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Halchenko", + "profile": "http://www.onerussian.com" + }, + { + "contributions": [ + "doc" + ], + "login": "yoni_ashar", + "name": "Yoni Ashar" + }, + { + "contributions": [ + "code" + ], + "login": "yuan_wang", + "name": "Yuan Wang" + }, + { + "contributions": [ + "doc" + ], + "login": "zachary_michael", + "name": "Zachary Michael" + }, + { + "avatar_url": [ + "https://avatars.githubusercontent.com/u/39155887?v=4" + ], + "contributions": [ + "code" + ], + "login": "ezemikulan", + "name": "ezemikulan", + "profile": "https://github.com/ezemikulan" + }, + { + "avatar_url": [ + "https://avatars.githubusercontent.com/u/9729281?v=4" + ], + "contributions": [ + "code" + ], + "login": "josator2", + "name": "josator2", + "profile": "https://github.com/josator2" + }, + { + "avatar_url": [ + "https://avatars.githubusercontent.com/u/8000597?v=4" + ], + "contributions": [ + "code" + ], + "login": "monkeyman192", + "name": "monkeyman192", + "profile": "https://github.com/monkeyman192" + }, + { + "contributions": [ + "data", + "code" + ], + "login": "étienne_bergeron", + "name": "Étienne Bergeron" + } + ], + "contributorsPerLine": 7 +} diff --git a/.circleci/config.yml b/.circleci/config.yml index f884388e0a..9e6b41fa62 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -66,14 +66,16 @@ jobs: build_docs_pdf: docker: - - image: danteev/texlive:latest + - image: texlive/texlive:latest steps: # checkout code to default ~/project - checkout - run: name: install dependencies command: | - apt-get update && apt install -y python3-pip + apt-get update && apt install -y python3-pip python3-venv pandoc + python3 -m venv .venv + source .venv/bin/activate python3 -m pip install --upgrade pip python3 -m pip install -r ~/project/requirements.txt python3 -m pip install ~/project/tools/schemacode/[render] @@ -83,6 +85,7 @@ jobs: - run: name: generate pdf version docs command: | + source .venv/bin/activate cd ~/project/pdf_build_src bash build_pdf.sh mv ~/project/pdf_build_src/bids-spec.pdf ~/project/bids-spec.pdf diff --git a/.codecov.yml b/.codecov.yml index 302b31ddce..b46689d13f 100644 --- a/.codecov.yml +++ b/.codecov.yml @@ -1,3 +1,5 @@ ignore: - - "*/*/tests/*" - - "**/tests/*" + - "*/*/tests/*" + - "**/tests/*" +codecov: + token: 7e84a7fb-8f7e-45f5-8dcc-9f5219fa3855 diff --git a/.codespell_dict b/.codespell_dict index 81adf22162..e4e9c7cc90 100644 --- a/.codespell_dict +++ b/.codespell_dict @@ -1,6 +1,11 @@ sub-directory->subdirectory +Sub-directory->Subdirectory sub-directories->subdirectories +Sub-directories->Subdirectories file name->filename +File name->Filename file names->filenames +File names->Filenames folder->directory -folders->directories +Folder->Directory +Folders->Directories diff --git a/.codespellrc b/.codespellrc index 28aeafee0c..4092a9a7bf 100644 --- a/.codespellrc +++ b/.codespellrc @@ -1,6 +1,8 @@ [codespell] -skip = *.js,*.svg,*.eps,.git -ignore-words-list = fo,te,als -builtin = clear,rare -dictionary = .codespell_dict +skip = *.js,*.svg,*.eps,.git,node_modules,env,venv,.mypy_cache,package-lock.json,CITATION.cff,tools/new_contributors.tsv,./tools/schemacode/docs/build +ignore-words-list = fo,te,als,Acknowledgements,acknowledgements,weill,bu,winn +builtin = clear,rare,en-GB_to_en-US +# this overloads default dictionaries and I have not yet figured out +# how to have multiple https://github.com/codespell-project/codespell/issues/2727 +# dictionary = .codespell_dict exclude-file = src/CHANGES.md diff --git a/.github/labeler.yml b/.github/labeler.yml new file mode 100644 index 0000000000..5c73894236 --- /dev/null +++ b/.github/labeler.yml @@ -0,0 +1,27 @@ +# labeler "full" schema +# https://github.com/marketplace/actions/auto-labeler + +# enable labeler on issues, prs, or both. +enable: + issues: false + prs: true +# comments object allows you to specify a different message for issues and prs + +comments: + prs: | + I have applied any labels matching special text in your title and description. + + Please review the labels and make any necessary changes. + +# Labels is an object where: +# - keys are labels +# - values are objects of { include: [ pattern ], exclude: [ pattern ] } +# - pattern must be a valid regex, and is applied globally to +# title + description of issues and/or prs (see enabled config above) +# - 'include' patterns will associate a label if any of these patterns match +# - 'exclude' patterns will ignore this label if any of these patterns match +labels: + exclude-from-changelog: + include: + - 'pre-commit\.ci' + exclude: [] diff --git a/.github/workflows/labeler.yml b/.github/workflows/labeler.yml new file mode 100644 index 0000000000..355ce3d2de --- /dev/null +++ b/.github/workflows/labeler.yml @@ -0,0 +1,21 @@ +name: "Label PRs" +# See https://github.com/marketplace/actions/auto-labeler + +on: + + pull_request_target: + types: [opened] + +jobs: + + labeler: + runs-on: ubuntu-latest + + if: github.repository_owner == 'bids-standard' + + steps: + - name: Check Labels + id: labeler + uses: jimschubert/labeler-action@v2 + with: + GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}} diff --git a/.github/workflows/redirect_circleci_artifacts.yml b/.github/workflows/redirect_circleci_artifacts.yml index 95810e311e..c40e051249 100644 --- a/.github/workflows/redirect_circleci_artifacts.yml +++ b/.github/workflows/redirect_circleci_artifacts.yml @@ -2,14 +2,17 @@ on: [status] jobs: circleci_artifacts_redirector_job: - if: "${{ startsWith(github.event.context, 'ci/circleci: build_docs_pdf') }}" runs-on: ubuntu-latest + if: "${{ startsWith(github.event.context, 'ci/circleci: build_docs_pdf') }}" + permissions: + statuses: write name: Run CircleCI artifacts redirector steps: - name: GitHub Action step uses: larsoner/circleci-artifacts-redirector-action@master with: repo-token: ${{ secrets.GITHUB_TOKEN }} + api-token: ${{ secrets.CIRCLECI_TOKEN }} artifact-path: 0/bids-spec.pdf circleci-jobs: build_docs_pdf job-title: Check the rendered PDF version here! diff --git a/.github/workflows/schema_docs.yaml b/.github/workflows/schema_docs.yaml deleted file mode 100644 index 70b1ac4bc9..0000000000 --- a/.github/workflows/schema_docs.yaml +++ /dev/null @@ -1,69 +0,0 @@ -name: "schemacode_docs" - -on: - push: - branches: - - "master" - tags: - - "schema-*" - workflow_dispatch: - inputs: - debug_enabled: - type: boolean - description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)' - required: false - default: false - -concurrency: - group: ${{ github.workflow }}-${{ github.ref }} - cancel-in-progress: true - -defaults: - run: - shell: bash - -jobs: - push_schema_for_docs: - runs-on: ${{ matrix.os }} - name: Push Schema to Schema Docs - strategy: - matrix: - os: ["ubuntu-latest"] - steps: - - uses: actions/checkout@v3 - - - name: Debug - uses: mxschmitt/action-tmate@v3 - if: ${{ inputs.debug_enabled }} - timeout-minutes: 15 - with: - limit-access-to-actor: true - - - name: Pull schema-docs and reqs from bids-specification - run: | - - pushd $HOME - git config --global user.name "${{ github.actor }}" - git config --global user.email "${{ github.actor}}@noreply.com" - git clone https://${{ github.repository_owner }}:${{ secrets.SCHEMA_DOCS_GITHUB_API_TOKEN }}@github.com/${{ github.repository_owner }}/schema-docs - popd - rsync --recursive --copy-links ${{ github.workspace }}/tools/schemacode/bidsschematools $HOME/schema-docs/ - rsync --recursive --copy-links ${{ github.workspace }}/tools/schemacode/docs $HOME/schema-docs/ - cat ${{ github.workspace }}/requirements.txt | grep -v tools/schemacode >> $HOME/schema-docs/requirements.txt - sort $HOME/schema-docs/requirements.txt | uniq > $HOME/schema-docs/requirements.txt.tmp - mv $HOME/schema-docs/requirements.txt.tmp $HOME/schema-docs/requirements.txt - - - name: Push Updates to schema-docs - run: | - - pushd $HOME/schema-docs - - git diff --exit-code > $HOME/gitdiff.log - if [[ $? == 0 ]]; then - echo "No changes found schema code, this workflow should only run when changes are made to schema-*." - echo "You must be up to no good." - else - git add --all - git commit -m "Auto update from bids-specification $GITHUB_SHA" - git push origin main - fi diff --git a/.github/workflows/schemacode_ci.yml b/.github/workflows/schemacode_ci.yml index 9d237200a3..8188370cdd 100644 --- a/.github/workflows/schemacode_ci.yml +++ b/.github/workflows/schemacode_ci.yml @@ -24,7 +24,7 @@ jobs: strategy: matrix: os: ["ubuntu-latest"] - python-version: ["3.10"] + python-version: ["3.11"] steps: - uses: actions/checkout@v3 - uses: actions/setup-python@v4 @@ -33,7 +33,7 @@ jobs: - name: "Install build dependencies" run: pip install --upgrade build twine - name: "Install test dependencies on tag" - run: pip install --upgrade pytest pyyaml pandas tabulate markdown-it-py + run: pip install --upgrade pytest pyyaml pandas tabulate markdown-it-py pyparsing if: ${{ startsWith(github.ref, 'refs/tags/schema-') }} - name: "Build archive on tag" run: pytest tools/schemacode/bidsschematools -k make_archive @@ -56,7 +56,7 @@ jobs: fail-fast: false matrix: os: ["ubuntu-latest"] - python-version: ["3.7", "3.8", "3.9", "3.10"] + python-version: ["3.8", "3.9", "3.10", "3.11"] include: - os: macos-latest python-version: 3 @@ -104,7 +104,7 @@ jobs: strategy: matrix: os: ["ubuntu-latest"] - python-version: ["3.10"] + python-version: ["3.11"] steps: - name: "Fetch packages" uses: actions/download-artifact@v3 diff --git a/.github/workflows/typescript_build.yml