instructor" + ], "language": [ "English" ], @@ -1011,7 +1034,7 @@ "imaging_modality": [ "Functional" ], - "open_dataset": null, + "open_dataset": false, "last_updated": "NA", "functionality": null, "assessment": true, @@ -1024,13 +1047,13 @@ "Julie Schneider", "Fellow-20" ], + "description": "Syllabus for reproducible neuroimaging multi-week course", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "problem-oriented (how to guides)" - ], - "description": "Syllabus for reproducible neuroimaging multi-week course" + ] }, { "id": 31, @@ -1043,7 +1066,9 @@ "Beginner" ], "platform": [ - "NA" + "Mac", + "Windows", + "Linux" ], "keywords": [ "syllabus", @@ -1055,7 +1080,9 @@ "instruction_medium": [ "notes" ], - "delivery": null, + "delivery": [ + "self-paced" + ], "language": [ "English" ], @@ -1068,7 +1095,7 @@ "imaging_modality": [ "MRI" ], - "open_dataset": null, + "open_dataset": false, "last_updated": "2020", "functionality": null, "assessment": false, @@ -1079,13 +1106,13 @@ "source": [ "ReproNim" ], + "description": "syllabus for tutorial; details unclear. Might be unfinished.", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "information-oriented (reference)" - ], - "description": "syllabus for tutorial; details unclear. Might be unfinished." + ] }, { "id": 32, @@ -1099,7 +1126,9 @@ "Intermediate" ], "platform": [ - "NA" + "Mac", + "Windows", + "Linux" ], "keywords": [ "DataLad", @@ -1126,7 +1155,7 @@ "imaging_modality": [ "NA" ], - "open_dataset": null, + "open_dataset": false, "last_updated": "2024", "functionality": "2025", "assessment": false, @@ -1137,14 +1166,14 @@ "ReproNim", "Adina Wagner" ], + "description": "very good resource for data provenance", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "information-oriented (reference)", "problem-oriented (how to guides)" - ], - "description": "very good resource for data provenance" + ] }, { "id": 33, @@ -1159,7 +1188,9 @@ "Beginner" ], "platform": [ - "NA" + "Mac", + "Windows", + "Linux" ], "keywords": [ "AI", @@ -1169,7 +1200,9 @@ "instruction_medium": [ "video" ], - "delivery": null, + "delivery": [ + "self-paced" + ], "language": [ "English", "German" @@ -1183,7 +1216,7 @@ "imaging_modality": [ "NA" ], - "open_dataset": null, + "open_dataset": false, "last_updated": "2024", "functionality": null, "assessment": false, @@ -1191,13 +1224,13 @@ "source": [ "AI campus" ], + "description": "Nice videos and course material on AI", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "understanding-oriented (explanation)" - ], - "description": "Nice videos and course material on AI" + ] }, { "id": 34, @@ -1212,7 +1245,9 @@ "Beginner" ], "platform": [ - "NA" + "Mac", + "Windows", + "Linux" ], "keywords": [ "Datalad", @@ -1223,7 +1258,9 @@ "instruction_medium": [ "video" ], - "delivery": null, + "delivery": [ + "self-paced" + ], "language": [ "English" ], @@ -1246,13 +1283,13 @@ "Lennart Wittkuhn", "Adina Wagner" ], + "description": "Good video", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "understanding-oriented (explanation)" - ], - "description": "Good video" + ] }, { "id": 35, @@ -1265,7 +1302,8 @@ "Intermediate" ], "platform": [ - "NA" + "Mac", + "Linux" ], "keywords": [ "Datalad", @@ -1299,14 +1337,16 @@ "Basic Git", "Unix" ], - "source": null, + "source": [ + "Adina Wagner", + "Max Planck Institute" + ], "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "problem-oriented (how to guides)" - ], - "description": "Course outline for Data Lad Course" + ] }, { "id": 36, @@ -1321,7 +1361,9 @@ "Beginner" ], "platform": [ - "NA" + "Mac", + "Windows", + "Linux" ], "keywords": [ "Git", @@ -1331,7 +1373,10 @@ "instruction_medium": [ "notes" ], - "delivery": null, + "delivery": [ + "self-paced", + "instructor" + ], "language": [ "English" ], @@ -1344,7 +1389,7 @@ "imaging_modality": [ "NA" ], - "open_dataset": null, + "open_dataset": false, "last_updated": "2024", "functionality": null, "assessment": false, @@ -1353,13 +1398,13 @@ "ReproNim", "Lennart Wittkuhn" ], + "description": "An open-access online book that teaches version control using Git, designed for researchers with no prior experience. It covers core Git concepts and workflows through hands-on exercises and practical examples relevant to scientific work.", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "information-oriented (reference)" - ], - "description": "An open-access online book that teaches version control using Git, designed for researchers with no prior experience. It covers core Git concepts and workflows through hands-on exercises and practical examples relevant to scientific work." + ] }, { "id": 38, @@ -1374,7 +1419,8 @@ "Beginner" ], "platform": [ - "NA" + "Jupyter", + "Linux" ], "keywords": [ "Git", @@ -1387,7 +1433,9 @@ "instruction_medium": [ "lecture" ], - "delivery": null, + "delivery": [ + "instructor" + ], "language": [ "English" ], @@ -1411,13 +1459,13 @@ "ReproNim", "Xihe Xie" ], + "description": "Review of previous materials, full course", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "understanding-oriented (explanation)" - ], - "description": "Review of previous materials, full course" + ] }, { "id": 39, @@ -1431,7 +1479,8 @@ "Beginner" ], "platform": [ - "NA" + "Mac", + "Linux" ], "keywords": [ "Syllabus", @@ -1446,7 +1495,9 @@ "instruction_medium": [ "notes" ], - "delivery": null, + "delivery": [ + "instructor" + ], "language": [ "English" ], @@ -1459,7 +1510,7 @@ "imaging_modality": [ "MRI" ], - "open_dataset": null, + "open_dataset": true, "last_updated": "2019", "functionality": null, "assessment": false, @@ -1472,13 +1523,13 @@ "Michael Dayan", "Fellow-19" ], + "description": "Syllabus for ReproNim workshop", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "information-oriented (reference)" - ], - "description": "Syllabus for ReproNim workshop" + ] }, { "id": 40, @@ -1503,7 +1554,9 @@ "notes", "outline" ], - "delivery": null, + "delivery": [ + "instructor" + ], "language": [ "English" ], @@ -1516,7 +1569,7 @@ "imaging_modality": [ "MRI" ], - "open_dataset": null, + "open_dataset": false, "last_updated": "2019", "functionality": null, "assessment": false, @@ -1529,13 +1582,13 @@ "Aaron Kemp", "Fellow-19" ], + "description": "Syllabus for Research Imaging Informatics course. Overview of neuroimaging methods and basic processing", "alias_links": null, "notes": null, "quadrants": [ "information-oriented (reference)", "understanding-oriented (explanation)" - ], - "description": "Syllabus for Research Imaging Informatics course. Overview of neuroimaging methods and basic processing" + ] }, { "id": 43, @@ -1550,7 +1603,7 @@ "Intermediate" ], "platform": [ - "NA" + "Linux" ], "keywords": [ "DataLad", @@ -1561,7 +1614,9 @@ "instruction_medium": [ "Hands-on tutorial / notebooks" ], - "delivery": null, + "delivery": [ + "instructor" + ], "language": [ "English" ], @@ -1586,13 +1641,13 @@ "source": [ "ReproNim" ], + "description": "Syllabus for workshop that has been given", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "problem-oriented (how to guides)" - ], - "description": "Syllabus for workshop that has been given" + ] }, { "id": 46, @@ -1607,7 +1662,8 @@ "Beginner" ], "platform": [ - "NA" + "Mac", + "Linux" ], "keywords": [ "fMRI", @@ -1617,7 +1673,9 @@ "instruction_medium": [ "lecture" ], - "delivery": null, + "delivery": [ + "self-paced" + ], "language": [ "English" ], @@ -1643,12 +1701,12 @@ "ReproNim", "Princeton" ], + "description": "Very nice overview of different fMRI topics", "alias_links": null, "notes": null, "quadrants": [ "information-oriented (reference)" - ], - "description": "Very nice overview of different fMRI topics" + ] }, { "id": 47, @@ -1663,7 +1721,8 @@ "Beginner" ], "platform": [ - "NA" + "Mac", + "Linux" ], "keywords": [ "fMRI analysis", @@ -1674,20 +1733,22 @@ "instruction_medium": [ "lecture" ], - "delivery": null, + "delivery": [ + "instructor" + ], "language": [ "English" ], "programming_language": [ - "NA" + "shell scripting" ], "neuroimaging_software": [ - "NA" + "FSL" ], "imaging_modality": [ "Functional" ], - "open_dataset": null, + "open_dataset": false, "last_updated": "2019", "functionality": null, "assessment": false, @@ -1699,14 +1760,14 @@ "ReproNim", "Etienne Roesch" ], + "description": "Pretty good if you want to teach fMRI analysis from scratch", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "understanding-oriented (explanation)", "information-oriented (reference)" - ], - "description": "Pretty good if you want to teach fMRI analysis from scratch" + ] }, { "id": 50, @@ -1732,7 +1793,9 @@ "instruction_medium": [ "lecture" ], - "delivery": null, + "delivery": [ + "instructor" + ], "language": [ "English" ], @@ -1745,7 +1808,7 @@ "imaging_modality": [ "NA" ], - "open_dataset": null, + "open_dataset": false, "last_updated": "2019", "functionality": null, "assessment": false, @@ -1756,13 +1819,13 @@ "ReproNim", "Sebastien Tourbier" ], + "description": "Single presentation, good for an intro class to data management and data version control", "alias_links": null, "notes": null, "quadrants": [ "information-oriented (reference)", "understanding-oriented (explanation)" - ], - "description": "Single presentation, good for an intro class to data management and data version control" + ] }, { "id": 51, @@ -1786,7 +1849,10 @@ "instruction_medium": [ "Hands-on tutorial / notebooks" ], - "delivery": null, + "delivery": [ + "self-paced", + "instructor" + ], "language": [ "English" ], @@ -1807,13 +1873,13 @@ "source": [ "Carpentries" ], + "description": "If you want to teach carpentries use this tool - not only shell scripting, but also intro to R, Python and HPC", "alias_links": "https://github.com/jdkent/incf-fellow-jdkent/blob/gh-pages/index.md", "notes": null, "quadrants": [ "learning-oriented (tutorials)", "problem-oriented (how to guides)" - ], - "description": "If you want to teach carpentries use this tool - not only shell scripting, but also intro to R, Python and HPC" + ] }, { "id": 52, @@ -1828,7 +1894,8 @@ "Beginner" ], "platform": [ - "NA" + "Mac", + "Linux" ], "keywords": [ "Lesson plan" @@ -1837,7 +1904,9 @@ "instruction_medium": [ "reference" ], - "delivery": null, + "delivery": [ + "self-paced" + ], "language": [ "English" ], @@ -1859,13 +1928,13 @@ "ReproNim", "David Warren" ], + "description": "For internal usage", "alias_links": null, "notes": "Link to Github Importer broken", "quadrants": [ "information-oriented (reference)", "understanding-oriented (explanation)" - ], - "description": "For internal usage" + ] }, { "id": 53, @@ -1912,22 +1981,25 @@ "MRI" ], "open_dataset": true, - "last_updated": null, + "last_updated": "2024", "functionality": null, - "assessment": null, + "assessment": true, "prerequisite": [ "Basic Python", "Introductory statistics", "Basic neuroimaging knowledge" ], - "source": null, + "source": [ + "McGill University", + "NeuroDataScience" + ], + "description": "An introduction to machine learning concepts and methods in the context of neuroimaging data, covering supervised learning, model evaluation, and practical implementation in Python. Part of the QLS612 multi-week curriculum at McGill University.", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "understanding-oriented (explanation)" - ], - "description": "An introduction to machine learning concepts and methods in the context of neuroimaging data, covering supervised learning, model evaluation, and practical implementation in Python. Part of the QLS612 multi-week curriculum at McGill University." + ] }, { "id": 54, @@ -1955,10 +2027,18 @@ "Python", "version control" ], - "course_length": "NA", - "instruction_medium": null, - "delivery": null, - "language": null, + "course_length": "1+ weeks", + "instruction_medium": [ + "lecture", + "Hands-on tutorial / notebooks", + "website" + ], + "delivery": [ + "instructor" + ], + "language": [ + "English" + ], "programming_language": [ "Python", "shell scripting", @@ -1971,24 +2051,29 @@ "Multiple" ], "imaging_modality": [ - "NA" + "Structural", + "Functional", + "EEG", + "MEG" ], "open_dataset": true, - "last_updated": null, + "last_updated": "2022", "functionality": null, - "assessment": null, + "assessment": true, "prerequisite": [ "Basic Python programming", "Familiarity with neuroimaging concepts" ], - "source": null, + "source": [ + "Brainhack School" + ], + "description": "Brainhack School is an intensive, project-based training program run by a consortium of Canadian universities that teaches open and reproducible neuroscience. Participants work on collaborative projects while learning modern data science tools applied to neuroimaging.", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "problem-oriented (how to guides)" - ], - "description": "Brainhack School is an intensive, project-based training program run by a consortium of Canadian universities that teaches open and reproducible neuroscience. Participants work on collaborative projects while learning modern data science tools applied to neuroimaging." + ] }, { "id": 55, @@ -2018,10 +2103,17 @@ "summer institute", "collaborative" ], - "course_length": "NA", - "instruction_medium": null, - "delivery": null, - "language": null, + "course_length": "1+ weeks", + "instruction_medium": [ + "lecture", + "Hands-on tutorial / notebooks" + ], + "delivery": [ + "instructor" + ], + "language": [ + "English" + ], "programming_language": [ "Python", "R", @@ -2040,22 +2132,24 @@ "Resting-State" ], "open_dataset": true, - "last_updated": null, + "last_updated": "2026", "functionality": null, - "assessment": null, + "assessment": true, "prerequisite": [ "Basic Python or programming experience", "Graduate-level neuroscience or related field" ], - "source": null, + "source": [ + "University of Washington" + ], + "description": "NeuroHackademy is a summer institute at the University of Washington focused on data science and open neuroscience, combining lectures and hands-on tutorials covering neuroimaging analysis, machine learning, and reproducible research practices.", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "understanding-oriented (explanation)", "problem-oriented (how to guides)" - ], - "description": "NeuroHackademy is a summer institute at the University of Washington focused on data science and open neuroscience, combining lectures and hands-on tutorials covering neuroimaging analysis, machine learning, and reproducible research practices." + ] }, { "id": 56, @@ -2082,37 +2176,48 @@ "open science", "tutorials" ], - "course_length": "NA", - "instruction_medium": null, - "delivery": null, - "language": null, + "course_length": "1+ weeks", + "instruction_medium": [ + "lecture", + "Hands-on tutorial / notebooks" + ], + "delivery": [ + "instructor" + ], + "language": [ + "English" + ], "programming_language": [ "Python" ], - "neuroimaging_software": null, + "neuroimaging_software": [ + "NA" + ], "imaging_modality": [ "Functional", "Resting-State", "Behavioral" ], "open_dataset": true, - "last_updated": null, + "last_updated": "2024", "functionality": null, - "assessment": null, + "assessment": true, "prerequisite": [ "Linear algebra", "Basic calculus", "Python programming", "Introductory neuroscience" ], - "source": null, + "source": [ + "Neuromatch Academy" + ], + "description": "Neuromatch Academy offers intensive online computational neuroscience and deep learning courses through lectures, tutorials, and projects designed to build skills in quantitative analysis of neural data. The curriculum covers modeling, data analysis, and machine learning applied to neuroscience.", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "understanding-oriented (explanation)" - ], - "description": "Neuromatch Academy offers intensive online computational neuroscience and deep learning courses through lectures, tutorials, and projects designed to build skills in quantitative analysis of neural data. The curriculum covers modeling, data analysis, and machine learning applied to neuroscience." + ] }, { "id": 57, @@ -2129,7 +2234,9 @@ "Advanced" ], "platform": [ - "NA" + "Mac", + "Windows", + "Linux" ], "keywords": [ "List of resources" @@ -2171,12 +2278,12 @@ "source": [ "Github Repo added by Charlotte Fraze" ], + "description": "Great resource", "alias_links": null, "notes": null, "quadrants": [ "information-oriented (reference)" - ], - "description": "Great resource" + ] }, { "id": 58, @@ -2186,39 +2293,25 @@ "course_name": "Andy's brain book", "url": "https://andysbrainbook.readthedocs.io/en/latest/", "course_length": "1+ weeks", - "level": null, - "platform": null, - "keywords": null, "instruction_medium": [ "blog post", "Hands-on tutorial / notebooks" ], - "open_dataset": true, - "last_updated": 2026, - "description": "Andy's Brain Book is a comprehensive, beginner-friendly online textbook covering neuroimaging analysis with major software packages including FSL, SPM, AFNI, and Freesurfer, using real datasets and step-by-step tutorials. It is widely used as an introductory reference for fMRI and structural MRI analysis.", - "level": [ - "Beginner", - "Intermediate" - ], - "platform": [ - "Mac", - "Windows", - "Linux" + "delivery": [ + "self-paced" ], - "keywords": [ - "fMRI", - "neuroimaging", - "FSL", - "SPM", - "AFNI", - "Freesurfer", - "tutorial", - "beginner", - "structural MRI", - "connectivity", - "tractography" + "language": [ + "English" ], + "assessment": false, + "open_dataset": true, "prerequisite": null, + "source": [ + "Andrew Jahn", + "University of Michigan" + ], + "last_updated": 2026, + "description": "Andy's Brain Book is a comprehensive, beginner-friendly online textbook covering neuroimaging analysis with major software packages including FSL, SPM, AFNI, and Freesurfer, using real datasets and step-by-step tutorials. It is widely used as an introductory reference for fMRI and structural MRI analysis.", "quadrants": [ "learning-oriented (tutorials)", "problem-oriented (how to guides)", @@ -2229,6 +2322,13 @@ "Python", "Matlab" ], + "neuroimaging_software": [ + "FSL", + "SPM", + "AFNI", + "Freesurfer", + "Multiple" + ], "imaging_modality": [ "Functional", "Structural", @@ -2236,12 +2336,27 @@ "Resting-State", "Task-based" ], - "neuroimaging_software": [ + "platform": [ + "Mac", + "Windows", + "Linux" + ], + "keywords": [ + "fMRI", + "neuroimaging", "FSL", "SPM", "AFNI", "Freesurfer", - "Multiple" + "tutorial", + "beginner", + "structural MRI", + "connectivity", + "tractography" + ], + "level": [ + "Beginner", + "Intermediate" ] }, { @@ -2269,9 +2384,16 @@ "open data" ], "course_length": "1+ weeks", - "instruction_medium": null, - "delivery": null, - "language": null, + "instruction_medium": [ + "video", + "Hands-on tutorial / notebooks" + ], + "delivery": [ + "Hybrid" + ], + "language": [ + "English" + ], "programming_language": [ "Python", "R", @@ -2287,23 +2409,26 @@ "DWI" ], "open_dataset": true, - "last_updated": null, + "last_updated": "2025", "functionality": null, - "assessment": null, + "assessment": true, "prerequisite": [ "Basic Python or R programming", "Introductory neuroimaging knowledge", "Familiarity with MRI data" ], - "source": null, + "source": [ + "ABCD-ReproNim", + "ReproNim" + ], + "description": "A comprehensive course on reproducible neuroimaging using the Adolescent Brain Cognitive Development (ABCD) dataset, covering data access, processing pipelines, and ReproNim reproducibility principles. Designed for researchers working with large-scale developmental neuroimaging data.", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "understanding-oriented (explanation)", "problem-oriented (how to guides)" - ], - "description": "A comprehensive course on reproducible neuroimaging using the Adolescent Brain Cognitive Development (ABCD) dataset, covering data access, processing pipelines, and ReproNim reproducibility principles. Designed for researchers working with large-scale developmental neuroimaging data." + ] }, { "id": 60, @@ -2326,9 +2451,16 @@ "course_length": [ "1+ weeks" ], - "instruction_medium": null, - "delivery": null, - "language": null, + "instruction_medium": [ + "video", + "website" + ], + "delivery": [ + "self-paced" + ], + "language": [ + "English" + ], "programming_language": [ "Python" ], @@ -2349,14 +2481,17 @@ "Basic Python programming", "Introductory machine learning concepts" ], - "source": null, + "source": [ + "ABCD-ReproNim", + "ReproNim" + ], + "description": "3 week machone learning course", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "problem-oriented (how to guides)" - ], - "description": "3 week machone learning course" + ] }, { "id": 61, @@ -2378,7 +2513,14 @@ "Best Practices", "Data Visualization" ], - "delivery": null, + "course_length": "1-4 hrs", + "instruction_medium": [ + "website", + "Hands-on tutorial / notebooks" + ], + "delivery": [ + "instructor" + ], "language": [ "English" ], @@ -2395,20 +2537,39 @@ "open_dataset": true, "last_updated": 2025, "functionality": null, - "assessment": null, + "assessment": false, "prerequisite": [ "Basic neuroimaging experience", "Familiarity with command-line tools", "Basic Python or shell scripting" ], - "source": null, + "source": [ + "Sina Mansour L.", + "OHBM 2025" + ], + "description": "Comprehensive website describing the necessity of reproducible research and how to achieve it (notebooks, visualisation)", "alias_links": null, "notes": null, "quadrants": [ "learning-oriented (tutorials)", "problem-oriented (how to guides)", "understanding-oriented (explanation)" + ] + }, + { + "id": 62, + "course_name": "test course", + "platform": [ + "Mac" + ], + "instruction_medium": [ + "blog post" ], - "description": "Comprehensive website describing the necessity of reproducible research and how to achieve it (notebooks, visualisation)" + "delivery": [ + "instructor" + ], + "imaging_modality": [ + "Behavioral" + ] } ] \ No newline at end of file diff --git a/model/reproinventory_data.yaml b/model/reproinventory_data.yaml index aa70b07..6448b56 100644 --- a/model/reproinventory_data.yaml +++ b/model/reproinventory_data.yaml @@ -36,15 +36,14 @@ open_dataset: false last_updated: '2023' assessment: false - prerequisite: null + prerequisite: source: - ReproNim - Johanna Bayer - Fellow-22 - description: A beginner-friendly course introducing Git and GitHub for version control - and collaboration, covering online GitHub workflows and local machine setup with - GitHub Desktop, progressing from basic concepts to managing merge conflicts. - notes: null + description: A beginner-friendly course introducing Git and GitHub for version control and collaboration, covering online + GitHub workflows and local machine setup with GitHub Desktop, progressing from basic concepts to managing merge conflicts. + notes: quadrants: - problem-oriented (how to guides) - learning-oriented (tutorials) @@ -53,8 +52,8 @@ - CW - JB course_name: 'Data Science in Communication: Python and Reproducible Research' - url: 'GitHub - yibeichan/COMM160DS: COMM 160DS: Data Science in Communication: Python - and Reproducible Research (Spring 2023, University of California, Santa Barbara)' + url: 'GitHub - yibeichan/COMM160DS: COMM 160DS: Data Science in Communication: Python and Reproducible Research (Spring + 2023, University of California, Santa Barbara)' level: - Beginner platform: @@ -86,7 +85,7 @@ - NA open_dataset: true last_updated: '2023' - functionality: null + functionality: assessment: true prerequisite: - Basic Python @@ -96,10 +95,9 @@ - Yibei Chen - Fellow-22 - UCSB - description: JupyterHub no longer accessible. Need to link GitHubClassroom to GitHub - (uclear if links work once you do that) - alias_links: null - notes: null + description: JupyterHub no longer accessible. Need to link GitHubClassroom to GitHub (unclear if links work once you do that) + alias_links: + notes: quadrants: - learning-oriented (tutorials) - id: 7 @@ -108,7 +106,8 @@ - CF - JB course_name: Reproducible Data Management with DataLad - University of Munster 18/11/22 - url: https://onedrive.live.com/?authkey=%21AFsNiGzveqZ750s&id=86184EF59C004002%21416672&cid=86184EF59C004002&parId=root&parQt=sharedby&o=OneUp + url: + https://onedrive.live.com/?authkey=%21AFsNiGzveqZ750s&id=86184EF59C004002%21416672&cid=86184EF59C004002&parId=root&parQt=sharedby&o=OneUp level: - Beginner platform: @@ -133,7 +132,7 @@ - NA open_dataset: false last_updated: '2022' - functionality: null + functionality: assessment: false prerequisite: - Basic Git @@ -143,7 +142,7 @@ - Fellow-22 - Donders Institute description: Short slide deck, very clear - alias_links: null + alias_links: notes: link does not work for me (JB) can someone double check quadrants: - understanding-oriented (explanation) @@ -152,7 +151,8 @@ - CW - CF course_name: Reproducible Data Management with DataLad - MEG/EEG Meeting DCCN 2022-11-28 - url: https://onedrive.live.com/?authkey=%21AANsp4ZosaSOK2o&id=86184EF59C004002%21416988&cid=86184EF59C004002&parId=root&parQt=sharedby&o=OneUp + url: + https://onedrive.live.com/?authkey=%21AANsp4ZosaSOK2o&id=86184EF59C004002%21416988&cid=86184EF59C004002&parId=root&parQt=sharedby&o=OneUp level: - Beginner platform: @@ -175,10 +175,11 @@ neuroimaging_software: - NA imaging_modality: - - NA + - EEG + - MEG open_dataset: false last_updated: '2022' - functionality: null + functionality: assessment: false prerequisite: - Basic Git @@ -187,10 +188,9 @@ - Julian Kosciessa - Fellow-22 - Donders Institute - description: Relatively quick overview - more just what is DataLad vs detailed how - to use - alias_links: null - notes: null + description: Relatively quick overview - more just what is DataLad vs detailed how to use + alias_links: + notes: quadrants: - information-oriented (reference) - understanding-oriented (explanation) @@ -200,7 +200,8 @@ - CF - JB course_name: Reusable (big) data management with DataLad - Donders Nexus - url: https://1drv.ms/b/s!AgJAAJz1ThiGms0Vdo-WifbI8FKPOA?e%3DourGa2&sa=D&source=editors&ust=1718948936539613&usg=AOvVaw0nBhMBkdri9NRmpgP0Wfu1 + url: + https://1drv.ms/b/s!AgJAAJz1ThiGms0Vdo-WifbI8FKPOA?e%3DourGa2&sa=D&source=editors&ust=1718948936539613&usg=AOvVaw0nBhMBkdri9NRmpgP0Wfu1 level: - Beginner platform: @@ -226,7 +227,7 @@ - NA open_dataset: false last_updated: '2022' - functionality: null + functionality: assessment: false prerequisite: - Basic Git @@ -236,8 +237,8 @@ - Fellow-22 - Donders Institute description: Very short slide deck on GIT - alias_links: null - notes: null + alias_links: + notes: quadrants: - understanding-oriented (explanation) - information-oriented (reference) @@ -271,17 +272,17 @@ - NA open_dataset: false last_updated: '2023' - functionality: null + functionality: assessment: false - prerequisite: null + prerequisite: source: - ReproNim - Julian Kosciessa - Fellow-22 - Donders Institute description: Practical intro to bash and git - alias_links: null - notes: null + alias_links: + notes: quadrants: - understanding-oriented (explanation) - id: 11 @@ -324,7 +325,7 @@ - MRI open_dataset: true last_updated: '2022' - functionality: null + functionality: assessment: true prerequisite: - MRI preprocessing @@ -334,10 +335,9 @@ - ReproNim - Celine Provins - Fellow-22 - description: Focuses on QC in reference to MRIQC; has lots of big picture info about - QC/QA in general - alias_links: null - notes: null + description: Focuses on QC in reference to MRIQC; has lots of big picture info about QC/QA in general + alias_links: + notes: quadrants: - learning-oriented (tutorials) - id: 16 @@ -370,7 +370,7 @@ - NA open_dataset: false last_updated: '2022' - functionality: null + functionality: assessment: false prerequisite: - Shell scripting @@ -379,8 +379,8 @@ - Avery Van De Water - Fellow-22 description: labeled as part 1 - unclear where part 2 is - alias_links: null - notes: null + alias_links: + notes: quadrants: - learning-oriented (tutorials) - id: 18 @@ -392,7 +392,8 @@ level: - Beginner platform: - - NA + - Mac + - Linux keywords: - Pre-registration - Plan @@ -407,11 +408,13 @@ language: - English programming_language: - - NA + - Python + - shell scripting neuroimaging_software: - - NA + - FSL imaging_modality: - - NA + - Functional + - Structural open_dataset: false last_updated: '2021' functionality: NA @@ -423,7 +426,7 @@ - ReproNim - Karolina Finc description: Some sections are under-developed - alias_links: null + alias_links: notes: Reproducible Neuroimaging, tutorial guide, for cog sci students audience quadrants: - learning-oriented (tutorials) @@ -436,7 +439,7 @@ level: - Beginner platform: - - NA + - Jupyter keywords: - BIDS - DataLad @@ -462,7 +465,7 @@ - MRI open_dataset: true last_updated: '2024' - functionality: null + functionality: assessment: true prerequisite: - Unix @@ -472,8 +475,8 @@ - MIchael Joseph - Fellow-20 description: Basic Imaging Overview. Focus on BIDS - alias_links: null - notes: null + alias_links: + notes: quadrants: - learning-oriented (tutorials) - understanding-oriented (explanation) @@ -486,7 +489,7 @@ level: - Beginner platform: - - NA + - Jupyter keywords: - nilearn - resting state @@ -512,7 +515,7 @@ - Functional open_dataset: true last_updated: '2024' - functionality: null + functionality: assessment: true prerequisite: - Python @@ -521,8 +524,8 @@ - MIchael Joseph - Fellow-20 description: Tutorial on functional neuroimaging in Python - alias_links: null - notes: null + alias_links: + notes: quadrants: - learning-oriented (tutorials) - problem-oriented (how to guides) @@ -534,7 +537,7 @@ level: - Beginner platform: - - NA + - Jupyter keywords: - dMRI - carpentries @@ -544,7 +547,8 @@ course_length: 1 day instruction_medium: - Hands-on tutorial / notebooks - delivery: null + delivery: + - self-paced language: - English programming_language: @@ -555,7 +559,7 @@ - DWI open_dataset: true last_updated: '2024' - functionality: null + functionality: assessment: true prerequisite: - Unix @@ -564,11 +568,10 @@ - ReproNim - MIchael Joseph - Fellow-20 - description: A Carpentries Incubator lesson introducing diffusion MRI concepts and - data organization using BIDS, with hands-on analysis using Python-based tools - like Dipy and Nibabel. - alias_links: null - notes: null + description: A Carpentries Incubator lesson introducing diffusion MRI concepts and data organization using BIDS, with hands-on + analysis using Python-based tools like Dipy and Nibabel. + alias_links: + notes: quadrants: - learning-oriented (tutorials) - problem-oriented (how to guides) @@ -592,7 +595,8 @@ course_length: 1 week instruction_medium: - notes - delivery: null + delivery: + - instructor language: - English programming_language: @@ -600,10 +604,11 @@ neuroimaging_software: - Multiple imaging_modality: - - NA - open_dataset: null + - Functional + - Structural + open_dataset: false last_updated: '2020' - functionality: null + functionality: assessment: false prerequisite: - Unix @@ -613,8 +618,8 @@ - Jennifer Legault - Fellow-20 description: example syllabus for hackathon/course - alias_links: null - notes: null + alias_links: + notes: quadrants: - understanding-oriented (explanation) - learning-oriented (tutorials) @@ -627,7 +632,9 @@ level: - Beginner platform: - - NA + - Mac + - Windows + - Linux keywords: - Rehabilitation - data sharing @@ -635,7 +642,9 @@ course_length: 1+ weeks instruction_medium: - video - delivery: null + delivery: + - self-paced + - instructor language: - English programming_language: @@ -647,7 +656,7 @@ - NA open_dataset: true last_updated: '2023' - functionality: null + functionality: assessment: false prerequisite: - Basic statistics @@ -658,8 +667,8 @@ - Fellow-20 - ReproRehab description: Entire first year bootcamp videos online - alias_links: null - notes: null + alias_links: + notes: quadrants: - learning-oriented (tutorials) - understanding-oriented (explanation) @@ -679,7 +688,8 @@ course_length: 1+ weeks instruction_medium: - Hands-on tutorial / notebooks - delivery: null + delivery: + - self-paced language: - English programming_language: @@ -690,7 +700,7 @@ - Functional open_dataset: true last_updated: '2020' - functionality: null + functionality: assessment: false prerequisite: - basic programming @@ -699,10 +709,9 @@ - Elizabeth McDevitt - Fellow-20 - Princeton - description: Jupyter tutorials from the basics to advanced machine learning analyses - on fMRI data - alias_links: null - notes: null + description: Jupyter tutorials from the basics to advanced machine learning analyses on fMRI data + alias_links: + notes: quadrants: - learning-oriented (tutorials) - problem-oriented (how to guides) @@ -714,7 +723,8 @@ level: - Intermediate platform: - - NA + - Mac + - Linux keywords: - Syllabus - MRI @@ -722,7 +732,8 @@ course_length: 1+ weeks instruction_medium: - lecture - delivery: null + delivery: + - instructor language: - English programming_language: @@ -734,7 +745,7 @@ - Functional open_dataset: true last_updated: '2020' - functionality: null + functionality: assessment: true prerequisite: - Basic neuroscience knowledge @@ -744,8 +755,8 @@ - Chris Rorden - Fellow-20 description: Syllabus for course on fMRI, including slides, from collection to inferencing - alias_links: null - notes: null + alias_links: + notes: quadrants: - learning-oriented (tutorials) - understanding-oriented (explanation) @@ -757,7 +768,9 @@ level: - Beginner platform: - - NA + - Mac + - Windows + - Linux keywords: - BIDS - fMRI @@ -765,7 +778,8 @@ course_length: 1+ weeks instruction_medium: - lecture - delivery: null + delivery: + - instructor language: - English programming_language: @@ -776,9 +790,9 @@ - Multiple imaging_modality: - Functional - open_dataset: null + open_dataset: false last_updated: NA - functionality: null + functionality: assessment: true prerequisite: - moderate programming experience @@ -788,8 +802,8 @@ - Julie