b/.github/workflows/typescript_build.yml deleted file mode 100644 index ad18e40bda..0000000000 --- a/.github/workflows/typescript_build.yml +++ /dev/null @@ -1,47 +0,0 @@ -name: "typescript_build" - -on: - push: - branches: - - "master" - paths: - - "tools/typescript/**" - - "src/schema/**" - pull_request: - branches: - - "*" - paths: - - "tools/typescript/**" - - "src/schema/**" - -concurrency: - group: ${{ github.workflow }}-${{ github.ref }} - cancel-in-progress: true - -jobs: - build_module: - runs-on: ${{ matrix.os }} - strategy: - fail-fast: false - matrix: - os: ["ubuntu-latest"] - deno-version: [1.21.3] - name: ${{ matrix.os }} with Deno ${{ matrix.deno-version }} - defaults: - run: - shell: bash - steps: - - uses: actions/checkout@v3 - - name: Use Deno Version ${{ matrix.deno-version }} - uses: denolib/setup-deno@v2 - with: - deno-version: ${{ matrix.deno-version }} - - name: Run tests - run: deno test --no-check - - name: Build module - run: deno run --allow-write --allow-read --no-check tools/typescript/build-schema-types.ts - - name: Save module - uses: actions/upload-artifact@v3 - with: - name: typescript-module - path: tools/typescript/output diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml index 91ba4d49e0..8e48d85bb6 100644 --- a/.github/workflows/validation.yml +++ b/.github/workflows/validation.yml @@ -81,3 +81,18 @@ jobs: run: | python no-bad-latin.py working-directory: tools + + # Validate CITATION.cff + validate_cff: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + - uses: actions/setup-python@v4 + with: + python-version: 3 + - name: Install dependencies + run: | + python -m pip install --upgrade pip setuptools + pip3 install cffconvert + - name: Validate CITATION.cff + run: make validate_citation_cff diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 9cdcbf36dc..53baab42b6 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -3,7 +3,7 @@ exclude: 'tools/schemacode/bidsschematools/tests/data/broken_dataset_description.json' repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.3.0 + rev: v4.4.0 hooks: - id: trailing-whitespace - id: end-of-file-fixer @@ -13,27 +13,53 @@ repos: - id: check-added-large-files - id: check-case-conflict - repo: https://github.com/psf/black - rev: 22.10.0 + rev: 23.7.0 hooks: - id: black + files: ^tools/(?!schemacode) + args: ["--verbose"] + - id: black + name: "black bidsschematools" files: tools/schemacode - args: [--verbose] + args: ["--config", "tools/schemacode/pyproject.toml", "--verbose"] - repo: https://github.com/pyCQA/isort - rev: 5.10.1 + rev: 5.12.0 hooks: - id: isort - files: tools/ + files: ^tools/(?!schemacode) + args: ["--profile", "black"] + - id: isort + name: "isort bidsschematools" + files: tools/schemacode + args: ["--settings-file", "tools/schemacode/pyproject.toml"] - repo: https://github.com/pyCQA/flake8 - rev: 5.0.4 + rev: 6.0.0 hooks: - id: flake8 args: [--config=tools/schemacode/setup.cfg] - repo: https://github.com/pre-commit/mirrors-prettier - rev: v3.0.0-alpha.2 + rev: v3.0.0 hooks: - id: prettier files: src/schema/.*/.*\.yaml - repo: https://github.com/codespell-project/codespell - rev: v2.2.2 + rev: v2.2.5 hooks: - id: codespell + args: ["--config=.codespellrc", "--dictionary=-", "--dictionary=.codespell_dict"] + - repo: https://github.com/pre-commit/mirrors-mypy + rev: v1.4.1 + hooks: + - id: mypy + # Sync with project.optional-dependencies.typing + additional_dependencies: + - click + - markdown-it-py + - importlib_resources + - pandas-stubs + - pyparsing + - pytest + - types-PyYAML + - types-tabulate + args: ["tools/schemacode/bidsschematools"] + pass_filenames: false diff --git a/.tributors b/.tributors new file mode 100644 index 0000000000..b325271c22 --- /dev/null +++ b/.tributors @@ -0,0 +1,3064 @@ +{ + "aaron_oliver-taylor": { + "contributions": [ + "doc" + ], + "name": "Aaron Oliver-Taylor" + }, + "adam2392": { + "bio": "I am a Postdoctoral Research Fellow at Columbia University in the Causal AI Lab. 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description: bids-specification + type: doi + value: 10.5281/zenodo.3686061 + +keywords: + - brain imaging data structure + - bids + - standards + - data-standards + +authors: + - given-names: Aaron + family-names: Oliver-Taylor + - given-names: Adam + family-names: Li + website: https://adam2392.github.io/ + - given-names: Adam + family-names: Thomas + website: https://cmn.nimh.nih.gov/dsst + orcid: https://orcid.org/0000-0002-2850-1419 + affiliation: + NIMH, Intramural Research Program, Bethesda, MD, 20891, United States of + America + email: adamt@nih.gov + - given-names: Adeen + family-names: Flinker + website: http://flinkerlab.org + orcid: https://orcid.org/0000-0003-1247-1283 + affiliation: + New York University, Department of Neurology, New York City, New York, + 10016, United States of America + email: adeen@nyu.edu + - given-names: Adina S. + family-names: Wagner + website: https://www.adina-wagner.com + orcid: https://orcid.org/0000-0003-2917-3450 + affiliation: + Institute of Neuroscience and Medicine (INM-7), Research Center Juelich, + Juelich, 52428, Germany + email: adina.wagner@t-online.de + - given-names: Agah + family-names: Karakuzu + website: https://agahkarakuzu.github.io + orcid: https://orcid.org/0000-0001-7283-271X + email: agahkarakuzu@gmail.com + - given-names: Aki + family-names: Nikolaidis + website: https://github.com/AkiNikolaidis + orcid: https://orcid.org/0000-0001-8960-1934 + - given-names: Alberto + family-names: Lazari + - given-names: Alejandro + family-names: de la Vega + website: https://github.com/adelavega + - given-names: Alessio + family-names: Giacomel + website: https://github.com/alegiac95 + orcid: https://orcid.org/0000-0002-7784-2041 + affiliation: GlaxoSmithKline Research and Development + - given-names: Alex + family-names: Rockhill + website: https://github.com/alexrockhill + orcid: https://orcid.org/0000-0003-3868-7453 + email: aprockhill@mailbox.org + - given-names: Alexander + family-names: Jones + - given-names: Alexander L. + family-names: Cohen + website: https://bchcohenlab.com + orcid: https://orcid.org/0000-0001-6557-5866 + affiliation: + Boston Children's Hospital, Department of Neurology, Boston, 02115, United + States of America + email: alexander.cohen2@childrens.harvard.edu + - given-names: Alexander + family-names: von Lautz + - given-names: Alexandre + family-names: Gramfort + website: http://alexandre.gramfort.net + orcid: https://orcid.org/0000-0001-9791-4404 + affiliation: Inria, Université Paris-Saclay + email: alexandre.gramfort@inria.fr + - given-names: Alexandre + family-names: Hutton + - given-names: Alexandre + family-names: Routier + website: https://github.com/alexandreroutier + orcid: https://orcid.org/0000-0003-1603-8049 + - given-names: Alexandru + family-names: Foias + website: https://github.com/alexfoias + orcid: https://orcid.org/0000-0001-5160-1402 + - given-names: Ali + family-names: Khan + - given-names: Ana + family-names: Fouto + - given-names: Anders + family-names: Eklund + website: https://github.com/wanderine + - given-names: Andrea + family-names: Pigorini + - given-names: Andrew + family-names: Hoopes + - given-names: Andrew + family-names: Jahn + - given-names: Andrew + family-names: Janke + website: http://apjanke.net + email: andrew@apjanke.net + - given-names: Anibal + family-names: Sólon + website: https://anibalsolon.com/ + orcid: https://orcid.org/0000-0002-2050-0614 + email: anibalsolon@gmail.com + - given-names: Anthony + family-names: Galassi + website: https://github.com/bendhouseart + orcid: https://orcid.org/0000-0001-6550-4574 + - given-names: Ariel + family-names: Rokem + website: https://arokem.org/ + orcid: https://orcid.org/0000-0003-0679-1985 + affiliation: + University of Washington, Psychology, Seattle, WA, 98107, United States of + America + email: arokem@uw.edu + - given-names: Arjen + family-names: Stolk + - given-names: Arnaud + family-names: Delorme + website: https://www.arnauddelorme.com + orcid: https://orcid.org/0000-0002-0799-3557 + affiliation: Swartz Center for Computational Neuroscience + email: adelorme@ucsd.edu + - given-names: Arnaud + family-names: Marcoux + website: https://github.com/arnaudmarcoux + - given-names: Arshitha + family-names: Basavaraj + website: https://github.com/Arshitha + orcid: https://orcid.org/0000-0002-6984-7969 + affiliation: + NIMH, Data Science and Sharing Team, Bethesda, MD, 20892, United States of + America + email: arsh2794@gmail.com + - given-names: Ashley G. + family-names: Gillman + website: https://github.com/ashgillman + - given-names: Athanasia + family-names: Monika Mowinckel + website: https://github.com/drmowinckels + orcid: https://orcid.org/0000-0002-5756-0223 + affiliation: University of Oslo + - given-names: Aysegul + family-names: Gunduz + - given-names: Azeez + family-names: Adebimpe + orcid: https://orcid.org/0000-0001-9049-0135 + affiliation: University of Pennsylvania + - given-names: B. + family-names: Nolan Nichols + - given-names: Balint + family-names: Kincses + - given-names: Benjamin + family-names: Beasley + website: https://github.com/musicinmybrain + - given-names: Benjamin + family-names: Dichter + - given-names: Benjamin + family-names: Gagl + orcid: https://orcid.org/0000-0002-2339-6293 + affiliation: University of Vienna + - given-names: Bertrand + family-names: Thirion + website: https://github.com/bthirion + orcid: https://orcid.org/0000-0001-5018-7895 + - given-names: Bradley + family-names: Voytek + website: https://www.voyteklab.com/ + orcid: https://orcid.org/0000-0003-1640-2525 + affiliation: + UC San Diego, Cognitive Science and Data Science, La Jolla, CA, 92093, + United States of America + - 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given-names: Christopher J. + family-names: Markiewicz + website: https://github.com/effigies + email: effigies@gmail.com + - given-names: Christopher + family-names: Lee-Messer + - given-names: Clara + family-names: Moreau + - given-names: Clint + family-names: Hansen + affiliation: Kiel University + email: c.hansen@neurologie.uni-kiel.de + - given-names: Cyril + family-names: Pernet + website: https://cpernet.github.io/ + orcid: https://orcid.org/0000-0003-4010-4632 + affiliation: + Neurobiology Research Unit, Copenhagen University Hospital + Rigshospitalet, DK-2100 Copenhagen, Denmark + email: wamcyril@gmail.com + - given-names: Cyrus + family-names: Eierud + website: https://trendscenter.org/cyrus-eierud/ + orcid: https://orcid.org/0000-0002-9942-676X + affiliation: Georgia State University + email: ceierud@gsu.edu + - given-names: D. + family-names: Sturgeon + website: https://dasturge.github.io + - given-names: Dan + family-names: Levitas + website: https://github.com/dlevitas + orcid: https://orcid.org/0000-0003-2279-7447 + affiliation: + Indiana University, Psychological & Brain Sciences, Bloomington, IN, + 47405, United States of America + email: dlevitas@iu.edu + - given-names: Dan + family-names: Lurie + website: https://github.com/danlurie + - given-names: Daniel A. + family-names: Handwerker + - given-names: David + family-names: Alsop + - given-names: David + family-names: Boas + website: http://bu.edu/neurophotonics + orcid: https://orcid.org/0000-0002-6709-7711 + affiliation: + Boston University, Biomedical Engineering, Boston, 02215, United States of + America + email: dboas@bu.edu + - given-names: David + family-names: Groppe + website: https://github.com/dmgroppe + orcid: https://orcid.org/0000-0002-3282-2514 + affiliation: + Persyst Development Corporation, R&D, Toronto, ON M4K 1W8 Canada + email: david.m.groppe@gmail.com + - given-names: David + family-names: Keator + website: https://github.com/dbkeator + orcid: https://orcid.org/0000-0001-5281-5576 + affiliation: Change Your Brain, Change Your Life Foundation + - given-names: David + family-names: McAlpine + - given-names: David + family-names: Thomas + - given-names: Dejan + family-names: Draschkow + orcid: https://orcid.org/0000-0003-1354-4835 + affiliation: University of Oxford + - given-names: Dianne + family-names: Patterson + website: https://profiles.arizona.edu/person/dkp + orcid: https://orcid.org/0000-0001-7518-3110 + affiliation: + University of Arizona, RII, Tucson Arizona 85721 United States of America + email: dkp@arizona.edu + - given-names: Dimitri + family-names: Papadopoulos Orfanos + website: https://github.com/DimitriPapadopoulos + - given-names: Dmitry + family-names: Petrov + - given-names: Dora + family-names: Hermes + website: https://github.com/dorahermes + - given-names: Dorien + family-names: Huijser + website: https://github.com/DorienHuijser + orcid: https://orcid.org/0000-0003-3282-8083 + affiliation: Utrecht University + - given-names: Douglas N. + family-names: Greve + website: https://github.com/dngreve + - given-names: Duncan + family-names: Macleod + - given-names: Dung + family-names: Truong + website: https://github.com/dungscout96 + affiliation: Swartz Center for Computational Neuroscience + email: dutruong@ucsd.edu + - given-names: Dylan + family-names: Nielson + website: https://github.com/Shotgunosine + orcid: https://orcid.org/0000-0003-4613-6643 + - given-names: Eduard + family-names: Ort + website: https://github.com/eort + orcid: https://orcid.org/0000-0001-5546-3561 + affiliation: + Heinrich-Heine-University, Department of Experimental Psychology, + Dusseldorf, 40224, Germany + - given-names: Eleonora + family-names: Marcantoni + orcid: https://orcid.org/0000-0003-1137-4983 + affiliation: + IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli di Brescia + - given-names: Elizabeth + family-names: Bock + - given-names: Elizabeth + family-names: DuPre + website: https://elizabeth-dupre.com + orcid: https://orcid.org/0000-0003-1358-196X + affiliation: + Stanford University, Department of Psychology, Stanford, CA, 94063, United + States of America + - given-names: Elke + family-names: Warmerdam + affiliation: Saarland University + email: elke.warmerdam@uni-saarland.de + - given-names: Erdal + family-names: Karaca + website: https://github.com/erdalkaraca + - given-names: Eric A. + family-names: Earl + website: https://ericearl.github.io/ + orcid: https://orcid.org/0000-0001-5512-0083 + affiliation: + NIMH Data Science & Sharing Team, Bethesda, MD, 20892, United States of + America + email: eric.earl@nih.gov + - given-names: Eric + family-names: Achten + website: https://github.com/rikAchten + - given-names: Eric + family-names: Bridgeford + - given-names: Erin W. + family-names: Dickie + website: http://imaging-genetics.camh.ca/ + - given-names: Ethan + family-names: Blackwood + orcid: https://orcid.org/0000-0002-3049-0640 + affiliation: University of Pennsylvania + - given-names: Eugene P. + family-names: Duff + website: http://eduff.github.io + orcid: https://orcid.org/0000-0001-8795-5472 + affiliation: UK Dementia Research Institute, Imperial College London, UK + email: eduff@imperial.ac.uk + - given-names: Ezequiel + family-names: Mikulan + orcid: https://orcid.org/0000-0001-7259-6120 + affiliation: University of Milan + - given-names: Felipe + family-names: Orihuela-Espina + - given-names: Fidel + family-names: Alfaro Almagro + - given-names: Filip + family-names: Szczepankiewicz + orcid: https://orcid.org/0000-0002-5251-587X + affiliation: Lund University + - given-names: Filippo + family-names: Maria Castelli + website: https://github.com/filippocastelli + orcid: https://orcid.org/0000-0001-8170-8905 + affiliation: + University of Florence, European Laboratory for NonLinear Spectroscopy, + Sesto Fiorentino, (FI), 50019, Italy + email: castelli@lens.unifi.it + - given-names: Franco + family-names: Pestilli + website: https://liberalarts.utexas.edu/psychology/faculty/fp4834 + - given-names: Franklin W. + family-names: Feingold + website: https://github.com/franklin-feingold + orcid: https://orcid.org/0000-0002-6533-2909 + affiliation: Stanford University + - given-names: François + family-names: Tadel + - given-names: Gaia + family-names: Rizzo + website: http://fair.dei.unipd.it/gaia-rizzo/ + orcid: https://orcid.org/0000-0001-7272-8576 + affiliation: + Invicro, Burlington Danes Building, Imperial College London, Hammersmith + Hospital, Du Cane Road, London, W12 0NN, UK + - given-names: Gang + family-names: Chen + website: https://github.com/afni-gangc + orcid: https://orcid.org/0000-0002-2960-089X + affiliation: + National Institutes of Health, Scientific and Statistical Computing Core, + NIMH, Bethesda, MD 20892, United States of America + email: gangchen@mail.nih.gov + - given-names: Gaël + family-names: Varoquaux + website: https://github.com/GaelVaroquaux + - given-names: Ghislain + family-names: Vaillant + website: https://github.com/ghisvail + orcid: https://orcid.org/0000-0003-0267-3033 + - given-names: Giacomo + family-names: Bertazzoli + orcid: https://orcid.org/0000-0003-1624-2576 + affiliation: Centro San Giovanni di Dio Fatebenefratelli + - given-names: Giacomo + family-names: Guidali + orcid: https://orcid.org/0000-0002-3741-0404 + affiliation: IRCCS Centro San Giovanni di Dio Fatebenefratelli + - given-names: Giacomo + family-names: Mazzamuto + website: https://github.com/gmazzamuto + orcid: https://orcid.org/0000-0003-3077-3904 + affiliation: National Institute of Optics, National Research Council + email: mazzamuto@lens.unifi.it + - given-names: Gilles + family-names: de Hollander + website: https://github.com/Gilles86 + - given-names: Gio + family-names: Piantoni + - given-names: Gitte M. + family-names: Knudsen + - given-names: Giulio + family-names: Castegnaro + - given-names: Giuseppe + family-names: Gallitto + orcid: https://orcid.org/0000-0001-5185-0206 + affiliation: Essen University Hospital + - given-names: Graham + family-names: Searle + - given-names: Granville J. + family-names: Matheson + website: http://www.granvillematheson.com + - given-names: Gregory + family-names: Kiar + website: https://github.com/gkiar + orcid: https://orcid.org/0000-0001-8915-496X + affiliation: Child Mind Institute + - given-names: Gregory + family-names: Noack + website: https://github.com/thinknoack + - given-names: Greydon + family-names: Gilmore + website: http://greydongilmore.com + orcid: https://orcid.org/0000-0001-7523-5734 + email: ggilmore@uwo.ca + - given-names: Guillaume + family-names: Flandin + website: https://www.fil.ion.ucl.ac.uk/team/spm-team/ + orcid: https://orcid.org/0000-0003-0077-7859 + affiliation: University College London + - given-names: Gunnar + family-names: Schaefer + orcid: https://orcid.org/0000-0001-9661-2121 + - given-names: Gustav + family-names: Nilsonne + website: https://nilsonne.net/about/ + orcid: https://orcid.org/0000-0001-5273-0150 + affiliation: + Karolinska Institutet, Department of Clinical Neuroscience, Stockholm, + 17177, Sweden + email: gustav.nilsonne@ki.se + - given-names: Hamish + family-names: Innes-Brown + orcid: https://orcid.org/0000-0002-1512-2823 + affiliation: Oticon A/S, Eriksholm Research Centre, Snekkersten, Denmark + email: hain@eriksholm.com + - given-names: Hanne D. + family-names: Hansen + orcid: https://orcid.org/0000-0001-5564-7627 + affiliation: + Copenhagen University Hospital, Neurobiology Research Unit, Section 8057, + Blegdamsvej 9, 2100 Copenhagen, Denmark + email: hanne.d.hansen@nru.dk + - given-names: Hanzhang + family-names: Lu + orcid: https://orcid.org/0000-0003-3871-1564 + affiliation: Johns Hopkins Medicine + - given-names: Hao-Ting + family-names: Wang + website: https://github.com/htwangtw + orcid: https://orcid.org/0000-0003-4078-2038 + affiliation: CRIUGM, Montreal, Quebec, H3W 1W5, Canada + email: htwangtw@gmail.com + - given-names: Helena + family-names: Cockx + website: https://github.com/helenacockx + orcid: https://orcid.org/0000-0001-7782-7178 + affiliation: Radboud University + email: helena.cockx@donders.ru.nl + - given-names: Henk + family-names: Mutsaerts + website: http://www.ExploreASL.org + orcid: https://orcid.org/0000-0003-0894-0307 + affiliation: + Amsterdam University Medical Centers, Radiology and Nuclear Department, + Amsterdam, 1013 EG, The Netherlands + email: h.j.mutsaerts@amsterdamumc.nl + - given-names: Hernando + family-names: Ombao + - given-names: Hugo + family-names: Boniface + website: https://github.com/Hboni + - given-names: Ilkay + family-names: Isik + website: https://github.com/ilkayisik + orcid: https://orcid.org/0000-0002-1652-9297 + affiliation: Max Planck Institute for Empirical Aesthetics + - given-names: Ilona + family-names: Lipp + website: https://github.com/IlonaLipp + - given-names: International + family-names: Neuroinformatics Coordinating Facility + website: https://github.com/INCF + - given-names: Iris + family-names: Groen + website: https://github.com/irisgroen + - given-names: Isla + family-names: Staden + orcid: https://orcid.org/0000-0002-0795-1154 + - given-names: Jaap + family-names: von der Aar + - given-names: Jakub + family-names: Kaczmarzyk + website: https://github.com/kaczmarj + orcid: https://orcid.org/0000-0002-5544-7577 + - given-names: James + family-names: Gholam + orcid: https://orcid.org/0000-0003-4513-2341 + - given-names: James + family-names: Kent + website: https://github.com/jdkent + - given-names: Jan + family-names: Mathijs Schoffelen + website: https://github.com/schoffelen + orcid: https://orcid.org/0000-0003-0923-6610 + affiliation: + Radboud University Nijmegen, Donders Institute, Nijmegen, 6500 HB, The + Netherlands + email: jm.schoffelen@gmail.com + - given-names: Jan + family-names: Petr + website: https://www.exploreasl.org + orcid: https://orcid.org/0000-0002-3201-6002 + affiliation: Helmholtz-Zentrum Dresden-Rossendorf, Dresden, 01309, Germany + email: j.petr@hzdr.de + - given-names: Jan-Mathijs + family-names: Schoffelen + - given-names: Jean-Baptiste + family-names: Poline + website: https://github.com/jbpoline + orcid: https://orcid.org/0000-0002-9794-749X + - given-names: Jean-Christophe + family-names: Houde + website: http://scil.dinf.usherbrooke.ca/jchoude + orcid: https://orcid.org/0000-0003-3026-021X + affiliation: Université de Sherbrooke + email: jean.christophe.houde@gmail.com + - given-names: Jean-Dominique + family-names: Gallezot + orcid: https://orcid.org/0000-0003-0399-8374 + affiliation: + Yale School of Medicine, Department of Radiology and Biomedical Imaging, + New Haven, CT, 06511, United States of America + email: jean-dominique.gallezot@yale.edu + - given-names: Jean-Philippe + family-names: Lachaux + orcid: https://orcid.org/0000-0002-9459-0667 + affiliation: INSERM + - given-names: Jeanette + family-names: Mumford + website: https://jeanettemumford.org/ + affiliation: Stanford, Department of Psychology, Stanford, CA + - given-names: Jeffrey G. + family-names: Ojemann + - given-names: Jeffrey S. + family-names: Grethe + website: http://profiles.ucsd.edu/jeffrey.grethe + - given-names: JegouA + website: https://github.com/JegouA + - given-names: Jelle + family-names: Dalenberg + website: https://github.com/jrdalenberg + orcid: https://orcid.org/0000-0001-8580-5358 + affiliation: + University of Groningen, University Medical Center Groningen, Department + of Neurology, Movement Disorders Groningen, Hanzeplein 1, 9713 GZ, + Groningen + email: j.r.dalenberg@umcg.nl + - given-names: Jeremy + family-names: Moreau + - given-names: Jessica A. + family-names: Turner + - given-names: Jochem + family-names: Rieger + website: https://uol.de/en/applied-neurocognitive-psychology + orcid: https://orcid.org/0000-0003-0955-2306 + affiliation: Oldenburg University, Dept. of Psychology, 26129, Germany + email: jochem.rieger@uni-oldenburg.de + - given-names: John + family-names: Detre + orcid: https://orcid.org/0000-0002-8115-6343 + affiliation: University of Pennsylvania + - given-names: John + family-names: Pellman + orcid: https://orcid.org/0000-0001-6810-4461 + - given-names: John T. + family-names: Wodder + website: https://github.com/jwodder + - given-names: Joke + family-names: Durnez + website: https://github.com/jokedurnez + orcid: https://orcid.org/0000-0001-9030-2202 + affiliation: Stanford University + - given-names: Jon + family-names: Haitz Legarreta Gorroño + website: https://github.com/jhlegarreta + orcid: https://orcid.org/0000-0002-9661-1396 + affiliation: + Université de Sherbrooke, Department of Computer Science, Sherbrooke, + (Québec), J1K 2R1, Canada + email: jon.haitz.legarreta@gmail.com + - given-names: Jonathan C. + family-names: Lau + - given-names: Jonathan + family-names: Winawer + website: https://github.com/JWinawer + - given-names: Joost + family-names: Kuijer + website: https://github.com/wadqc + orcid: https://orcid.org/0000-0002-4181-0427 + affiliation: + Amsterdam University Medical Centers, Radiology and Nuclear Medicine, + Amsterdam, 1081 HV, The Netherlands + email: jpa.kuijer@amsterdamumc.nl + - given-names: Jose + family-names: Manuel Saborit + - given-names: Joseph + family-names: Wexler + orcid: https://orcid.org/0000-0001-9086-8484 + affiliation: Loyola University Chicago + - given-names: Joseph + family-names: Woods + website: https://www.ndcn.ox.ac.uk/team/joseph-woods + orcid: https://orcid.org/0000-0002-0329-824X + affiliation: + University of Oxford, Nuffield Department of Clinical Neuroscience, + Oxford, UK + email: joseph.woods@ndcn.ox.ac.uk + - given-names: Julia + family-names: Guiomar Niso Galán + website: http://guiomarniso.com + orcid: https://orcid.org/0000-0001-5872-8924 + affiliation: Indiana University + - given-names: Julia + family-names: Sprenger + website: https://github.com/juliasprenger + orcid: https://orcid.org/0000-0002-9986-7477 + affiliation: + Institute de Neuroscience de la Timone, CNRS, Marseille, 13005, France + email: julia.sprenger@univ-amu.fr + - given-names: Julien + family-names: Cohen-Adad + website: https://www.neuro.polymtl.ca + orcid: https://orcid.org/0000-0003-3662-9532 + affiliation: + Polytechnique Montreal, Department of Electrical Engineering, Montreal, + QC, Canada + - given-names: Julius + family-names: Welzel + website: https://github.com/JuliusWelzel + orcid: https://orcid.org/0000-0001-8958-0934 + affiliation: Kiel University + email: julius.welzel@gmail.com + - given-names: Kai J. + family-names: Miller + - given-names: Kangjoo + family-names: Lee + website: https://github.com/Kangjoo + orcid: https://orcid.org/0000-0002-7760-8079 + affiliation: Yale School of Medicine + - given-names: Katja + family-names: Heuer + website: https://github.com/katjaq + orcid: https://orcid.org/0000-0002-7237-0196 + affiliation: Institut Pasteur + - given-names: Kay + family-names: Robbins + website: http://www.cs.utsa.edu/~krobbins + orcid: https://orcid.org/0000-0002-7147-5797 + affiliation: + University of Texas at San Antonio Department of Computer Science San + Antonio, TX 78249 United States of America + email: kay.robbins@utsa.edu + - given-names: Kevin + family-names: Larcher + - given-names: Kimberly + family-names: Ray + orcid: https://orcid.org/0000-0003-1302-2834 + affiliation: UT Austin + email: kimberlylray@gmail.com + - given-names: Kirstie + family-names: Whitaker + website: https://whitakerlab.github.io + orcid: https://orcid.org/0000-0001-8498-4059 + affiliation: University of Cambridge + email: kwhitaker@turing.ac.uk + - given-names: Klara + family-names: Gregorova + website: https://github.com/greckla + orcid: https://orcid.org/0000-0002-3828-9386 + - given-names: Klaus + family-names: Gramann + affiliation: Technical University Berlin + email: klaus.gramann@tu-berlin.de + - given-names: Kris + family-names: Thielemans + website: https://iris.ucl.ac.uk/iris/browse/profile?upi=KTHIE60 + - given-names: Kristofer + family-names: Bouchard + website: https://bouchardlab.lbl.gov + orcid: https://orcid.org/0000-0002-1974-4603 + affiliation: LBNL, Scientific Data Division + email: kristofer.bouchard@gmail.com + - given-names: Kurt + family-names: Schilling + website: https://github.com/schillkg + - given-names: Laura + family-names: and John Arnold Foundation + - given-names: Leandro + family-names: Beltrachini + orcid: https://orcid.org/0000-0003-4602-1416 + affiliation: + Cardiff University, Cardiff University Brain Research Imaging Centre + (CUBRIC), UK + email: BeltrachiniL@cardiff.ac.uk + - given-names: Lee + family-names: Kamentsky + website: https://github.com/LeeKamentsky + orcid: https://orcid.org/0000-0002-8161-3604 + affiliation: MIT + - given-names: Lennart + family-names: Walger + orcid: https://orcid.org/0000-0002-3300-6877 + - given-names: Lennart + family-names: Wittkuhn + website: https://github.com/lnnrtwttkhn + orcid: https://orcid.org/0000-0003-2966-6888 + affiliation: Max Planck Institute for Human Development + - given-names: Liberty + family-names: Hamilton + website: https://github.com/libertyh + - given-names: Luca + family-names: Pollonini + website: https://polloninilab.com + orcid: https://orcid.org/0000-0003-2955-6355 + affiliation: + University of Houston, Dept. of Engineering Technology, Houston TX 77204, + United States of America + email: lpollonini@uh.edu + - given-names: Luis + family-names: Hernandez-Garcia + - given-names: Luke J. + family-names: Edwards + orcid: https://orcid.org/0000-0002-8320-7298 + affiliation: Max Planck Institute for Human Cognitive and Brain Sciences + - given-names: Lyuba + family-names: Zehl + website: https://github.com/lzehl + orcid: https://orcid.org/0000-0002-5947-9939 + affiliation: Forschungszentrum Jülich, Jülich, 52428, Germany + - given-names: Mainak + family-names: Jas + website: http://jasmainak.github.io/ + orcid: https://orcid.org/0000-0002-3199-9027 + - given-names: Manjari + family-names: Narayan + - given-names: Manuel + family-names: Mercier + orcid: https://orcid.org/0000-0001-6358-4734 + affiliation: + Dynamics of Cognitive Processes Group Institut de Neurosciences des + Systèmes, INS - UMR 1106 Inserm Aix-Marseille Université, France + - given-names: Maqsood + family-names: Yaqub + orcid: https://orcid.org/0000-0003-2122-740X + affiliation: Amsterdam UMC, locatie VUmc + - given-names: Marc + family-names: Lalancette + website: https://github.com/Moo-Marc + orcid: https://orcid.org/0000-0003-1161-3972 + affiliation: + Montreal Neurological Institute-Hospital, McConnell Brain Imaging Center, + Montreal, Quebec, H2A + - given-names: Marco + family-names: Castellaro + website: https://github.com/marcocastellaro + orcid: https://orcid.org/0000-0002-1203-2670 + affiliation: + University of Padova, Department of Information Engineering, Padova, Italy + email: marco.castellaro@gmail.com + - given-names: Maria + family-names: de la Iglesia + website: https://bimcv.cipf.es + orcid: https://orcid.org/0000-0003-4505-8399 + affiliation: + FISABIO, Join Unit Biomedical Imagin, Valencia, Valencia, 46006, Spain + email: delaiglesia_mar@gva.es + - given-names: Marie-Hélène + family-names: Bourget + website: https://github.com/mariehbourget + - given-names: Mark + family-names: Mikkelsen + website: https://vivo.weill.cornell.edu/display/cwid-mam4041 + orcid: https://orcid.org/0000-0002-0349-3782 + affiliation: + Weill Cornell Medicine, Department of Radiology, New York, NY, 10021, + United States of America + email: mam4041@med.cornell.edu + - given-names: Markus + family-names: Morawski + orcid: https://orcid.org/0000-0002-3817-5186 + affiliation: Universität Leipzig + - given-names: Marta + family-names: Bortoletto + orcid: https://orcid.org/0000-0002-8489-8043 + affiliation: IRCCS Centro S Giovanni di Dio Fatebenefratelli + - given-names: Martin + family-names: Craig + - given-names: Martin + family-names: Noergaard + website: https://profiles.stanford.edu/martin-noergaard + orcid: https://orcid.org/0000-0003-2131-5688 + affiliation: + Stanford University, Department of Psychology, CA, 94304, United States of + America + email: noergard@stanford.edu + - given-names: Martin + family-names: Szinte + website: http://www.martinszinte.net + orcid: https://orcid.org/0000-0003-2040-4005 + affiliation: + CNRS, Institut des Neurosciences de la Timone, Marseille, 13008, France + email: mail@martinszinte.net + - given-names: Martin + family-names: Wilson + - given-names: Martina + family-names: Bulgari + orcid: https://orcid.org/0000-0003-1594-9617 + affiliation: IRCCS Centro San Giovanni di Dio Fatebenefratelli + - given-names: Mateusz + family-names: Pawlik + website: https://github.com/mateuszpawlik + email: mateusz.pawlik@plus.ac.at + - given-names: Mathias + family-names: Goncalves + website: https://github.com/mgxd + orcid: https://orcid.org/0000-0002-7252-7771 + affiliation: + Psychology Department, Stanford University, Palo Alto, CA, 94305, United + States of America + email: mathiasg@stanford.edu + - given-names: Mathieu + family-names: Boudreau + website: https://github.com/mathieuboudreau + orcid: https://orcid.org/0000-0002-7726-4456 + affiliation: Polytechnique Montréal + - given-names: Matt + family-names: Sanderson + - given-names: Matteo + family-names: Tonietto + website: https://github.com/matteotonietto + orcid: https://orcid.org/0000-0001-9591-5710 + affiliation: + Hoffmann-La Roche Ltd, Research and Early Development, Basel, 4070, + Switzerland + - given-names: Matthias + family-names: Günther + - given-names: Matthias + family-names: Van Osch + - given-names: Maureen + family-names: J Shader + - given-names: Maurice + family-names: Pasternak + - given-names: Max A. + family-names: van den Boom + website: https://github.com/MaxvandenBoom + orcid: https://orcid.org/0000-0001-5481-1659 + affiliation: + Mayo Clinic, Department of neurosurgery, Rochester, MN, United States of + America + email: m.a.vandenboom84@gmail.com + - given-names: Melanie + family-names: Ganz-Benjaminsen + website: https://sites.google.com/view/melanieganz/home + orcid: https://orcid.org/0000-0002-9120-8098 + affiliation: + University of Copenhagen, Department of Computer Science, Copenhagen, + 2100, Denmark + - given-names: Michael + family-names: Chappell + - given-names: Michael + family-names: Hanke + website: https://github.com/mih + - given-names: Michael P. + family-names: Harms + - given-names: Michael P. + family-names: Milham + - given-names: Michael P. + family-names: Notter + - given-names: Michael + family-names: Schirner + website: https://www.brainsimulation.org + orcid: https://orcid.org/0000-0001-8227-8476 + affiliation: + Charité—Universitätsmedizin Berlin, Department of Neurology, Berlin, + 10115, Germany + email: michael.schirner@charite.de + - given-names: Mikaël + family-names: Naveau + website: https://www.cyceron.fr + orcid: https://orcid.org/0000-0002-4685-0057 + affiliation: UAR3408-US50 CYCERON, Caen, 14000, France + - given-names: Nader + family-names: Pouratian + orcid: https://orcid.org/0000-0002-0426-3241 + - given-names: Natalia + family-names: Petridou + orcid: https://orcid.org/0000-0002-0783-0387 + affiliation: + High Field Dpt, Center for Image Sciences, University Medical Center + Utrecht, 3584 CX Utrecht, NL + - given-names: National + family-names: Institute of Mental Health + - given-names: Nell + family-names: Hardcastle + website: https://github.com/nellh + orcid: https://orcid.org/0000-0002-3837-0707 + - given-names: Nicholas + family-names: Traut + - given-names: Nick F. + family-names: Ramsey + - given-names: Nicole C. + family-names: Swann + - given-names: Nima + family-names: Bigdely Shamlo + orcid: https://orcid.org/0000-0001-6403-892X + - given-names: Olivier + family-names: David + - given-names: Orrin + family-names: Devinsky + orcid: https://orcid.org/0000-0003-0044-4632 + affiliation: NYU School of Medicine + - given-names: Oscar + family-names: Esteban + website: http://www.axonlab.org + orcid: https://orcid.org/0000-0001-8435-6191 + affiliation: + Department of Radiology, Lausanne University Hospital, Lausanne, CH-1011, + Switzerland + email: phd@oscaresteban.es + - given-names: Pamela + family-names: LaMontagne + orcid: https://orcid.org/0000-0002-6752-8518 + - given-names: Parul + family-names: Sethi + website: https://github.com/parulsethi + - given-names: Patricia + family-names: Clement + website: https://github.com/patsycle + orcid: https://orcid.org/0000-0001-8546-0134 + affiliation: + Department of Medical Imaging / Department of Medical Sciences, Ghent + University Hospital / Ghent University, Ghent, Belgium + email: patricia.clement@ugent.be + - given-names: Patrick + family-names: Park + website: https://github.com/Park-Patrick + - given-names: Paule-Joanne + family-names: Toussaint + orcid: https://orcid.org/0000-0002-7446-150X + affiliation: + McGill University Faculty of Medicine and Health Sciences, Montréal, + Québec, Canada + - given-names: Peer + family-names: Herholz + website: https://peerherholz.github.io/ + orcid: https://orcid.org/0000-0002-9840-6257 + affiliation: + NeuroDataScience - ORIGAMI lab, McConnell Brain Imaging Centre, Montreal + Neurological Institute and Hospital, McGill University, Montreal, Québec, + Canada + email: herholz.peer@gmail.com + - given-names: Petra + family-names: Ritter + website: https://www.brainsimulation.org + orcid: https://orcid.org/0000-0002-4643-4782 + affiliation: + Charité University Medicine Berlin, Berlin Institute of Health, Berlin, + 10115, Germany + email: petra.ritter@charite.de + - given-names: Pierre + family-names: Rioux + website: https://github.com/prioux + - given-names: Pieter + family-names: Vandemaele + website: https://github.com/pvdemael + orcid: https://orcid.org/0000-0002-4523-2476 + affiliation: Ghent University Hospital + - given-names: Pradeep + family-names: Reddy Raamana + website: https://github.com/raamana + - given-names: R. + family-names: Cameron Craddock + website: https://github.com/ccraddock + - given-names: Remi + family-names: Gau + website: https://remi-gau.github.io/ + orcid: https://orcid.org/0000-0002-1535-9767 + affiliation: Université catholique de Louvain + email: remi.gau@tuebingen.mpg.de + - given-names: Richard + family-names: Höchenberger + website: https://hoechenberger.net/ + orcid: https://orcid.org/0000-0002-0380-4798 + affiliation: Inria Saclay - Île-de-France Research Centre + email: richard.hoechenberger@gmail.com + - given-names: Richard N. + family-names: Henson + website: http://www.mrc-cbu.cam.ac.uk/people/rik.henson/personal + orcid: https://orcid.org/0000-0002-0712-2639 + affiliation: MRC CBU, University of Cambridge, UK + email: Rik.Henson@mrc-cbu.cam.ac.uk + - given-names: Robert B. + family-names: Innis + website: https://www.nimh.nih.gov/research/research-conducted-at-nimh/research-areas/clinics-and-labs/mib/molecular-imaging-branch-mib + orcid: https://orcid.org/0000-0003-1238-7209 + affiliation: + NIMH Intramural Research Program, Bethesda, MD 20850 United States of + America, MD 20892 United States of America + email: robert.innis@nih.gov + - given-names: Robert E. + family-names: Smith + website: http://www.mrtrix.org + orcid: https://orcid.org/0000-0003-3636-4642 + affiliation: + The Florey Institute of Neuroscience and Mental Health, Epilepsy + Neuroinformatics Laboratory, Heidelberg, Victoria, 3084, Australia + email: robert.smith@florey.edu.au + - given-names: Robert + family-names: Knight + - given-names: Robert + family-names: Luke + website: https://github.com/rob-luke + - given-names: Robert + family-names: Oostenveld + website: https://robertoostenveld.nl + orcid: https://orcid.org/0000-0002-1974-1293 + affiliation: + Radboud University, Donders Institute, Nijmegen, 6525 EN, The Netherlands + email: r.oostenveld@donders.ru.nl + - given-names: Roberto + family-names: Toro + website: https://github.com/r03ert0 + - given-names: Rohan + family-names: Goyal + - given-names: Ross W. + family-names: Blair + website: https://github.com/rwblair + - given-names: Russell A. + family-names: Poldrack + website: http://www.poldracklab.org + orcid: https://orcid.org/0000-0001-6755-0259 + affiliation: + Stanford University, Stanford, CA 94305 United States of America + email: russpold@stanford.edu + - given-names: Rémi + family-names: Adon + website: https://github.com/remiadon + - given-names: Samir + family-names: Das + website: https://github.com/samirdas + - given-names: Samuel + family-names: Garcia + - given-names: Samuel + family-names: Nastase + website: https://snastase.github.io/ + orcid: https://orcid.org/0000-0001-7013-5275 + affiliation: Princeton University + email: sam.nastase@gmail.com + - given-names: Sara + family-names: Elgayar + - given-names: Sasha + family-names: D'Ambrosio + orcid: https://orcid.org/0000-0002-6600-6419 + affiliation: + University of Milan, Department of Biomedical and Clinical Sciences, + Milan, 20137, Italy + email: sasha.dambrosio@unimi.it + - given-names: Satrajit S. + family-names: Ghosh + website: https://satra.cogitatum.org + orcid: https://orcid.org/0000-0002-5312-6729 + affiliation: + MIT, McGovern Institute for Brain Research, Cambridge, 02139, United + States of America + email: satra@mit.edu + - given-names: Scott + family-names: Makeig + website: https://sccn.ucsd.edu/~scott + orcid: https://orcid.org/0000-0002-9048-8438 + affiliation: + Institute for Neural Computation, University of California San Diego, La + Jolla, CA 92-93-0955, United States of America + email: smakeig@gmail.com + - given-names: Sein + family-names: Jeung + website: https://github.com/sjeung + orcid: https://orcid.org/0000-0002-0247-087X + affiliation: Technical University Berlin + email: seinjeung@gmail.com + - given-names: Shashank + family-names: Bansal + - given-names: Sjoerd B. + family-names: Vos + website: https://research-repository.uwa.edu.au/en/persons/sjoerd-vos + orcid: https://orcid.org/0000-0002-8502-4487 + affiliation: + University of Western Australia;Centre for Microscopy, Characterisation, + and Analysis;Perth;WA;6009;Australia + - given-names: Soichi + family-names: Hayashi + website: https://github.com/soichih + orcid: https://orcid.org/0000-0003-3641-3491 + affiliation: Indiana University + - given-names: Stefan + family-names: Appelhoff + website: https://www.stefanappelhoff.com + orcid: https://orcid.org/0000-0001-8002-0877 + affiliation: Max Planck Institute for Human Development + email: stefan.appelhoff@mailbox.org + - given-names: Stephan + family-names: Bickel + - given-names: Suyash + family-names: Bhogawar + website: https://www.linkedin.com/in/suyashb/ + - given-names: Sylvain + family-names: Baillet + website: https://github.com/sbaillet + - given-names: Sylvain + family-names: Takerkart + website: https://github.com/SylvainTakerkart + orcid: https://orcid.org/0000-0001-8410-0962 + affiliation: + CNRS, Institut des Neurosciences de la Timone, Marseille, France + email: sylvain.takerkart@univ-amu.fr + - given-names: Sébastien + family-names: Tourbier + website: https://github.com/sebastientourbier + orcid: https://orcid.org/0000-0002-4441-899X + affiliation: + Lausanne University Hospital (CHUV), Department of Clinical Neurosciences + (DNC), Lausanne, 1007, Switzerland + email: sebastien.tourbier1@gmail.com + - given-names: Sören + family-names: Grothkopp + affiliation: Technical University Berlin + email: s.grothkopp@secure.mailbox.org + - given-names: Tal + family-names: Pal Attia + website: https://github.com/tpatpa + - given-names: Tal + family-names: Yarkoni + website: https://github.com/tyarkoni + orcid: https://orcid.org/0000-0002-6558-5113 + - given-names: Tamas + family-names: Spisak + website: https://pni-lab.github.io/ + orcid: https://orcid.org/0000-0002-2942-0821 + affiliation: + University Hospital Essen, Center for Translational and Behavioral + Neuroscience, Department of Diagnostic and Interventional Radiology and + Neuroradiology + email: tamas.spisak@uk-essen.de + - given-names: Tamás + family-names: Józsa + - given-names: Taylor + family-names: Salo + website: https://tsalo.github.io + orcid: https://orcid.org/0000-0001-9813-3167 + affiliation: + University of Pennsylvania, Department of Psychiatry, Philadelphia, + Pennsylvania, 19104, United States of America + email: tsalo006@fiu.edu + - given-names: Teon L. + family-names: Brooks + website: https://teonbrooks.com + orcid: https://orcid.org/0000-0001-7344-3230 + email: teon.brooks@gmail.com + - given-names: Thomas E. + family-names: Nichols + website: http://nisox.org + orcid: https://orcid.org/0000-0002-4516-5103 + affiliation: University of Oxford, Big Data Institute, Oxford, OX3 7LF, UK + email: thomas.nichols@BDI.OX.AC.UK + - given-names: Thomas + family-names: Funck + website: https://github.com/tfunck + - given-names: Thomas + family-names: Kirk + - given-names: Thomas + family-names: Okell + orcid: https://orcid.org/0000-0001-8258-0659 + affiliation: University of Oxford + - given-names: Tibor + family-names: Auer + website: https://tiborauer.github.io + orcid: https://orcid.org/0000-0001-5153-1424 + affiliation: + University of Surrey, School of Psychology, Guildford, GU2 7XH, UK + email: tibor.auer@gmail.com + - given-names: Timo + family-names: Dickscheid + website: https://go.fzj.de/dickscheid + orcid: https://orcid.org/0000-0002-9051-3701 + affiliation: + Forschungszentrum Jülich, Institute of Neuroscience and Medicine, Jülich, + 52428, Germany + email: t.dickscheid@fz-juelich.de + - given-names: Timotheus + family-names: Berg + website: https://github.com/timo-berg + orcid: https://orcid.org/0000-0002-0746-3679 + affiliation: Technical University Berlin + email: timo.berg@campus.tu-berlin.de + - given-names: Tobey + family-names: Betthauser + orcid: https://orcid.org/0000-0001-8856-1352 + affiliation: University of Wisconsin-Madison + - given-names: Tobias + family-names: Bengfort + website: http://tobib.spline.de + email: tobias.bengfort@posteo.de + - given-names: Tom + family-names: Hampshire + - given-names: Tor + family-names: Wager + website: https://github.com/torwager + - given-names: Travis + family-names: Riddle + orcid: https://orcid.org/0000-0001-8160-3986 + affiliation: National Police Foundation + - given-names: Tristan + family-names: Glatard + website: https://github.com/glatard + orcid: https://orcid.org/0000-0003-2620-5883 + - given-names: Ulrike + family-names: Bingel + orcid: https://orcid.org/0000-0002-9528-3204 + - given-names: Vanessa + family-names: Sochat + website: https://github.com/vsoch + orcid: https://orcid.org/0000-0002-4387-3819 + - given-names: Vasudev + family-names: Raguram + - given-names: Vince D. + family-names: Calhoun + website: http://trendscenter.org + affiliation: + Tri-institutional Center for Translational Research in Neuroimaging and + Data Science (TReNDS), Georgia State, Georgia Tech, and Emory, Atlanta, GA + 30030 + email: vcalhoun@gsu.edu + - given-names: Vittorio + family-names: Iacovella + orcid: https://orcid.org/0000-0002-0853-1573 + - given-names: Vladimir + family-names: Litvak + orcid: https://orcid.org/0000-0001-8535-7452 + affiliation: UCL Queen Square Institute of Neurology + - given-names: Wietske + family-names: van der Zwaag + - given-names: William + family-names: Clarke + - given-names: William + family-names: Triplett + - given-names: Wouter V. + family-names: Potters + website: https://www.wouterpotters.nl + orcid: https://orcid.org/0000-0003-1249-1196 + - given-names: Xiangrui + family-names: Li + website: https://github.com/xiangruili + affiliation: The Ohio State University, United States of America + email: xiangrui.li@gmail.com + - given-names: Yaroslav O. + family-names: Halchenko + website: http://www.onerussian.com + orcid: https://orcid.org/0000-0003-3456-2493 + affiliation: Dartmouth College, United States of America + email: debian@onerussian.com + - given-names: Yoni + family-names: Ashar + orcid: https://orcid.org/0000-0001-5602-5619 + - given-names: Yuan + family-names: Wang + - given-names: Zachary + family-names: Michael + - given-names: ezemikulan + website: https://github.com/ezemikulan + - given-names: josator2 + website: https://github.com/josator2 + - given-names: monkeyman192 + website: https://github.com/monkeyman192 + - given-names: Étienne + family-names: Bergeron + orcid: https://orcid.org/0000-0002-8329-7852 + affiliation: Collège Sainte-Anne de Lachine diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index e74bbf98f4..40fae2e3ea 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -157,6 +157,8 @@ Some others need to fixed manually: to some readers and try to replace them by common English equivalents such as `"for example"`, `"that is"`, `"and so on"`. +The BIDS specification is written in American English. + #### Soft rules We follow certain "soft rules" in the way we format the specification in Markdown. @@ -716,7 +718,7 @@ either make a change to the part of a pull request or you can edit this [page](https://github.com/bids-standard/bids-specification/wiki/Recent-Contributors) of the specification WIKI. -The WIKI is then synced with the specification with evert new release of the specifications. +The WIKI is then synced with the specification with every new release of the specifications. ## Thank you! diff --git a/DECISION-MAKING.md b/DECISION-MAKING.md index eef8568a18..05e4c91887 100644 --- a/DECISION-MAKING.md +++ b/DECISION-MAKING.md @@ -14,20 +14,22 @@ BIDS governance. ### Steering Group -Curent and past members of the steering group can be found +Current and past members of the steering group can be found [here](https://bids.neuroimaging.io/governance.html#bids-steering-group). ### Maintainers Group -| Name | Time commitment | Scope | -|--------------------------------------------------------------------------------|-----------------|----------------------------------| -| Stefan Appelhoff ([@sappelhoff](https://github.com/sappelhoff)) | 5h/week | Lead Maintainer | -| Chris Markiewicz ([@effigies](https://github.com/effigies)) | 5h/week | | -| Taylor Salo ([@tsalo](https://github.com/tsalo)) | 3h/week | MRI | -| Remi Gau ([@Remi-Gau](https://github.com/Remi-Gau)) | 3h/week | Community development, MRI | -| Anthony Galassi ([@bendhouseart](https://github.com/bendhouseart)) | 3h/week | PET, Community development | -| Eric Earl ([@ericearl](https://github.com/ericearl)) | 2h/week | | -| Ross Blair ([@rwblair](https://github.com/rwblair)) | | Maintainer of the bids-validator | +| Name | Time commitment | Scope | Joined | +|---------------------------------------------------------------------------|-----------------|---------------------------------------|----------| +| Stefan Appelhoff ([@sappelhoff](https://github.com/sappelhoff)) | 5h/week | Lead Maintainer | Mar 2020 | +| Chris Markiewicz ([@effigies](https://github.com/effigies)) | 5h/week | | Mar 2020 | +| Ross Blair ([@rwblair](https://github.com/rwblair)) | | Maintainer of the bids-validator | Mar 2020 | +| Taylor Salo ([@tsalo](https://github.com/tsalo)) | 3h/week | MRI | Sep 2020 | +| Remi Gau ([@Remi-Gau](https://github.com/Remi-Gau)) | 3h/week | Community development, MRI | Oct 2020 | +| Anthony Galassi ([@bendhouseart](https://github.com/bendhouseart)) | 3h/week | PET, Community development | Sep 2021 | +| Eric Earl ([@ericearl](https://github.com/ericearl)) | 2h/week | | Dec 2021 | +| Christine Rogers ([@christinerogers](https://github.com/christinerogers)) | 2h/mo | Interoperability, EEG and multi-modal | Apr 2023 | +| Nell Hardcastle ([@nellh](https://github.com/nellh)) | 2h/week | | Jul 2023 | In addition to the [BIDS Governance](https://bids.neuroimaging.io/governance.html#bids-maintainers-group) classification of a maintainer, maintainers may declare a limited scope of responsibility. @@ -39,9 +41,9 @@ contributions elsewhere are welcome, as well. #### Past maintainers group members -| Name | -|--------------------------------------------------------------------------------| -| Franklin Feingold ([@franklin-feingold](https://github.com/franklin-feingold)) | +| Name | Duration | +|--------------------------------------------------------------------------------|---------------------| +| Franklin Feingold ([@franklin-feingold](https://github.com/franklin-feingold)) | Mar 2020 - Jul 2022 | ### BEP Leads Group diff --git a/Makefile b/Makefile index 2662661f38..a56b672d82 100644 --- a/Makefile +++ b/Makefile @@ -1,3 +1,12 @@ +.PHONY: tools/contributors.tsv + +validate_citation_cff: CITATION.cff + cffconvert --validate + +update_contributors: + python tools/add_contributors.py + python tools/print_contributors.py + yarn all-contributors generate runprettier: prettier --write "src/schema/**/*.yaml" diff --git a/README.md b/README.md index 796a057f65..54b7bd11d7 100644 --- a/README.md +++ b/README.md @@ -7,11 +7,12 @@ bids-logo The [Brain Imaging Data Structure (BIDS)](https://bids.neuroimaging.io) is an emerging standard for the -organisation of neuroimaging data. +organization of neuroimaging data. In this repository, we develop the [BIDS specification](https://bids-specification.readthedocs.io/en/latest/). + # When to use BIDS To organize your data in BIDS, all you need is neuro data, a computer, and the @@ -28,6 +29,7 @@ BIDS currently supports the following data modalities with more to come in the f - PET - microscopy - NIRS +- motion # Formatting your data with BIDS @@ -59,3 +61,431 @@ We ask that all contributions to BIDS across all project-related spaces (includi [GitHub](https://github.com/bids-standard), the [Google group](https://groups.google.com/forum/#!forum/bids-discussion), and newsletter emails), adhere to our [code of conduct](https://github.com/bids-standard/bids-specification/blob/master/CODE_OF_CONDUCT.md). + +## Contributors + +Thanks goes to these wonderful people. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

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+ + + + + diff --git a/Release_Protocol.md b/Release_Protocol.md index cb1363f750..5773da78e3 100644 --- a/Release_Protocol.md +++ b/Release_Protocol.md @@ -42,6 +42,10 @@ git checkout -b rel/1.2.0 upstream/master ### 2. Update the version, contributors list, previous version URLs, and the Changelog +#### 2.1 Update the version + +Update the version in CITATION.cff. + Change the "Unreleased" heading in [src/CHANGES.md](https://github.com/bids-standard/bids-specification/blob/master/src/CHANGES.md) to `v`, and link to the target ReadTheDocs URL. @@ -64,17 +68,38 @@ In the figure below, we update `v1.2.0-dev` to `v1.2.0`. Additionally, implement the same change in the version name perform above in the `src/schema/BIDS_VERSION` file. -Note: this will make our continuous integration ([CircleCI](https://circleci.com/)) fail. This fails because the URL of the new ReadTheDocs rendering has not been generated at this time. It will be generated once the GitHub release has been completed. +Note: +this will make our continuous integration ([CircleCI](https://circleci.com/)) fail. +This fails because the URL of the new ReadTheDocs rendering has not been generated at this time. +It will be generated once the GitHub release has been completed. + +#### 2.2 Update the contributors list Synchronize the [Contributors appendix](https://github.com/bids-standard/bids-specification/blob/master/src/appendices/contributors.md) with the [Contributors wiki page](https://github.com/bids-standard/bids-specification/wiki/Contributors) to ensure all contributors are duly credited. Be sure not to remove credits if both have been edited. +- add new contributors info to the `tools/new_contributors.tsv` file. +- make sure that you have installed + - all the python packages listed in `tools/requirements.txt` + - the [allcontributors](https://allcontributors.org/docs/en/cli/installation) package +- run: +```bash +make update_contributors +``` +- you may need to fix some errors in the contributions names in case of crash +- make sure to review the changes and not commit them blindly +- commit the changes + +#### 2.3 Update the previous version URLs + Please change the previous version links from GitHub to ReadTheDocs. In the figure below, we update v1.2.2. ![github-to-rtd](release_images/GitHub_to_RTD_spec_rendering.png "github-to-rtd") +#### 2.4 Update the Changelog + Review `src/CHANGES.md` to ensure that the document produces a changelog that is useful to a reader of the specification. For example, several small PRs fixing typos might be merged into a single line-item, or less @@ -214,6 +239,8 @@ on the expected next version. Additionally, the same version name set above in `mkdocs.yaml` should be set in the `src/schema/BIDS_VERSION` schema version file. +Similarly update the version in CITATION.cff with a `dev` suffix. + ### 10. Uploading the stable PDF to Zenodo 1. Open a private browser window diff --git a/macros_doc.md b/macros_doc.md index bf8b10dae6..6ec9fcf5a2 100644 --- a/macros_doc.md +++ b/macros_doc.md @@ -92,6 +92,7 @@ All the macros we use are in listed in this | make_suffix_table | Generate a markdown table of suffix information. | Yes | [link](https://github.com/bids-standard/bids-specification/blob/9201b203ffaa72d83b2fa30d1c61f46f089f77de/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md?plain=1#L199) | | define_common_principles | List the common principles and definitions. | Yes | [link](https://github.com/bids-standard/bids-specification/blob/831ee55577b91aaa110153e9269e7829b095fb6f/src/02-common-principles.md?plain=1#L12) | | define_allowed_top_directories | Create a list of allowed top-level directories with their descriptions. | Yes | [link](https://github.com/bids-standard/bids-specification/blob/2a701fd034d51c25e8fe18ba67bb7b76621ba477/src/02-common-principles.md?plain=1#L124) | +| render_description | Renders the description of an object in the schema. | Yes | [link] (???) | ## When should I use a macro? diff --git a/mkdocs.yml b/mkdocs.yml index e633f544e2..1a24697360 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -1,4 +1,4 @@ -site_name: Brain Imaging Data Structure v1.8.1-dev +site_name: Brain Imaging Data Structure v1.9.0-dev site_url: https://bids-specification.readthedocs.io/en/stable/ nav: - The BIDS Specification: @@ -17,6 +17,7 @@ nav: - Positron Emission Tomography: modality-specific-files/positron-emission-tomography.md - Microscopy: modality-specific-files/microscopy.md - Near-Infrared Spectroscopy: modality-specific-files/near-infrared-spectroscopy.md + - Motion: modality-specific-files/motion.md - Derivatives: - BIDS Derivatives: derivatives/introduction.md - Common data types and metadata: derivatives/common-data-types.md diff --git a/pdf_build_src/pandoc_script.py b/pdf_build_src/pandoc_script.py index 54e6ec1ba5..b7b1842b96 100644 --- a/pdf_build_src/pandoc_script.py +++ b/pdf_build_src/pandoc_script.py @@ -2,7 +2,6 @@ This is done once the duplicate src directory is processed. """ -import os import subprocess import yaml from pathlib import Path diff --git a/readthedocs.yml b/readthedocs.yml index b5e50426b3..cc3f461fc7 100644 --- a/readthedocs.yml +++ b/readthedocs.yml @@ -3,7 +3,7 @@ version: 2 build: os: ubuntu-22.04 tools: - python: "3.10" + python: "3.11" jobs: pre_build: - bst -v export --output src/schema.json diff --git a/src/CHANGES.md b/src/CHANGES.md index 59849ec54c..261bb25a44 100644 --- a/src/CHANGES.md +++ b/src/CHANGES.md @@ -2,7 +2,38 @@ ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD) +- \[FIX] Update links to BIDS examples [#1545](https://github.com/bids-standard/bids-specification/pull/1545) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[FIX] match subject label in folder and filename in func example [#1536](https://github.com/bids-standard/bids-specification/pull/1536) ([Remi-Gau](https://github.com/Remi-Gau)) +- FIX: Trail MEG directory formats with `/` [#1534](https://github.com/bids-standard/bids-specification/pull/1534) ([effigies](https://github.com/effigies)) +- \[ENH] Permit CITATION.cff as structured alternative to some dataset_description fields [#1525](https://github.com/bids-standard/bids-specification/pull/1525) ([effigies](https://github.com/effigies)) +- \[FIX] Add missing column description in physio example [#1514](https://github.com/bids-standard/bids-specification/pull/1514) ([sappelhoff](https://github.com/sappelhoff)) +- \[ENH] Clarify that data files must be uniquely identified by entities/suffix [#1508](https://github.com/bids-standard/bids-specification/pull/1508) ([sappelhoff](https://github.com/sappelhoff)) +- DOC: Auto-generate full API docs [#1505](https://github.com/bids-standard/bids-specification/pull/1505) ([effigies](https://github.com/effigies)) +- \[INFRA] Publish schema tools API docs to additional ReadTheDocs site [#1491](https://github.com/bids-standard/bids-specification/pull/1491) ([bendhouseart](https://github.com/bendhouseart)) +- \[FIX] Remove references to unspecified aslcontext.json [#1485](https://github.com/bids-standard/bids-specification/pull/1485) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[FIX] Revert index (entity format) definition to be a non-negative number, permitting zero [#1482](https://github.com/bids-standard/bids-specification/pull/1482) ([TheChymera](https://github.com/TheChymera)) +- ENH: Add version list to schema.meta and a warning on unknown BIDSVersion [#1472](https://github.com/bids-standard/bids-specification/pull/1472) ([effigies](https://github.com/effigies)) +- \[FIX] Clean up qMRI RB1COR notes [#1465](https://github.com/bids-standard/bids-specification/pull/1465) ([lukeje](https://github.com/lukeje)) +- \[ENH] Allow fractional seconds in StartTime [#1459](https://github.com/bids-standard/bids-specification/pull/1459) ([sappelhoff](https://github.com/sappelhoff)) +- \[MISC] consistently list filename templates; `ext` --> `extension`; `\_photo.jpg` --> `\_photo.\` [#1458](https://github.com/bids-standard/bids-specification/pull/1458) ([sappelhoff](https://github.com/sappelhoff)) +- \[FIX] Demote `sample` and `value` columns in `events.tsv` from OPTIONAL to arbitrary [#1457](https://github.com/bids-standard/bids-specification/pull/1457) ([sappelhoff](https://github.com/sappelhoff)) +- ENH: Clarify shape of PDT2 images and recommend acq entity for split PDw/T2w images [#1448](https://github.com/bids-standard/bids-specification/pull/1448) ([effigies](https://github.com/effigies)) +- \[ENH] clarify guiding principles for requirement levels [#1444](https://github.com/bids-standard/bids-specification/pull/1444) ([sappelhoff](https://github.com/sappelhoff)) +- \[FIX] Clarify that dataset_description.Genetics object is required for genetics data [#1442](https://github.com/bids-standard/bids-specification/pull/1442) ([sappelhoff](https://github.com/sappelhoff)) +- \[ENH] Clarify that BIDS specification is in American English [#1439](https://github.com/bids-standard/bids-specification/pull/1439) ([yarikoptic](https://github.com/yarikoptic)) +- \[MISC] Link to new BEP guidelines. [#1426](https://github.com/bids-standard/bids-specification/pull/1426) ([arokem](https://github.com/arokem)) +- \[FIX] reorganize anat filename templates [#1419](https://github.com/bids-standard/bids-specification/pull/1419) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[FIX] Rename `channels.tsv` column: `orientation\_component` to `component` [#1417](https://github.com/bids-standard/bids-specification/pull/1417) ([sjeung](https://github.com/sjeung)) +- \[ENH] Some missing docstrings for bidsschematools [#1413](https://github.com/bids-standard/bids-specification/pull/1413) ([anibalsolon](https://github.com/anibalsolon)) +- \[FIX] fixing some minor issues introduced recently [#1411](https://github.com/bids-standard/bids-specification/pull/1411) ([yarikoptic](https://github.com/yarikoptic)) +- SCHEMA: Implement some fairly easy rules [#1410](https://github.com/bids-standard/bids-specification/pull/1410) ([effigies](https://github.com/effigies)) +- \[REF] refactor institution and task tables [#1397](https://github.com/bids-standard/bids-specification/pull/1397) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[ENH] Add paragraph about richness versus distinctness in filenames [#1392](https://github.com/bids-standard/bids-specification/pull/1392) ([CPernet](https://github.com/CPernet)) +- \[FIX] Updated HED score library version [#1390](https://github.com/bids-standard/bids-specification/pull/1390) ([VisLab](https://github.com/VisLab)) +- \[FIX] Updated links and fixed typos in hed appendix [#1383](https://github.com/bids-standard/bids-specification/pull/1383) ([VisLab](https://github.com/VisLab)) +- \[ENH] add screen parameters metadata [#1369](https://github.com/bids-standard/bids-specification/pull/1369) ([Remi-Gau](https://github.com/Remi-Gau)) - RF: allow for any "recording" file to be listed in \_scans.tsv not just "neural recording" [#1368](https://github.com/bids-standard/bids-specification/pull/1368) ([yarikoptic](https://github.com/yarikoptic)) +- \[FIX] wrong usage of DOI in SourceDatasets example [#1361](https://github.com/bids-standard/bids-specification/pull/1361) ([sappelhoff](https://github.com/sappelhoff)) - \[FIX] make references to Neuromag/Elekta/MEGIN consistent [#1359](https://github.com/bids-standard/bids-specification/pull/1359) ([sappelhoff](https://github.com/sappelhoff)) - \[DOC] link to steering group section on bids website [#1358](https://github.com/bids-standard/bids-specification/pull/1358) ([Remi-Gau](https://github.com/Remi-Gau)) - \[ENH] Add reference for ASL BEP [#1357](https://github.com/bids-standard/bids-specification/pull/1357) ([Remi-Gau](https://github.com/Remi-Gau)) @@ -11,8 +42,12 @@ - \[ENH] Recommend gzip header fields be set to empty values [#1349](https://github.com/bids-standard/bids-specification/pull/1349) ([kousu](https://github.com/kousu)) - \[FIX] clarify TriggerChannelCount and TRIG type [#1342](https://github.com/bids-standard/bids-specification/pull/1342) ([sappelhoff](https://github.com/sappelhoff)) - \[ENH] Add qMRI fieldmap filename templates [#1336](https://github.com/bids-standard/bids-specification/pull/1336) ([Remi-Gau](https://github.com/Remi-Gau)) +- ENH: Introduce GIFTI formats in derivatives [#1333](https://github.com/bids-standard/bids-specification/pull/1333) ([effigies](https://github.com/effigies)) - \[ENH] Add ParallelReductionFactorOutOfPlane to MRI metadata [#1221](https://github.com/bids-standard/bids-specification/pull/1221) ([lukeje](https://github.com/lukeje)) - \[ENH]\[SCHEMA] Adding an OPTIONAL \_task-\