Schneider - Fellow-20 description: Syllabus for reproducible neuroimaging multi-week course - alias_links: null - notes: null + alias_links: + notes: quadrants: - learning-oriented (tutorials) - problem-oriented (how to guides) @@ -801,7 +815,9 @@ level: - Beginner platform: - - NA + - Mac + - Windows + - Linux keywords: - syllabus - BIDS @@ -810,7 +826,8 @@ course_length: 1-3 days instruction_medium: - notes - delivery: null + delivery: + - self-paced language: - English programming_language: @@ -819,9 +836,9 @@ - Freesurfer imaging_modality: - MRI - open_dataset: null + open_dataset: false last_updated: '2020' - functionality: null + functionality: assessment: false prerequisite: - UNIX @@ -829,8 +846,8 @@ source: - ReproNim description: syllabus for tutorial; details unclear. Might be unfinished. - alias_links: null - notes: null + alias_links: + notes: quadrants: - learning-oriented (tutorials) - information-oriented (reference) @@ -843,7 +860,9 @@ level: - Intermediate platform: - - NA + - Mac + - Windows + - Linux keywords: - DataLad - version control @@ -862,7 +881,7 @@ - NA imaging_modality: - NA - open_dataset: null + open_dataset: false last_updated: '2024' functionality: '2025' assessment: false @@ -872,8 +891,8 @@ - ReproNim - Adina Wagner description: very good resource for data provenance - alias_links: null - notes: null + alias_links: + notes: quadrants: - learning-oriented (tutorials) - information-oriented (reference) @@ -888,14 +907,17 @@ level: - Beginner platform: - - NA + - Mac + - Windows + - Linux keywords: - AI - chatbots course_length: 1+ weeks instruction_medium: - video - delivery: null + delivery: + - self-paced language: - English - German @@ -905,16 +927,16 @@ - NA imaging_modality: - NA - open_dataset: null + open_dataset: false last_updated: '2024' - functionality: null + functionality: assessment: false - prerequisite: null + prerequisite: source: - AI campus description: Nice videos and course material on AI - alias_links: null - notes: null + alias_links: + notes: quadrants: - learning-oriented (tutorials) - understanding-oriented (explanation) @@ -928,7 +950,9 @@ level: - Beginner platform: - - NA + - Mac + - Windows + - Linux keywords: - Datalad - Version Control @@ -936,7 +960,8 @@ course_length: 1-4 hrs instruction_medium: - video - delivery: null + delivery: + - self-paced language: - English programming_language: @@ -947,16 +972,16 @@ - NA open_dataset: false last_updated: '2021' - functionality: null + functionality: assessment: false - prerequisite: null + prerequisite: source: - ReproNim - Lennart Wittkuhn - Adina Wagner description: Good video - alias_links: null - notes: null + alias_links: + notes: quadrants: - learning-oriented (tutorials) - understanding-oriented (explanation) @@ -968,7 +993,8 @@ level: - Intermediate platform: - - NA + - Mac + - Linux keywords: - Datalad - MPI @@ -988,15 +1014,17 @@ - NA open_dataset: false last_updated: '2020' - functionality: null + functionality: assessment: false prerequisite: - Basic Git - Unix - source: null - description: Course outline for Data Lad Course - alias_links: null - notes: null + source: + - Adina Wagner + - Max Planck Institute + description: Course outline for Data Lad Course + alias_links: + notes: quadrants: - learning-oriented (tutorials) - problem-oriented (how to guides) @@ -1010,14 +1038,18 @@ level: - Beginner platform: - - NA + - Mac + - Windows + - Linux keywords: - Git - Version Control course_length: 1+ weeks instruction_medium: - notes - delivery: null + delivery: + - self-paced + - instructor language: - English programming_language: @@ -1026,20 +1058,18 @@ - NA imaging_modality: - NA - open_dataset: null + open_dataset: false last_updated: '2024' - functionality: null + functionality: assessment: false - prerequisite: null + prerequisite: source: - ReproNim - Lennart Wittkuhn - description: An open-access online book that teaches version control using Git, - designed for researchers with no prior experience. It covers core Git concepts - and workflows through hands-on exercises and practical examples relevant to scientific - work. - alias_links: null - notes: null + description: An open-access online book that teaches version control using Git, designed for researchers with no prior experience. + It covers core Git concepts and workflows through hands-on exercises and practical examples relevant to scientific work. + alias_links: + notes: quadrants: - learning-oriented (tutorials) - information-oriented (reference) @@ -1053,7 +1083,8 @@ level: - Beginner platform: - - NA + - Jupyter + - Linux keywords: - Git - Reproducibility @@ -1063,7 +1094,8 @@ course_length: 1+ weeks instruction_medium: - lecture - delivery: null + delivery: + - instructor language: - English programming_language: @@ -1074,7 +1106,7 @@ - NA open_dataset: true last_updated: '2021' - functionality: null + functionality: assessment: false prerequisite: - Basic familiarity with Python recommended @@ -1082,8 +1114,8 @@ - ReproNim - Xihe Xie description: Review of previous materials, full course - alias_links: null - notes: null + alias_links: + notes: quadrants: - learning-oriented (tutorials) - understanding-oriented (explanation) @@ -1096,7 +1128,8 @@ level: - Beginner platform: - - NA + - Mac + - Linux keywords: - Syllabus - shell scripting @@ -1108,7 +1141,8 @@ course_length: 1-3 days instruction_medium: - notes - delivery: null + delivery: + - instructor language: - English programming_language: @@ -1117,9 +1151,9 @@ - Python imaging_modality: - MRI - open_dataset: null + open_dataset: true last_updated: '2019' - functionality: null + functionality: assessment: false prerequisite: - Basic Python @@ -1129,8 +1163,8 @@ - Michael Dayan - Fellow-19 description: Syllabus for ReproNim workshop - alias_links: null - notes: null + alias_links: + notes: quadrants: - learning-oriented (tutorials) - information-oriented (reference) @@ -1151,7 +1185,8 @@ instruction_medium: - notes - outline - delivery: null + delivery: + - instructor language: - English programming_language: @@ -1160,9 +1195,9 @@ - NA imaging_modality: - MRI - open_dataset: null + open_dataset: false last_updated: '2019' - functionality: null + functionality: assessment: false prerequisite: - Computational Methods @@ -1171,10 +1206,9 @@ - ReproNim - Aaron Kemp - Fellow-19 - description: Syllabus for Research Imaging Informatics course. Overview of neuroimaging - methods and basic processing - alias_links: null - notes: null + description: Syllabus for Research Imaging Informatics course. Overview of neuroimaging methods and basic processing + alias_links: + notes: quadrants: - information-oriented (reference) - understanding-oriented (explanation) @@ -1188,7 +1222,7 @@ level: - Intermediate platform: - - NA + - Linux keywords: - DataLad - Boutiques @@ -1196,7 +1230,8 @@ course_length: 1-3 days instruction_medium: - Hands-on tutorial / notebooks - delivery: null + delivery: + - instructor language: - English programming_language: @@ -1207,7 +1242,7 @@ - NA open_dataset: false last_updated: '2020' - functionality: null + functionality: assessment: true prerequisite: - Basic Python @@ -1216,8 +1251,8 @@ source: - ReproNim description: Syllabus for workshop that has been given - alias_links: null - notes: null + alias_links: + notes: quadrants: - learning-oriented (tutorials) - problem-oriented (how to guides) @@ -1231,14 +1266,16 @@ level: - Beginner platform: - - NA + - Mac + - Linux keywords: - fMRI - Multivariate analysis course_length: 1+ weeks instruction_medium: - lecture - delivery: null + delivery: + - self-paced language: - English programming_language: @@ -1250,7 +1287,7 @@ - Functional open_dataset: true last_updated: '2021' - functionality: null + functionality: assessment: false prerequisite: - Basic familiarity with neuroimaging concepts @@ -1259,8 +1296,8 @@ - ReproNim - Princeton description: Very nice overview of different fMRI topics - alias_links: null - notes: null + alias_links: + notes: quadrants: - information-oriented (reference) - id: 47 @@ -1273,7 +1310,8 @@ level: - Beginner platform: - - NA + - Mac + - Linux keywords: - fMRI analysis - clinical @@ -1281,18 +1319,19 @@ course_length: 1 week instruction_medium: - lecture - delivery: null + delivery: + - instructor language: - English programming_language: - - NA + - shell scripting neuroimaging_software: - - NA + - FSL imaging_modality: - Functional - open_dataset: null + open_dataset: false last_updated: '2019' - functionality: null + functionality: assessment: false prerequisite: - Basic MRI knowledge @@ -1301,8 +1340,8 @@ - ReproNim - Etienne Roesch description: Pretty good if you want to teach fMRI analysis from scratch - alias_links: null - notes: null + alias_links: + notes: quadrants: - learning-oriented (tutorials) - understanding-oriented (explanation) @@ -1325,7 +1364,8 @@ course_length: 1-4 hrs instruction_medium: - lecture - delivery: null + delivery: + - instructor language: - English programming_language: @@ -1334,19 +1374,18 @@ - NA imaging_modality: - NA - open_dataset: null + open_dataset: false last_updated: '2019' - functionality: null + functionality: assessment: false prerequisite: - Basic neuroimaging knowledge source: - ReproNim - Sebastien Tourbier - description: Single presentation, good for an intro class to data management and - data version control - alias_links: null - notes: null + description: Single presentation, good for an intro class to data management and data version control + alias_links: + notes: quadrants: - information-oriented (reference) - understanding-oriented (explanation) @@ -1366,7 +1405,9 @@ course_length: 1+ weeks instruction_medium: - Hands-on tutorial / notebooks - delivery: null + delivery: + - self-paced + - instructor language: - English programming_language: @@ -1377,15 +1418,15 @@ - NA open_dataset: false last_updated: '2024' - functionality: null + functionality: assessment: false - prerequisite: null + prerequisite: source: - Carpentries - description: If you want to teach carpentries use this tool - not only shell scripting, - but also intro to R, Python and HPC + description: If you want to teach carpentries use this tool - not only shell scripting, but also intro to R, Python and + HPC alias_links: https://github.com/jdkent/incf-fellow-jdkent/blob/gh-pages/index.md - notes: null + notes: quadrants: - learning-oriented (tutorials) - problem-oriented (how to guides) @@ -1399,13 +1440,15 @@ level: - Beginner platform: - - NA + - Mac + - Linux keywords: - Lesson plan course_length: <1 hr instruction_medium: - reference - delivery: null + delivery: + - self-paced language: - English programming_language: @@ -1416,14 +1459,14 @@ - NA open_dataset: false last_updated: NA - functionality: null + functionality: assessment: false - prerequisite: null + prerequisite: source: - ReproNim - David Warren description: For internal usage - alias_links: null + alias_links: notes: Link to Github Importer broken quadrants: - information-oriented (reference) @@ -1462,19 +1505,21 @@ imaging_modality: - MRI open_dataset: true - last_updated: null - functionality: null - assessment: null + last_updated: '2024' + functionality: + assessment: true prerequisite: - Basic Python - Introductory statistics - Basic neuroimaging knowledge - source: null - description: An introduction to machine learning concepts and methods in the context - of neuroimaging data, covering supervised learning, model evaluation, and practical - implementation in Python. Part of the QLS612 multi-week curriculum at McGill University. - alias_links: null - notes: null + source: + - McGill University + - NeuroDataScience + description: An introduction to machine learning concepts and methods in the context of neuroimaging data, covering supervised + learning, model evaluation, and practical implementation in Python. Part of the QLS612 multi-week curriculum at McGill + University. + alias_links: + notes: quadrants: - learning-oriented (tutorials) - understanding-oriented (explanation) @@ -1499,10 +1544,15 @@ - collaboration - Python - version control - course_length: NA - instruction_medium: null - delivery: null - language: null + course_length: 1+ weeks + instruction_medium: + - lecture + - Hands-on tutorial / notebooks + - website + delivery: + - instructor + language: + - English programming_language: - Python - shell scripting @@ -1513,21 +1563,24 @@ - Python - Multiple imaging_modality: - - NA + - Structural + - Functional + - EEG + - MEG open_dataset: true - last_updated: null - functionality: null - assessment: null + last_updated: '2022' + functionality: + assessment: true prerequisite: - Basic Python programming - Familiarity with neuroimaging concepts - source: null - description: Brainhack School is an intensive, project-based training program run - by a consortium of Canadian universities that teaches open and reproducible neuroscience. - Participants work on collaborative projects while learning modern data science - tools applied to neuroimaging. - alias_links: null - notes: null + source: + - Brainhack School + description: Brainhack School is an intensive, project-based training program run by a consortium of Canadian universities + that teaches open and reproducible neuroscience. Participants work on collaborative projects while learning modern data + science tools applied to neuroimaging. + alias_links: + notes: quadrants: - learning-oriented (tutorials) - problem-oriented (how to guides) @@ -1554,10 +1607,14 @@ - Python - summer institute - collaborative - course_length: NA - instruction_medium: null - delivery: null - language: null + course_length: 1+ weeks + instruction_medium: + - lecture + - Hands-on tutorial / notebooks + delivery: + - instructor + language: + - English programming_language: - Python - R @@ -1573,19 +1630,19 @@ - Structural - Resting-State open_dataset: true - last_updated: null - functionality: null - assessment: null + last_updated: '2026' + functionality: + assessment: true prerequisite: - Basic Python or programming experience - Graduate-level neuroscience or related field - source: null - description: NeuroHackademy is a summer institute at the University of Washington - focused on data science and open neuroscience, combining lectures and hands-on - tutorials covering neuroimaging analysis, machine learning, and reproducible research + source: + - University of Washington + description: NeuroHackademy is a summer institute at the University of Washington focused on data science and open neuroscience, + combining lectures and hands-on tutorials covering neuroimaging analysis, machine learning, and reproducible research practices. - alias_links: null - notes: null + alias_links: + notes: quadrants: - learning-oriented (tutorials) - understanding-oriented (explanation) @@ -1610,33 +1667,38 @@ - online course - open science - tutorials - course_length: NA - instruction_medium: null - delivery: null - language: null + course_length: 1+ weeks + instruction_medium: + - lecture + - Hands-on tutorial / notebooks + delivery: + - instructor + language: + - English programming_language: - Python - neuroimaging_software: null + neuroimaging_software: + - NA imaging_modality: - Functional - Resting-State - Behavioral open_dataset: true - last_updated: null - functionality: null - assessment: null + last_updated: '2024' + functionality: + assessment: true prerequisite: - Linear algebra - Basic calculus - Python programming - Introductory neuroscience - source: null - description: Neuromatch Academy offers intensive online computational neuroscience - and deep learning courses through lectures, tutorials, and projects designed to - build skills in quantitative analysis of neural data. The curriculum covers modeling, + source: + - Neuromatch Academy + description: Neuromatch Academy offers intensive online computational neuroscience and deep learning courses through lectures, + tutorials, and projects designed to build skills in quantitative analysis of neural data. The curriculum covers modeling, data analysis, and machine learning applied to neuroscience. - alias_links: null - notes: null + alias_links: + notes: quadrants: - learning-oriented (tutorials) - understanding-oriented (explanation) @@ -1652,7 +1714,9 @@ - Intermediate - Advanced platform: - - NA + - Mac + - Windows + - Linux keywords: - List of resources course_length: 1+ weeks @@ -1682,12 +1746,12 @@ last_updated: '2024' functionality: '2024' assessment: false - prerequisite: null + prerequisite: source: - Github Repo added by Charlotte Fraze description: Great resource - alias_links: null - notes: null + alias_links: + notes: quadrants: - information-oriented (reference) - id: 58 @@ -1696,18 +1760,23 @@ course_name: Andy's brain book url: https://andysbrainbook.readthedocs.io/en/latest/ course_length: 1+ weeks - level: null - platform: null - keywords: null instruction_medium: - blog post - Hands-on tutorial / notebooks + delivery: + - self-paced + language: + - English + assessment: false open_dataset: true - last_updated: 2026 - description: Andy's Brain Book is a comprehensive, beginner-friendly online textbook - covering neuroimaging analysis with major software packages including FSL, SPM, - AFNI, and Freesurfer, using real datasets and step-by-step tutorials. It is widely - used as an introductory reference for fMRI and structural MRI analysis. + prerequisite: + source: + - Andrew Jahn + - University of Michigan + last_updated: '2026' + description: Andy's Brain Book is a comprehensive, beginner-friendly online textbook covering neuroimaging analysis with + major software packages including FSL, SPM, AFNI, and Freesurfer, using real datasets and step-by-step tutorials. It is + widely used as an introductory reference for fMRI and structural MRI analysis. quadrants: - learning-oriented (tutorials) - problem-oriented (how to guides) @@ -1768,9 +1837,13 @@ - open data course_length: 1+ weeks - instruction_medium: null - delivery: null - language: null + instruction_medium: + - video + - Hands-on tutorial / notebooks + delivery: + - Hybrid + language: + - English programming_language: - Python - R @@ -1783,14 +1856,16 @@ - Resting-State - DWI open_dataset: true - last_updated: null + last_updated: '2025' functionality: null - assessment: null + assessment: true prerequisite: - Basic Python or R programming - Introductory neuroimaging knowledge - Familiarity with MRI data - source: null + source: + - ABCD-ReproNim + - ReproNim description: A comprehensive course on reproducible neuroimaging using the Adolescent Brain Cognitive Development (ABCD) dataset, covering data access, processing pipelines, and ReproNim reproducibility principles. Designed for researchers working with @@ -1816,9 +1891,13 @@ - Machine Learning course_length: - 1+ weeks - instruction_medium: null - delivery: null - language: null + instruction_medium: + - video + - website + delivery: + - self-paced + language: + - English programming_language: - Python neuroimaging_software: @@ -1835,8 +1914,10 @@ - ABCD ReproNim course or equivalent - Basic Python programming - Introductory machine learning concepts - source: null - description: 3 week machone learning course + source: + - ABCD-ReproNim + - ReproNim + description: 3 week machine learning course alias_links: null notes: null quadrants: @@ -1857,9 +1938,12 @@ - Reproducible Pipelines - Best Practices - Data Visualization - course_length: null - instruction_medium: null - delivery: null + course_length: 1-4 hrs + instruction_medium: + - website + - Hands-on tutorial / notebooks + delivery: + - instructor language: - English programming_language: @@ -1872,14 +1956,15 @@ open_dataset: true last_updated: 2025 functionality: null - assessment: null + assessment: false prerequisite: - Basic neuroimaging experience - Familiarity with command-line tools - Basic Python or shell scripting - source: null - description: Comprehensive website describing the necessity of reproducible research - and how to achieve it (notebooks, visualisation) + source: + - Sina Mansour L. + - OHBM 2025 + description: Comprehensive website describing the necessity of reproducible research and how to achieve it (notebooks, visualisation) alias_links: null notes: null quadrants: