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Potters", + "profile": "https://www.wouterpotters.nl" + }, + { + "avatar_url": "https://avatars.githubusercontent.com/u/19894855?v=4", + "contributions": [ + "doc", + "code" + ], + "login": "xiangruili", + "name": "Xiangrui Li", + "profile": "https://github.com/xiangruili" + }, + { + "avatar_url": [ + "https://avatars.githubusercontent.com/u/39889?v=4" + ], + "contributions": [ + "doc", + "talk", + "tool", + "question", + "bug", + "code", + "data", + "fundingFinding", + "ideas", + "plugin", + "review", + "userTesting", + "infra" + ], + "login": "yarikoptic", + "name": "Yaroslav O. 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 f884388e..ee82d5b0 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -2,7 +2,7 @@ version: 2.1 jobs: build_docs: docker: - - image: cimg/python:3.8 + - image: cimg/python:3.12-node steps: # checkout code to default ~/project - checkout @@ -21,14 +21,15 @@ jobs: - persist_to_workspace: # the mkdocs build outputs are in ~/project/site root: ~/project - paths: site + paths: + - site - store_artifacts: path: ~/project/site/ destination: dev_docs check_links: docker: - - image: cimg/python:3.8 + - image: cimg/python:3.12 steps: # checkout code to default ~/project - checkout @@ -66,14 +67,16 @@ 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 +86,7 @@ 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 @@ -128,7 +132,8 @@ jobs: - persist_to_workspace: # raw generated changelog in ~/changelog_build/CHANGES.md root: ~/. - paths: changelog_build + paths: + - changelog_build # Lint and fix the auto generated changes.md file lint_generated_changelog: @@ -161,7 +166,8 @@ jobs: - persist_to_workspace: # linted and fixed changelog in ~/changelog_build/CHANGES.md root: ~/. - paths: changelog_build + paths: + - changelog_build # Push built changelog to repo commit_generated_changelog: @@ -175,7 +181,7 @@ jobs: - attach_workspace: # fixed+linted changelog in ~/changelog_build/CHANGES.md at: ~/. - - deploy: + - run: name: Changelog deployment # $CHANGE_TOKEN is generated via the GitHub web UI, and then securely stored within CircleCI web UI command: | @@ -194,7 +200,6 @@ jobs: fi workflows: - version: 2 search_build: jobs: - build_docs diff --git a/.codecov.yml b/.codecov.yml index 552591d6..b46689d1 100644 --- a/.codecov.yml +++ b/.codecov.yml @@ -1,4 +1,5 @@ ignore: - - "*/*/tests/*" - - "**/tests/*" - + - "*/*/tests/*" + - "**/tests/*" +codecov: + token: 7e84a7fb-8f7e-45f5-8dcc-9f5219fa3855 diff --git a/.codespell_dict b/.codespell_dict new file mode 100644 index 00000000..e4e9c7cc --- /dev/null +++ b/.codespell_dict @@ -0,0 +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 +Folder->Directory +Folders->Directories diff --git a/.codespellrc b/.codespellrc new file mode 100644 index 00000000..22cd48ca --- /dev/null +++ b/.codespellrc @@ -0,0 +1,8 @@ +[codespell] +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,manuel +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 00000000..5c738942 --- /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/codespell.yml b/.github/workflows/codespell.yml deleted file mode 100644 index db5f92e7..00000000 --- a/.github/workflows/codespell.yml +++ /dev/null @@ -1,20 +0,0 @@ ---- -name: Codespell - -on: - push: - branches: [master] - pull_request: - branches: [master] - -jobs: - codespell: - name: Check for spelling errors - runs-on: ubuntu-latest - - steps: - - uses: actions/checkout@v3 - - uses: codespell-project/actions-codespell@master - with: - skip: js,*.svg - ignore_words_list: fo,te,als diff --git a/.github/workflows/labeler.yml b/.github/workflows/labeler.yml new file mode 100644 index 00000000..355ce3d2 --- /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/markdown_style.yml b/.github/workflows/markdown_style.yml deleted file mode 100644 index d587f572..00000000 --- a/.github/workflows/markdown_style.yml +++ /dev/null @@ -1,17 +0,0 @@ -name: Check Markdown style - -on: [push, pull_request] - -jobs: - markdown-style: - runs-on : ubuntu-latest - steps: - - uses: actions/checkout@v3 - - name: Setup NodeJS - uses: actions/setup-node@v3 - with: - node-version: 14 - - name: Install dependencies - run: npm install `cat npm-requirements.txt` - - name: Run style checks - run: npx remark src/*.md src/*/*.md --frail --rc-path .remarkrc diff --git a/.github/workflows/no-bad-latin.yml b/.github/workflows/no-bad-latin.yml deleted file mode 100644 index e6e699e5..00000000 --- a/.github/workflows/no-bad-latin.yml +++ /dev/null @@ -1,57 +0,0 @@ - -# This action initially adopted from The Turing Way from in October 2020. -# doi:10.5281/zenodo.3233853 -# https://github.com/alan-turing-institute/the-turing-way/blob/af98c94/.github/workflows/no-bad-latin.yml -# -# This action triggers the script tools/no-bad-latin.py to and will throw an error if any latin expression (like e.g. or i.e.) is detected: -# -# This action will be triggered -# - on a push to master -# - on a PR to the master branch and will only check files that were modified in src - -name: Check for Latin Phrases - -# Decide when to run the tests -# -# This configuration sets the test to run on pushes to master -# and on pull requests that are opened to master -on: - push: - branches: - - master - pull_request: - branches: - - master - -# Set up the Continuous Integration job -jobs: - latin-phrases: - # Run on the latest Ubuntu distribution - runs-on: ubuntu-latest - # This section collects together the steps involved in running the test - steps: - # Checkout the repository. Relies on another GH-Action. - - uses: actions/checkout@v3 - # Set up the Python version. Relies on another GH-Action. - - name: Setup Python 3.7 - uses: actions/setup-python@v4 - with: - python-version: 3.7 - # Install Python dependencies - - name: Install dependencies - working-directory: ./tools - run: | - python -m pip install --upgrade pip - python -m pip install -r requirements.txt - # Run a Python script - - name: Run Python script to check for latin phrases - Master - working-directory: ./tools - if: github.event_name == 'push' && github.ref == 'refs/heads/master' - run: | - python no-bad-latin.py - - - name: Run Python script to check for latin phrases - Pull Request - working-directory: ./tools - if: github.event.pull_request - run: | - python no-bad-latin.py --pull-request ${{ github.event.pull_request.number }} diff --git a/.github/workflows/redirect_circleci_artifacts.yml b/.github/workflows/redirect_circleci_artifacts.yml index ff8eb5f5..c40e0512 100644 --- a/.github/workflows/redirect_circleci_artifacts.yml +++ b/.github/workflows/redirect_circleci_artifacts.yml @@ -1,13 +1,18 @@ on: [status] + jobs: circleci_artifacts_redirector_job: runs-on: ubuntu-latest + if: "${{ 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/schemacode_ci.yml b/.github/workflows/schemacode_ci.yml index ffc95096..6cf4dbcd 100644 --- a/.github/workflows/schemacode_ci.yml +++ b/.github/workflows/schemacode_ci.yml @@ -10,6 +10,10 @@ on: branches: - "*" +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + defaults: run: shell: bash @@ -20,16 +24,16 @@ jobs: strategy: matrix: os: ["ubuntu-latest"] - python-version: ["3.10"] + python-version: ["3.11"] steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: "Install build dependencies" run: pip install --upgrade build twine - name: "Install test dependencies on tag" - run: pip install --upgrade pytest pyyaml pandas tabulate + 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 @@ -40,7 +44,7 @@ jobs: run: python -m build tools/schemacode - name: "Check distribution metadata" run: twine check tools/schemacode/dist/* - - uses: actions/upload-artifact@v3 + - uses: actions/upload-artifact@v4 with: name: dist path: tools/schemacode/dist/ @@ -52,21 +56,27 @@ 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", "3.12"] + include: + - os: macos-latest + python-version: 3 + - os: windows-latest + python-version: 3 name: ${{ matrix.os }} with Python ${{ matrix.python-version }} steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: "Set up Python" - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} + allow-prereleases: true - name: "Display Python version" run: python -c "import sys; print(sys.version)" - name: "Fetch packages" - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 with: name: dist path: dist/ @@ -78,10 +88,10 @@ jobs: - name: "Run tests" run: | python -m pytest -vs --pyargs bidsschematools -m "not validate_schema" \ - --cov-append --cov-report=xml --cov=bidsschematools + --cov-append --cov-report=xml --cov=bidsschematools --doctest-modules - name: Upload artifacts - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: unit_${{ matrix.os }}_${{ matrix.python-version }} path: coverage.xml @@ -95,10 +105,10 @@ jobs: strategy: matrix: os: ["ubuntu-latest"] - python-version: ["3.10"] + python-version: ["3.11"] steps: - name: "Fetch packages" - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 with: name: dist path: dist/ @@ -116,38 +126,16 @@ jobs: user: __token__ password: ${{ secrets.PYPI_API_TOKEN }} - flake8-lint: - runs-on: ubuntu-latest - name: Lint schemacode - steps: - - name: Check out source repository - uses: actions/checkout@v3 - - - name: Set up Python environment - uses: actions/setup-python@v4 - with: - python-version: "3.7" - - - name: Install the schemacode package - run: | - python -m pip install --progress-bar off --upgrade pip setuptools wheel - python -m pip install -e ./tools/schemacode[all] - - - name: Run flake8 - working-directory: ./tools/schemacode/ - run: | - flake8 . - validate_schema: runs-on: ubuntu-latest name: Validate schema steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Set Up Python environment - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: - python-version: "3.9" + python-version: "3.11" - name: Install the schemacode package run: | @@ -158,7 +146,7 @@ jobs: run: python -m pytest --pyargs bidsschematools -m "validate_schema" --cov-append --cov-report=xml --cov=bidsschematools - name: Upload artifacts - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: schema_validation path: coverage.xml @@ -170,12 +158,13 @@ jobs: needs: [test, validate_schema] steps: - name: Checkout - uses: actions/checkout@v2 + uses: actions/checkout@v4 - name: Download artifacts - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 - name: Upload to CodeCov - uses: codecov/codecov-action@v3 + uses: codecov/codecov-action@v4 with: + token: ${{ secrets.CODECOV_TOKEN }} # not required but might help API rate limits fail_ci_if_error: true diff --git a/.github/workflows/typescript_build.yml b/.github/workflows/typescript_build.yml deleted file mode 100644 index fd539181..00000000 --- a/.github/workflows/typescript_build.yml +++ /dev/null @@ -1,45 +0,0 @@ -name: "typescript_build" - -on: - push: - branches: - - "master" - paths: - - "tools/typescript/**" - - "src/schema/**" - pull_request: - branches: - - "*" - paths: - - "tools/typescript/**" - - "src/schema/**" - -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 new file mode 100644 index 00000000..5be42a5b --- /dev/null +++ b/.github/workflows/validation.yml @@ -0,0 +1,98 @@ +--- +name: Validation + +on: + push: + branches: [master] + pull_request: + branches: [master] + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +jobs: + # Check for common misspellings + codespell: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: codespell-project/actions-codespell@master + + # Markdown formatting + remark: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-node@v4 + with: + node-version: 14 + - name: Install dependencies + run: npm install `cat npm-requirements.txt` + - name: Run style checks + run: npx remark src/**/*.md --frail --rc-path .remarkrc + + # YAML + yamllint: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + with: + python-version: 3 + - name: Install dependencies + run: pip install yamllint + - name: Lint yml files in src/schema + run: yamllint -f standard src/schema/ -c .yamllint.yml + + # Python best practices + python-style: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + with: + python-version: 3 + - run: python -m pip install --upgrade flake8 black isort[colors] + - run: black --diff --color --check tools/schemacode + - run: isort --diff --color --check tools/schemacode + - run: flake8 + working-directory: tools/schemacode + + # Avoid Latin phrases to improve readability + latin-phrases: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + with: + python-version: 3 + - name: Install dependencies + run: | + python -m pip install --upgrade pip + python -m pip install -r tools/requirements.txt + - name: Run Python script to check for Latin phrases - Master + if: github.event_name == 'push' && github.ref == 'refs/heads/master' + run: | + python no-bad-latin.py + working-directory: tools + - name: Run Python script to check for Latin phrases - Pull Request + if: github.event.pull_request + run: | + python no-bad-latin.py + working-directory: tools + + # Validate CITATION.cff + validate_cff: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + 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/.github/workflows/yml_lint.yml b/.github/workflows/yml_lint.yml deleted file mode 100644 index 8adaff7b..00000000 --- a/.github/workflows/yml_lint.yml +++ /dev/null @@ -1,20 +0,0 @@ -name: Lint yml files - -on: [push, pull_request] - -jobs: - yml-lint: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: 3.9 - - name: Install dependencies - run: pip install yamllint - - name: Lint yml files in src/schema - # for config, see: - # https://yamllint.readthedocs.io/en/stable/configuration.html#custom-configuration-without-a-config-file - run: | - yamllint -f standard src/schema/ -c .yamllint.yml diff --git a/.gitignore b/.gitignore index 2ef07dac..9e8cf66a 100644 --- a/.gitignore +++ b/.gitignore @@ -7,6 +7,7 @@ venvs pdf_build_src/bids-spec.pdf pdf_build_src/bids-spec_pandoc_log.json pdf_build_src/src_copy +pdf_build_src/tests/data/output # JS/NPM package-lock.json @@ -142,6 +143,9 @@ venv.bak/ # mkdocs documentation /site +# schema docs documentation +tools/schemacode/build/* + # mypy .mypy_cache/ .dmypy.json diff --git a/.lgtm.yml b/.lgtm.yml deleted file mode 100644 index 07342104..00000000 --- a/.lgtm.yml +++ /dev/null @@ -1,8 +0,0 @@ ---- -# This file contains configuration for the LGTM tool: https://lgtm.com/ -# The bids-specification repository is continuously scanned by the LGTM tool -# for any security and/or code vulnerabilities. You can find the alert here: -# https://lgtm.com/projects/g/bids-standard/bids-specification/ -queries: - # https://lgtm.com/rules/6770079/ - - exclude: py/unused-import diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0cfb3c4e..baab7834 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,8 +1,9 @@ # See https://pre-commit.com for more information # See https://pre-commit.com/hooks.html for more hooks +exclude: 'tools/schemacode/bidsschematools/tests/data/broken_dataset_description.json' repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.0.1 + rev: v4.5.0 hooks: - id: trailing-whitespace - id: end-of-file-fixer @@ -11,3 +12,55 @@ repos: - id: check-ast - id: check-added-large-files - id: check-case-conflict + - repo: https://github.com/psf/black + rev: 24.3.0 + hooks: + - id: black + files: ^tools/(?!schemacode) + args: ["--verbose"] + - id: black + name: "black bidsschematools" + files: tools/schemacode + args: ["--config", "tools/schemacode/pyproject.toml", "--verbose"] + - repo: https://github.com/pyCQA/isort + rev: 5.13.2 + hooks: + - id: isort + 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: 7.0.0 + hooks: + - id: flake8 + args: [--config=tools/schemacode/setup.cfg] + - repo: https://github.com/pre-commit/mirrors-prettier + rev: v4.0.0-alpha.8 + hooks: + - id: prettier + entry: env PRETTIER_LEGACY_CLI=1 prettier # temporary fix for https://github.com/prettier/prettier/issues/15742 + files: src/schema/.*/.*\.yaml + - repo: https://github.com/codespell-project/codespell + rev: v2.2.6 + hooks: + - id: codespell + args: ["--config=.codespellrc", "--dictionary=-", "--dictionary=.codespell_dict"] + - repo: https://github.com/pre-commit/mirrors-mypy + rev: v1.9.0 + 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/.remarkrc b/.remarkrc index fc065759..8d6c2648 100644 --- a/.remarkrc +++ b/.remarkrc @@ -10,6 +10,7 @@ ["lint-maximum-heading-length", false], ["lint-no-shortcut-reference-link", false], ["lint-no-trailing-spaces"], + ["remark-lint-code-block-style", false], ["lint-no-undefined-references", false] ] } diff --git a/.tributors b/.tributors new file mode 100644 index 00000000..fa5b1a18 --- /dev/null +++ b/.tributors @@ -0,0 +1,3128 @@ +{ + "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: PDFs of the BIDS specification for versions 1.9.0 and above + type: doi + value: 10.5281/zenodo.10175845 + - description: PDFs of the BIDS specification for versions 1.0.0 to 1.8.0 + 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, USA + 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, USA + 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, MA, + 02115, USA + 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: Alizee + family-names: Wickenheiser + affiliation: LORIS, MCIN, Montreal Neurological Institute, McGill University + email: alizee.wickenheiser@mcin.ca + - 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, USA + 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, + USA + - given-names: Brett L. + family-names: Foster + - given-names: Brian A. + family-names: Wandell + - given-names: Brian N. + family-names: Lundstrom + - given-names: Camille + family-names: Maumet + website: https://camillemaumet.com/ + orcid: https://orcid.org/0000-0002-6290-553X + affiliation: Inria, Univ Rennes, CNRS, Inserm, Rennes, 35042, France + - given-names: Carlo + family-names: Miniussi + orcid: https://orcid.org/0000-0002-5436-4745 + affiliation: University of Trento + - given-names: Cecile + family-names: Madjar + affiliation: LORIS, MCIN, Montreal Neurological Institute, McGill University + email: cecile.madjar@mcin.ca + - given-names: Chloé + family-names: Pasturel + - given-names: Chris + family-names: Benjamin + - given-names: Chris + family-names: Gahnström + - given-names: Chris + family-names: Holdgraf + website: http://chrisholdgraf.com + orcid: https://orcid.org/0000-0002-9420-9301 + - given-names: Chris J. + family-names: Gorgolewski + website: http://chrisgorgolewski.org + orcid: https://orcid.org/0000-0003-3321-7583 + affiliation: Google LLC + email: krzysztof.gorgolewski@gmail.com + - given-names: Chris + family-names: Rorden + website: https://www.mricro.com + orcid: https://orcid.org/0000-0002-7554-6142 + affiliation: University of South Carolina, Department of Psychology, Columbia, + SC, 29016, USA + email: crorden6@gmail.com + - given-names: Christian + family-names: Büchel + - given-names: Christian + family-names: Horea + website: http://www.chymera.eu + orcid: https://orcid.org/0000-0001-7037-2449 + affiliation: Dartmouth College, PBS, Hanover NH/USA + email: chr@chymera.eu + - given-names: Christine + family-names: Rogers + orcid: https://orcid.org/0000-0002-9893-8448 + affiliation: McGill Centre for Integrative Neuroscience, Montreal Neurological + Institute + email: christine.rogers@mcgill.ca + - given-names: Christophe + family-names: Phillips + website: https://www.uliege.be/cms/c_9054334/en/directory/?uid=U016440 + orcid: https://orcid.org/0000-0002-4990-425X + affiliation: University of Liège, GIGA CRC in vivo imaging, Liège, 4000, Belgium + email: c.phillips@uliege.be + - given-names: Christopher J. + family-names: Honey + website: https://www.honeylab.org + orcid: https://orcid.org/0000-0002-0745-5089 + affiliation: Johns Hopkins University, Psychological and Brain Sciences, Baltimore, + MD, 21218, United States + - 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, USA + 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, MA 02215 USA + 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 USA + 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, + USA + - 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, USA + 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, USA + 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, USA + 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: Jefferson + family-names: Casimir + affiliation: LORIS, MCIN, Montreal Neurological Institute, McGill University + email: jefferson.casimir@mcin.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 USA + 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: Laetitia + family-names: Fesselier + affiliation: LORIS, MCIN, Montreal Neurological Institute, McGill University + email: laetitia.fesselier@mcin.ca + - 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, USA + 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 + - 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, + USA + 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, USA + 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, + USA + 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, USA + 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 + - 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 USA, MD 20892 USA + 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 USA + 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, MA 02139, + USA + 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, USA + 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: Steven + family-names: Meisler + orcid: https://orcid.org/0000-0002-8888-1572 + affiliation: Program in Speech and Hearing Bioscience and Technology, Harvard + University + email: smeisler@g.harvard.edu + - 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 de Neurosciences de la Timone (INT), 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 + 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, United + Kingdom + 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 + (INM-1), 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: Tyler + family-names: Collins + affiliation: BrockU, LORIS, MCIN, Montreal Neurological Institute, McGill University + email: tyler.collins@mcin.ca + - 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 + 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 + 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/CODEOWNERS b/CODEOWNERS index ec56a06d..54d256bb 100644 --- a/CODEOWNERS +++ b/CODEOWNERS @@ -5,19 +5,15 @@ # Request for Review) please add your GitHub username next to the file you want to # monitor below. -# Add your GitHub name below to get notified about proposed releases -/src/CHANGES.md @chrisgorgo @sappelhoff @CPernet - # Individual sections -/src/01-common-principles.md @chrisgorgo @DimitriPapadopoulos -/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md @chrisgorgo -/src/04-modality-specific-files/03-electroencephalography.md @sappelhoff @ezemikulan -/src/04-modality-specific-files/04-intracranial-electroencephalography.md @ezemikulan -/src/05-derivatives/03-imaging.md @effigies -/src/05-derivatives/04-structural-derivatives.md @edickie @ahoopes -/src/05-derivatives/05-functional-derivatives.md @effigies -/src/05-derivatives/06-diffusion-derivatives.md @francopestilli @oesteban @Lestropie -/src/appendices/meg-file-formats.md @monkeyman192 +/src/common-principles.md @chrisgorgo @DimitriPapadopoulos +/src/modality-specific-files/magnetic-resonance-imaging-data.md @chrisgorgo +/src/modality-specific-files/electroencephalography.md @sappelhoff @ezemikulan +/src/modality-specific-files/intracranial-electroencephalography.md @ezemikulan +/src/derivatives/imaging.md @effigies +/src/derivatives/structural-derivatives.md @edickie @ahoopes +/src/derivatives/functional-derivatives.md @effigies +/src/derivatives/diffusion-derivatives.md @francopestilli @oesteban @Lestropie # The schema /src/schema/ @tsalo @erdalkaraca diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index e04c2374..c34f9cb5 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -157,11 +157,13 @@ 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. -These rules are sometimes for internal consistency in terms of styling and aesthetics, +These rules are sometimes for internal consistency in terms of styling and esthetics, but several of them are also there because they help the workflow of tracking changes, reviewing them on GitHub, and making code suggestions. @@ -224,6 +226,37 @@ That would look like this: |--------------|----------------------------------------------------------| | Manufacturer | Manufacturer of the equipment, for example (`"Siemens"`) | + +#### MkDocs admonitions + +It is possible to use [Mkdocs admonitions](https://squidfunk.github.io/mkdocs-material/reference/admonitions/#inline-blocks-inline-end) +to highlight certain aspect of the specification. + +Admonitions are written like this: + +```` +!!! note "displayed heading is preceded by a keyword and 3 `!`" + + Body of the admonition + can be written on several lines, + but must be always preceded by 4 spaces. +```` + +The keyword for the heading must be one of the following: + +- note +- abstract +- info +- tip +- success +- question +- warning +- failure: octicons +- danger +- bug +- example +- quote + ## Using macros We use [mkdocs-macros](https://mkdocs-macros-plugin.readthedocs.io/en/latest/) @@ -310,8 +343,8 @@ The third command ensures to install the BIDS schema code as an "editable" insta so that if you make changes to the schema files, these are automatically reflected in the sourcecode. -Note that if you need to work on the some of the Python code -that is used to render the specification, +Note that if you need to work on the some of the Python code +that is used to render the specification, you will probably have to also run: ```bash @@ -696,6 +729,8 @@ the `master` branch of the specification via a "Merge commit" see the [GitHub help page](https://help.github.com/en/articles/about-merge-methods-on-github) for more information on merge methods). +![merge-commit](release_images/merge_commit.png "merge-commit") + Note that for pull requests starting with `REL:`, no changelog is generated. To exclude pull requests from showing up in the changelog, they have to be labeled with @@ -707,16 +742,14 @@ BIDS follows the [all-contributors](https://github.com/kentcdodds/all-contributors) specification, so we welcome and recognize all contributions from documentation to testing to code development. -You can see a list of current contributors in the -[BIDS specification](https://github.com/bids-standard/bids-specification/blob/master/src/appendices/contributors.md). - -If you have made any type of contributions to the BIDS specifications, you can -either make a change to the -[contributors document](./src/appendices/contributors.md) and commit as -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. +You can see a list of contributors in the +[contributors appendix](https://bids-specification.readthedocs.io/en/stable/appendices/contributors.html) +of the BIDS specification. + +If you have made any type of contributions to BIDS, +we encourage you to enter or update your information in the +[Contributors wiki page](https://github.com/bids-standard/bids-specification/wiki/Recent-Contributors) +according to the instructions listed there. ## Thank you! diff --git a/DECISION-MAKING.md b/DECISION-MAKING.md index 8ad8bbdb..a29b4b86 100644 --- a/DECISION-MAKING.md +++ b/DECISION-MAKING.md @@ -14,31 +14,23 @@ BIDS governance. ### Steering Group -| Name | -|------------------------------------------------------------------------------| -| Guiomar Niso ([@guiomar](https://github.com/guiomar)) | -| Melanie Ganz ([@melanieganz](https://github.com/melanieganz)) | -| Robert Oostenveld ([@robertoostenveld](https://github.com/robertoostenveld)) | -| Russell Poldrack ([@poldrack](https://github.com/poldrack)) | -| Ariel Rokem ([@arokem](https://github.com/arokem)) | - -#### Past steering group members - -| Name | -|------------------------------------------------------------------------------| -| Kirstie Whitaker ([@KirstieJane](https://github.com/KirstieJane)) | +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 | +| Kimberly Ray ([@KimberlyLRay](https://github.com/KimberlyLRay)) | 1h/week | | Nov 2022 | 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. @@ -50,9 +42,9 @@ 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 @@ -61,11 +53,12 @@ Leaders of BIDS Extension Proposals are listed in the ### Contributors Group -Contributors are listed in the [Contributors appendix](https://bids-specification.readthedocs.io/en/stable/appendices/contributors.html) -of the BIDS specification. Contributors who have not yet entered their name -into this list are encouraged to edit the [Contributors WIKI page](https://github.com/bids-standard/bids-specification/wiki/Contributors) -with their name, using the emojis listed in the WIKI to indicate their -contributions. +Contributors are listed in the +[Contributors appendix](https://bids-specification.readthedocs.io/en/stable/appendices/contributors.html) +of the BIDS specification. +Contributors who have not yet entered their name into this list are encouraged to edit the +[Contributors wiki page](https://github.com/bids-standard/bids-specification/wiki/Recent-Contributors) +according to the instructions listed there. ### Other groups diff --git a/LICENSE b/LICENSE index d5919783..22091e01 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ Attribution 4.0 International -Copyright (c) 2018-2022, BIDS Contributors. +Copyright (c) 2018, BIDS Contributors. ======================================================================= diff --git a/Makefile b/Makefile index 2662661f..a56b672d 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 aefe81c8..6474f470 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,14 @@ -[![Check Markdown style](https://github.com/bids-standard/bids-specification/actions/workflows/markdown_style.yml/badge.svg)](https://github.com/bids-standard/bids-specification/actions/workflows/markdown_style.yml) +[![Validation](https://github.com/bids-standard/bids-specification/actions/workflows/validation.yml/badge.svg)](https://github.com/bids-standard/bids-specification/actions/workflows/validation.yml) [![CircleCI](https://circleci.com/gh/bids-standard/bids-specification.svg?style=shield)](https://circleci.com/gh/bids-standard/bids-specification) -[![@BIDSstandard](http://img.shields.io/twitter/follow/bidsstandard.svg?style=social)](https://twitter.com/BIDSstandard) +[![Mastodon Follow](https://img.shields.io/mastodon/follow/109520103085644521?domain=https%3A%2F%2Ffosstodon.org%2F)](https://fosstodon.org/@bidsstandard) +[![@BIDSstandard](https://img.shields.io/twitter/follow/bidsstandard.svg?style=social)](https://x.com/BIDSstandard) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3686061.svg)](https://doi.org/10.5281/zenodo.3686061) bids-logo 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/). @@ -27,6 +28,8 @@ BIDS currently supports the following data modalities with more to come in the f - physiological - PET - microscopy +- NIRS +- motion # Formatting your data with BIDS @@ -40,10 +43,7 @@ The specification is provided in the form of a webpage, built using 1. Read some introductory material, most likely the very basic problems have already been addressed! - [BIDS Starter Kit](https://github.com/bids-standard/bids-starter-kit) for tutorials, wikis, templates, ... 2. Post your question in one of several channels where BIDS members are active - - the [NeuroStars](https://neurostars.org/tags/bids) discourse forum - - the [BrainHack Mattermost](https://mattermost.brainhack.org), for instant messaging (see also this [news item](https://bids.neuroimaging.io/2020/06/24/Join-the-BIDS-community-on-the-BrainHack-Mattermost.html)) - - the [Google group](https://groups.google.com/forum/#!forum/bids-discussion), for broader discussions surrounding BIDS - - the [specification repository issue page](https://github.com/bids-standard/bids-specification/issues), if you found inconsistencies, typos, or other issues with the BIDS specification itself + - see: [BIDS communication channels](#bids-communication-channels) # Contributing to BIDS @@ -54,7 +54,466 @@ For a current list of our contributors, please see our [Contributors appendix](h When you're ready to get started, check out [our contributing guidelines](https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md). -We ask that all contributions to BIDS across all project-related spaces (including but not limited to: -[GitHub](https://github.com/bids-standard), -the [Google group](https://groups.google.com/forum/#!forum/bids-discussion), and newsletter emails), +We ask that all contributions to BIDS across all project-related spaces +(including but not limited to: +[GitHub](https://github.com/bids-standard), and the +[Google group](https://groups.google.com/forum/#!forum/bids-discussion); see +[BIDS communication channels](#bids-communication-channels)) adhere to our [code of conduct](https://github.com/bids-standard/bids-specification/blob/master/CODE_OF_CONDUCT.md). + +# BIDS communication channels + +## Main communication channels + + - "Issue" pages on the different GitHub repositories of the [`bids-standard` GitHub organization](https://github.com/bids-standard), + such as the [BIDS specification repository](https://github.com/bids-standard/bids-specification/issues), + for reporting problems or making suggestions + - The [NeuroStars Discourse forum](https://neurostars.org/tags/bids), for asking usage questions + - The [BrainHack Mattermost](https://mattermost.brainhack.org), for instant messaging + (see also this [news item](https://bids.neuroimaging.io/2020/06/24/Join-the-BIDS-community-on-the-BrainHack-Mattermost.html)) + - The [Google group](https://groups.google.com/forum/#!forum/bids-discussion), for broader discussions and announcements surrounding BIDS + - The [BIDS website "news"](https://bids.neuroimaging.io/news.html), similar to the Google group, for broader discussions and announcements + +## Social media channels + +- [X](https://x.com/BIDSstandard) +- [Mastodon](https://fosstodon.org/@bidsstandard) +- [Bluesky](https://bsky.app/profile/bidsstandard.bsky.social) +- [Youtube](https://www.youtube.com/channel/UCxZUcYfd_nvIVWAbzRB1tlw) +- [Instagram](https://www.instagram.com/bidsstandard/) + +## Contributors + +Thanks goes to these wonderful people. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Aaron Oliver-Taylor
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Dejan Draschkow
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Duncan Macleod
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+ + + + + diff --git a/Release_Protocol.md b/Release_Protocol.md index 67d34e4c..c93c039a 100644 --- a/Release_Protocol.md +++ b/Release_Protocol.md @@ -8,10 +8,14 @@ The protocol assumes that you have a [fork](https://help.github.com/en/articles/ of the bids-standard/bids-specification repository and have [cloned](https://help.github.com/en/articles/cloning-a-repository) your fork locally to a directory called `bids-specification`. -NOTE: Before you start a release, you have to ensure that the automatically generated changelog is -**up to date**. See the relevant [section in CONTRIBUTING.md](CONTRIBUTING.md#how-is-the-changelog-generated) -for further information. In practice this means ensuring that the most recently merged pull request was -merged into the `master` branch using the "Merge commit" option. +### 0. Cleaning up the changelog + +Before you start a release, you have to ensure that the automatically generated changelog is **up to date**. +See the relevant [section in CONTRIBUTING.md](CONTRIBUTING.md#how-is-the-changelog-generated) for further information. +In practice this means ensuring that the most recently merged pull request +was merged into the `master` branch using the "Merge commit" option. + +![merge-commit](release_images/merge_commit.png.png "merge-commit") ### 1. Fetch the latest version of the [master branch of the BIDS-specification](https://github.com/bids-standard/bids-specification/tree/master) @@ -20,15 +24,15 @@ You should have a remote, which we will call `upstream`, for the repository: ```Shell -$ git remote get-url upstream +git remote get-url upstream git@github.com:bids-standard/bids-specification.git ``` If you do not, add it with: ```Shell -$ cd bids-specification -$ git remote add upstream git@github.com:bids-standard/bids-specification.git +cd bids-specification +git remote add upstream git@github.com:bids-standard/bids-specification.git ``` Fetch the current repository state and create a new `rel/` branch based on @@ -36,21 +40,25 @@ Fetch the current repository state and create a new `rel/` branch based For example, if releasing version `1.2.0`: ```Shell -$ git fetch upstream -$ git checkout -b rel/1.2.0 upstream/master +git fetch upstream +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. +to ``, and link to the target ReadTheDocs URL. If the target release date is known, include the date in YYYY-MM-DD in parentheses after the link. ```Diff - ## Unreleased -+ ## [v1.2.0](https://bids-specification.readthedocs.io/en/v1.2.0/) (2019-03-04) ++ ## [1.2.0](https://bids-specification.readthedocs.io/en/1.2.0/) (2019-03-04) ``` The date can be changed or added later, so accurate prediction is not necessary. @@ -59,32 +67,58 @@ Remove the `-dev` from the version in [mkdocs.yml](https://github.com/bids-standard/bids-specification/blob/master/mkdocs.yml) configuration, so the title will be correct for the released specification. If the version preceding the `-dev` is not the target version, update the version as well. -In the figure below, we update `v1.2.0-dev` to `v1.2.0`. +In the figure below, we update `1.2.0-dev` to `1.2.0`. ![dev-to-stable](release_images/site_name_release_1.2dev-1.2.png "dev-to-stable") 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. -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. +#### 2.2 Update the contributors list -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") +We want to ensure that all contributors are duly credited. -Remove `REL:` entries in [src/CHANGES.md](https://github.com/bids-standard/bids-specification/blob/master/src/CHANGES.md). +To 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/Recent-Contributors), +please follow these steps: -```Diff -- REL: v1.2.2 #405 (franklin-feingold) +- be sure not to remove credits if both the contributors appendix AND + the contributors wiki page have been edited (or the `.tributors` or `.all-contributorsrc` files) +- 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 + +In `src/CHANGES.md`, +please change the previous version links from GitHub to ReadTheDocs. +In the figure below, we update 1.2.2. +![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 important changes might be moved down the list to ensure that large changes are more prominent. +You can also make use of the `exclude-from-changelog` label. +Adding this label to PRs in the GitHub web interface will prevent the changelog generator from +considering this item for inclusion in the changelog. ### 3. Commit changes and push to upstream @@ -92,14 +126,17 @@ By pushing `rel/` branches to the main repository, the chances of continuous int discrepancies is reduced. ```Shell -$ git add src/CHANGES.md mkdocs.yml src/appendices/contributors.md -$ git commit -m 'REL: v1.2.0' -$ git push -u upstream rel/1.2.0 +git add src/CHANGES.md mkdocs.yml src/appendices/contributors.md src/schema/BIDS_VERSION +git commit -m 'REL: 1.2.0' +git push -u upstream rel/1.2.0 ``` ### 4. Open a pull request against the master branch -Important note: The pull request title **must** be named "REL: vX.Y.Z" (for example, "REL: v1.2.0"). +**Important notes:** + +1. The pull request title **must** be named "REL: X.Y.Z" (for example, "REL: 1.2.0") +1. The pull request **must** get a GitHub label called `exclude-from-changelog` **This will open a period of discussion for 5 business days regarding if we are ready to release.** @@ -118,10 +155,10 @@ probably wait. If `master` is updated, it should be merged into the `rel/` branch: ```Shell -$ git fetch upstream -$ git checkout rel/1.2.0 -$ git merge upstream/master -$ git push rel/1.2.0 +git fetch upstream +git checkout rel/1.2.0 +git merge upstream/master +git push rel/1.2.0 ``` ### 5. Set release date and merge @@ -133,24 +170,28 @@ The date should be placed after the link to the versioned URL. For example: ```Diff -- ## [v1.2.0](https://bids-specification.readthedocs.io/en/v1.2.0/) -+ ## [v1.2.0](https://bids-specification.readthedocs.io/en/v1.2.0/) (2019-03-04) +- ## [1.2.0](https://bids-specification.readthedocs.io/en/1.2.0/) ++ ## [1.2.0](https://bids-specification.readthedocs.io/en/1.2.0/) (2019-03-04) ``` -Verify that the pull request title matches "REL: vX.Y.Z" and merge the pull request. +Verify that the pull request title matches "REL: X.Y.Z" and merge the pull request. -### 6. Get the built PDF +### 6. Get the built PDF and `CITATION.cff` file Upon each commit to the `master` branch, CircleCI builds a PDF version of the specification (see `.circleci/config.yml` and the `pdf_build_src` directory). So after merging the new "stable" version into `master`, wait for the CircleCI -jobs to finish and then check the built PDF using this link: +jobs to finish and then check the built PDF using the following steps: -`https://circleci.com/api/v1.1/project/github/bids-standard/bids-specification/latest/artifacts/0/bids-spec.pdf?branch=master` +1. Go to the [list of recent commits](https://github.com/bids-standard/bids-specification/commits/master) +1. Click on the "CI checks" for the most recent commit (should be a green checkmark) +1. From the list of CI checks, click on the one called: `Check the rendered PDF version here!` +1. Download the PDF and check that the date and version on the first page are as expected +1. Hold the PDF ready for upload to our Zenodo archive (see the *Uploading the stable PDF to Zenodo* step below) -Download the PDF and hold it ready for upload to our Zenodo archive. See the -*Uploading the stable PDF to Zenodo* step below. +Furthermore, **copy the `CITATION.cff`** file in its current state from the root of the repository +and hold it ready for facilitating the upload of the PDF to our Zenodo archive. ### 7. Tag the release @@ -160,9 +201,9 @@ To do this, `fetch` the current state of `upstream` (see step 1), tag `upstream/ `push` the tag to `upstream`. ```Shell -$ git fetch upstream -$ git tag -a -m "v1.2.0 (2019-03-04)" v1.2.0 upstream/master -$ git push upstream v1.2.0 +git fetch upstream +git tag -a -m "1.2.0 (2019-03-04)" 1.2.0 upstream/master +git push upstream 1.2.0 ``` There are four components to the tag command: @@ -187,7 +228,7 @@ Click [Draft a new release](https://github.com/bids-standard/bids-specification/ ![GH-release-2](release_images/GH-release_2.png "GH-release-2") -Set the tag version and release title to "vX.Y.Z", and paste the current changelog as the +Set the tag version and release title to "X.Y.Z", and paste the current changelog as the description: ![GH-release-3](release_images/GH-release_3.png "GH-release-3") @@ -200,8 +241,14 @@ for `stable` and the most recent tag. ### 9. Edit the mkdocs.yml file site_name to set a new development version -Please commit to `master` with the title `REL: -dev`. +Please open a pull request and create a merge commit to `master` with the title `REL: -dev`. + +![merge-commit](release_images/merge_commit.png.png "merge-commit") + This should be the first commit in the new version. + +This will reset the URLs that were [manually changed before in step 2.3](#2.3-update-the-previous-version-URLs). + This process is illustrated below. ![stable-to-dev](release_images/site_name_release_1.2-1.3dev.png "stable-to-dev") @@ -213,24 +260,23 @@ 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 -1. Log into https://github.com with the `bids-maintenance` user (credentials - are available from the BIDS maintainer group) -1. Open a new tab at https://zenodo.org and "log in via GitHub", you'll then - be on the `bids-maintenance` Zenodo account -1. Navigate to the [archive of our BIDS specification PDFs](https://doi.org/10.5281/zenodo.3686061) -1. Click on "add new version" -1. For a new version, upload the new PDF, naming it consistently with the other - PDFs: `BIDS-Specification-vX.X.X.pdf` (replace `X.X.X` with the new version) -1. Remove all other files from the upload -1. Edit the following fields: - 1. publication date - 1. version -1. Double check that everything is in order, then save and publish - -### 11. Sharing news of the release - -Please share news of the release on the [identified platforms](https://docs.google.com/spreadsheets/d/16SAGK3zG93WM2EWuoZDcRIC7ygPc5b7PDNGpFyC3obA/edit#gid=0). +1. In a previous step you have secured a PDF version of the BIDS specification and the corresponding `CITATION.cff` file. +1. Follow the steps described here: https://github.com/bids-standard/bids-specification-pdf-releases#release-instructions + +### 11. Update the BIDS website data + +Update the following files in the BIDS website repository (https://github.com/bids-standard/bids-website) if applicable: + +- `tools/timeline.csv` +- `_data/beps.yml` +- `_data/beps_completed.yml` +- `_data/beps_other.yml` + +### 12. Sharing news of the release + +Please share news of the release on the [identified platforms](https://github.com/bids-standard/bids-specification?tab=readme-ov-file#BIDS-communication-channels). Please use our previous release posts as a guide. diff --git a/macros_doc.md b/macros_doc.md index 1aa378ac..6ec9fcf5 100644 --- a/macros_doc.md +++ b/macros_doc.md @@ -80,17 +80,20 @@ consistency. All the macros we use are in listed in this [Python file](https://github.com/bids-standard/bids-specification/blob/master/tools/mkdocs_macros_bids/macros.py). -| Name | Purpose | Uses schema | Example | -| ------------------------ | -------------------------------------------------------------------------------------- | ----------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| make_columns_table | Generate a markdown table of TSV column information. | Yes | [link](https://github.com/bids-standard/bids-specification/blob/9201b203ffaa72d83b2fa30d1c61f46f089f77de/src/03-modality-agnostic-files.md?plain=1#L202) | -| make_entity_table | Generate an entity table from the schema, based on specific filters. | Yes | [link](https://github.com/bids-standard/bids-specification/blob/9201b203ffaa72d83b2fa30d1c61f46f089f77de/src/99-appendices/04-entity-table.md?plain=1#L23) | -| make_entity_definitions | Generate definitions and other relevant information for entities in the specification. | Yes | [link](https://github.com/bids-standard/bids-specification/blob/9201b203ffaa72d83b2fa30d1c61f46f089f77de/src/99-appendices/09-entities.md?plain=1#L16) | -| make_filename_template | Generate a filename template from the schema, based on specific filters. | Yes | [link](https://github.com/bids-standard/bids-specification/blob/9201b203ffaa72d83b2fa30d1c61f46f089f77de/src/04-modality-specific-files/10-microscopy.md?plain=1#L21) | -| make_filetree_example | Generate a filetree snippet from example content. | No | [link](https://github.com/bids-standard/bids-specification/blob/9201b203ffaa72d83b2fa30d1c61f46f089f77de/src/02-common-principles.md?plain=1#L268) | -| make_glossary | | Yes | [link](https://github.com/bids-standard/bids-specification/blob/9201b203ffaa72d83b2fa30d1c61f46f089f77de/src/99-appendices/14-glossary.md?plain=1#L9) | -| make_metadata_table | Generate a markdown table of metadata field information. | Yes | [link](https://github.com/bids-standard/bids-specification/blob/9201b203ffaa72d83b2fa30d1c61f46f089f77de/src/02-common-principles.md?plain=1#L462) | -| 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) | +| Name | Purpose | Uses schema | Example | +| ------------------------------ | -------------------------------------------------------------------------------------- | ----------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| make_columns_table | Generate a markdown table of TSV column information. | Yes | [link](https://github.com/bids-standard/bids-specification/blob/9201b203ffaa72d83b2fa30d1c61f46f089f77de/src/03-modality-agnostic-files.md?plain=1#L202) | +| make_entity_table | Generate an entity table from the schema, based on specific filters. | Yes | [link](https://github.com/bids-standard/bids-specification/blob/9201b203ffaa72d83b2fa30d1c61f46f089f77de/src/99-appendices/04-entity-table.md?plain=1#L23) | +| make_entity_definitions | Generate definitions and other relevant information for entities in the specification. | Yes | [link](https://github.com/bids-standard/bids-specification/blob/9201b203ffaa72d83b2fa30d1c61f46f089f77de/src/99-appendices/09-entities.md?plain=1#L16) | +| make_filename_template | Generate a filename template from the schema, based on specific filters. | Yes | [link](https://github.com/bids-standard/bids-specification/blob/9201b203ffaa72d83b2fa30d1c61f46f089f77de/src/04-modality-specific-files/10-microscopy.md?plain=1#L21) | +| make_filetree_example | Generate a filetree snippet from example content. | No | [link](https://github.com/bids-standard/bids-specification/blob/9201b203ffaa72d83b2fa30d1c61f46f089f77de/src/02-common-principles.md?plain=1#L268) | +| make_glossary | | Yes | [link](https://github.com/bids-standard/bids-specification/blob/9201b203ffaa72d83b2fa30d1c61f46f089f77de/src/99-appendices/14-glossary.md?plain=1#L9) | +| make_metadata_table | Generate a markdown table of metadata field information. | Yes | [link](https://github.com/bids-standard/bids-specification/blob/9201b203ffaa72d83b2fa30d1c61f46f089f77de/src/02-common-principles.md?plain=1#L462) | +| 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 cba7f3e4..051aa2aa 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -1,94 +1,151 @@ -site_name: Brain Imaging Data Structure v1.7.1-dev +site_name: Brain Imaging Data Structure 1.10.0-dev site_url: https://bids-specification.readthedocs.io/en/stable/ -theme: - name: material - favicon: images/favicon.png - logo: images/logo.png - features: - - navigation.sections -copyright: Copyright © 2018-2022, BIDS Contributors - CC BY 4.0 -extra: - generator: false - social: - - icon: fontawesome/brands/twitter - link: https://twitter.com/BIDSstandard/ - - icon: fontawesome/brands/github - link: https://github.com/bids-standard/bids-specification/ - - icon: fontawesome/brands/google - link: https://groups.google.com/g/bids-discussion -extra_javascript: - - js/jquery-3.6.0.min.js -markdown_extensions: - - toc: - anchorlink: true - - pymdownx.superfences -plugins: - - search - - branchcustomization: - update_config: - - branch: /(?!^master$)/ - +extra_css: - - css/watermark.css - - macros: - module_name: tools/mkdocs_macros_bids/main - - redirects: - redirect_maps: - '99-appendices/14-glossary.md': 'glossary.md' - '99-appendices/01-contributors.md': 'appendices/contributors.md' - '99-appendices/02-licenses.md': 'appendices/licenses.md' - '99-appendices/03-hed.md': 'appendices/hed.md' - '99-appendices/04-entity-table.md': 'appendices/entity-table.md' - '99-appendices/05-units.md': 'appendices/units.md' - '99-appendices/06-meg-file-formats.md': 'appendices/meg-file-formats.md' - '99-appendices/07-meg-systems.md': 'appendices/meg-systems.md' - '99-appendices/08-coordinate-systems.md': 'appendices/coordinate-systems.md' - '99-appendices/09-entities.md': 'appendices/entities.md' - '99-appendices/10-file-collections.md': 'appendices/file-collections.md' - '99-appendices/11-qmri.md': 'appendices/qmri.md' - '99-appendices/12-arterial-spin-labeling.md': 'appendices/arterial-spin-labeling.md' - '99-appendices/13-cross-modality-correspondence.md': 'appendices/cross-modality-correspondence.md' -docs_dir: 'src' -use_directory_urls: false +repo_url: https://github.com/bids-standard/bids-specification nav: - - The BIDS Specification: - - Introduction: 01-introduction.md - - Common principles: 02-common-principles.md - - Modality agnostic files: 03-modality-agnostic-files.md + - The BIDS Specification: + - Introduction: introduction.md + - Common principles: common-principles.md + - Modality agnostic files: modality-agnostic-files.md - Modality specific files: - - Magnetic Resonance Imaging: 04-modality-specific-files/01-magnetic-resonance-imaging-data.md - - Magnetoencephalography: 04-modality-specific-files/02-magnetoencephalography.md - - Electroencephalography: 04-modality-specific-files/03-electroencephalography.md - - Intracranial Electroencephalography: 04-modality-specific-files/04-intracranial-electroencephalography.md - - Task events: 04-modality-specific-files/05-task-events.md - - Physiological and other continuous recordings: 04-modality-specific-files/06-physiological-and-other-continuous-recordings.md - - Behavioral experiments (with no neural recordings): 04-modality-specific-files/07-behavioral-experiments.md - - Genetic Descriptor: 04-modality-specific-files/08-genetic-descriptor.md - - Positron Emission Tomography: 04-modality-specific-files/09-positron-emission-tomography.md - - Microscopy: 04-modality-specific-files/10-microscopy.md + - Magnetic Resonance Imaging: modality-specific-files/magnetic-resonance-imaging-data.md + - Magnetoencephalography: modality-specific-files/magnetoencephalography.md + - Electroencephalography: modality-specific-files/electroencephalography.md + - Intracranial Electroencephalography: modality-specific-files/intracranial-electroencephalography.md + - Task events: modality-specific-files/task-events.md + - Physiological and other continuous recordings: modality-specific-files/physiological-and-other-continuous-recordings.md + - Behavioral experiments (with no neural recordings): modality-specific-files/behavioral-experiments.md + - Genetic Descriptor: modality-specific-files/genetic-descriptor.md + - 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: 05-derivatives/01-introduction.md - - Common data types and metadata: 05-derivatives/02-common-data-types.md - - Imaging data types: 05-derivatives/03-imaging.md - - Diffusion derivatives: 05-derivatives/05-diffusion-derivatives.md - - Longitudinal and multi-site studies: 06-longitudinal-and-multi-site-studies.md + - BIDS Derivatives: derivatives/introduction.md + - Common data types and metadata: derivatives/common-data-types.md + - Imaging data types: derivatives/imaging.md + - Longitudinal and multi-site studies: longitudinal-and-multi-site-studies.md - Glossary: glossary.md - - BIDS Extension Proposals: 07-extensions.md + - BIDS Extension Proposals: extensions.md - Appendix: - - Contributors: appendices/contributors.md - - Licenses: appendices/licenses.md - - Entity table: appendices/entity-table.md - - Entities: appendices/entities.md - - File collections: appendices/file-collections.md - - Units: appendices/units.md - - Hierarchical Event Descriptors: appendices/hed.md - - MEG file formats: appendices/meg-file-formats.md - - MEG systems: appendices/meg-systems.md - - Coordinate systems: appendices/coordinate-systems.md - - Quantitative MRI: appendices/qmri.md - - Arterial Spin Labeling: appendices/arterial-spin-labeling.md - - Cross modality correspondence: appendices/cross-modality-correspondence.md + - Schema: appendices/schema.md + - Contributors: appendices/contributors.md + - Licenses: appendices/licenses.md + - Entity table: appendices/entity-table.md + - Entities: appendices/entities.md + - File collections: appendices/file-collections.md + - Units: appendices/units.md + - Hierarchical Event Descriptors: appendices/hed.md + - MEG file formats: appendices/meg-file-formats.md + - MEG systems: appendices/meg-systems.md + - Coordinate systems: appendices/coordinate-systems.md + - Quantitative MRI: appendices/qmri.md + - Arterial Spin Labeling: appendices/arterial-spin-labeling.md + - Cross modality correspondence: appendices/cross-modality-correspondence.md - Changelog: CHANGES.md - - The BIDS Starter Kit: - - Website: https://bids-standard.github.io/bids-starter-kit + - The BIDS Starter Kit: + - Website: https://bids-standard.github.io/bids-starter-kit/ - Tutorials: https://bids-standard.github.io/bids-starter-kit/tutorials/tutorials.html - GitHub repository: https://github.com/bids-standard/bids-starter-kit +theme: + name: material + favicon: images/favicon.png + logo: images/logo.png + features: + - navigation.sections + - content.action.edit + icon: + repo: fontawesome/brands/github + edit: material/pencil + palette: + # Palette toggle for automatic mode + - media: (prefers-color-scheme) + toggle: + icon: material/brightness-auto + name: Switch to light mode + # Palette toggle for light mode + - media: "(prefers-color-scheme: light)" + scheme: default + toggle: + icon: material/brightness-7 + name: Switch to dark mode + # Palette toggle for dark mode + - media: "(prefers-color-scheme: dark)" + scheme: slate + toggle: + icon: material/brightness-4 + name: Switch to system preference + +edit_uri: https://github.com/bids-standard/bids-specification/edit/master/src/ + +copyright: Copyright © BIDS Contributors - CC BY 4.0 + +extra: + generator: false + social: + - icon: fontawesome/brands/github + link: https://github.com/bids-standard/bids-specification/ + - icon: fontawesome/brands/x-twitter + link: https://x.com/BIDSstandard/ + - icon: fontawesome/brands/mastodon + link: https://fosstodon.org/@bidsstandard + - icon: fontawesome/brands/google + link: https://groups.google.com/g/bids-discussion + - icon: fontawesome/brands/instagram + link: https://www.instagram.com/bidsstandard/ + - icon: fontawesome/brands/youtube + link: https://www.youtube.com/channel/UCxZUcYfd_nvIVWAbzRB1tlw + +extra_javascript: + - js/jquery-3.6.0.min.js +markdown_extensions: + - toc: + anchorlink: true + - pymdownx.superfences + - admonition + - pymdownx.details +plugins: + - search + - branchcustomization: + update_config: + - branch: /(?!^master$)/ + +extra_css: + - css/watermark.css + - macros: + module_name: tools/mkdocs_macros_bids/main + - redirects: + redirect_maps: + "01-introduction.md": "introduction.md" + "02-common-principles.md": "common-principles.md" + "03-modality-agnostic-files.md": "modality-agnostic-files.md" + "04-modality-specific-files/01-magnetic-resonance-imaging-data.md": "modality-specific-files/magnetic-resonance-imaging-data.md" + "04-modality-specific-files/02-magnetoencephalography.md": "modality-specific-files/magnetoencephalography.md" + "04-modality-specific-files/03-electroencephalography.md": "modality-specific-files/electroencephalography.md" + "04-modality-specific-files/04-intracranial-electroencephalography.md": "modality-specific-files/intracranial-electroencephalography.md" + "04-modality-specific-files/05-task-events.md": "modality-specific-files/task-events.md" + "04-modality-specific-files/06-physiological-and-other-continuous-recordings.md": "modality-specific-files/physiological-and-other-continuous-recordings.md" + "04-modality-specific-files/07-behavioral-experiments.md": "modality-specific-files/behavioral-experiments.md" + "04-modality-specific-files/08-genetic-descriptor.md": "modality-specific-files/genetic-descriptor.md" + "04-modality-specific-files/09-positron-emission-tomography.md": "modality-specific-files/positron-emission-tomography.md" + "04-modality-specific-files/10-microscopy.md": "modality-specific-files/microscopy.md" + "04-modality-specific-files/11-near-infrared-spectroscopy.md": "modality-specific-files/near-infrared-spectroscopy.md" + "05-derivatives/01-introduction.md": "derivatives/introduction.md" + "05-derivatives/02-common-data-types.md": "derivatives/common-data-types.md" + "05-derivatives/03-imaging.md": "derivatives/imaging.md" + "06-longitudinal-and-multi-site-studies.md": "longitudinal-and-multi-site-studies.md" + "07-extensions.md": "extensions.md" + "99-appendices/14-glossary.md": "glossary.md" + "99-appendices/01-contributors.md": "appendices/contributors.md" + "99-appendices/02-licenses.md": "appendices/licenses.md" + "99-appendices/03-hed.md": "appendices/hed.md" + "99-appendices/04-entity-table.md": "appendices/entity-table.md" + "99-appendices/05-units.md": "appendices/units.md" + "99-appendices/06-meg-file-formats.md": "appendices/meg-file-formats.md" + "99-appendices/07-meg-systems.md": "appendices/meg-systems.md" + "99-appendices/08-coordinate-systems.md": "appendices/coordinate-systems.md" + "99-appendices/09-entities.md": "appendices/entities.md" + "99-appendices/10-file-collections.md": "appendices/file-collections.md" + "99-appendices/11-qmri.md": "appendices/qmri.md" + "99-appendices/12-arterial-spin-labeling.md": "appendices/arterial-spin-labeling.md" + "99-appendices/13-cross-modality-correspondence.md": "appendices/cross-modality-correspondence.md" +docs_dir: "src" +use_directory_urls: false diff --git a/pdf_build_src/pandoc_script.py b/pdf_build_src/pandoc_script.py index be7d399c..e9710482 100644 --- a/pdf_build_src/pandoc_script.py +++ b/pdf_build_src/pandoc_script.py @@ -2,9 +2,18 @@ This is done once the duplicate src directory is processed. """ -import os -import pathlib + import subprocess +import yaml +from pathlib import Path + +HERE = Path(__file__).absolute() + + +def _find(path, filename): + return next( + parent / filename for parent in path.parents if Path.is_file(parent / filename) + ) def build_pdf(filename="bids-spec.pdf", logfile="bids-spec_pandoc_log.json"): @@ -17,52 +26,56 @@ def build_pdf(filename="bids-spec.pdf", logfile="bids-spec_pandoc_log.json"): logfile : str Name of the log file. Defaults to "bids-spec_pandoc_log.json". """ - # Files that are not supposed to be built into the PDF - EXCLUDE = ["./index.md", "./schema/README.md", "./pregh-changes.md"] - - # Get all input files - markdown_list = [] - for root, dirs, files in os.walk('.'): - for file in files: - fpath = os.path.join(root, file) - if fpath.endswith(".md") and fpath not in EXCLUDE: - markdown_list.append(fpath) - elif fpath.endswith('index.md'): - # Special role for index.md - index_page = fpath + + def _flatten_values(lst): + """Flatten a list of dicts of lists to a list of values.""" + for obj in lst: + for val in obj.values(): + if isinstance(val, str): + yield val + else: + yield from _flatten_values(val) + + fname_mkdocs_yml = _find(HERE, "mkdocs.yml") + + with open(fname_mkdocs_yml, "r") as stream: + mkdocs_yml = yaml.safe_load(stream) + + sections = mkdocs_yml["nav"][0]["The BIDS Specification"] + + # special files + index_page = "./index.md" + pandoc_metadata = _find(HERE, "metadata.yml") # Prepare the command options cmd = [ - 'pandoc', - '--from=markdown_github+yaml_metadata_block', - '--include-before-body=./cover.tex', - '--include-in-header=./header.tex', - '--include-in-header=./header_setup.tex', - '--pdf-engine=xelatex', - f'--log={logfile}', - f'--output={filename}', + "pandoc", + "--from=markdown_github+yaml_metadata_block", + "--include-before-body=./cover.tex", + "--include-in-header=./header.tex", + "--include-in-header=./header_setup.tex", + "--pdf-engine=xelatex", + f"--log={logfile}", + f"--output={filename}", ] - # location of this file: This is also the working directory when - # the pdf is being built using `cd build_pdf_src` and then - # `bash build_pdf.sh` - root = pathlib.Path(__file__).parent.absolute() - # Resources are searched relative to the working directory, but # we can add additional search paths using :, ... # When in one of the appendices/ files there is a reference to # "../04-modality-specific-files/images/...", then we need to use # appendices/ as a resource-path so that the relative files can # be found. - cmd += [f'--resource-path=.:{str(root / "appendices")}'] + build_root = HERE.parent + cmd += [f'--resource-path=.:{build_root / "appendices"}'] # Add input files to command # The filenames in `markdown_list` will ensure correct order when sorted - cmd += [str(root / index_page)] - cmd += [str(root / i) for i in ["../../metadata.yml"] + sorted(markdown_list)] + cmd += [str(build_root / index_page)] + cmd += [str(pandoc_metadata)] + cmd += [str(build_root / md) for md in _flatten_values(sections)] # print and run - print('running: \n\n' + '\n'.join(cmd)) + print("pandoc command being run: \n\n" + "\n".join(cmd)) subprocess.run(cmd) diff --git a/pdf_build_src/process_markdowns.py b/pdf_build_src/process_markdowns.py index 6145d33b..705daa8b 100644 --- a/pdf_build_src/process_markdowns.py +++ b/pdf_build_src/process_markdowns.py @@ -17,6 +17,8 @@ import numpy as np +from remove_admonitions import remove_admonitions + sys.path.append("../tools/") # functions from module macros are called by eval() later on from mkdocs_macros_bids import macros # noqa: F401 @@ -24,11 +26,12 @@ def run_shell_cmd(command): """Run shell/bash commands passed as a string using subprocess module.""" - process = subprocess.Popen(command.split(), stdout=subprocess.PIPE, - stderr=subprocess.PIPE) + process = subprocess.Popen( + command.split(), stdout=subprocess.PIPE, stderr=subprocess.PIPE + ) output = process.stdout.read() - return output.decode('utf-8') + return output.decode("utf-8") def copy_src(): @@ -63,7 +66,7 @@ def copy_images(root_path): # and copy contents to the 'images' directory in the duplicate src # directory for root, dirs, files in sorted(os.walk(root_path)): - if 'images' in dirs: + if "images" in dirs: subdir_list.append(root) for each in subdir_list: @@ -75,14 +78,16 @@ def extract_header_string(): """Extract the latest release's version number and date from CHANGES.md.""" run_shell_cmd("cp ../mkdocs.yml src_copy/") - with open(os.path.join(os.path.dirname(__file__), 'src_copy/mkdocs.yml'), 'r') as file: + with open( + os.path.join(os.path.dirname(__file__), "src_copy/mkdocs.yml"), "r" + ) as file: data = file.readlines() header_string = data[0].split(": ")[1] title = " ".join(header_string.split()[0:4]) version_number = header_string.split()[-1] - build_date = datetime.today().strftime('%Y-%m-%d') + build_date = datetime.today().strftime("%Y-%m-%d") return title, version_number, build_date @@ -95,14 +100,14 @@ def add_header(): # creating a header string with latest version number and date header_string = r"\fancyhead[L]{ " + header + " }" - with open('header.tex', 'r') as file: + with open("header.tex", "r") as file: data = file.readlines() # insert the header, note that you have to add a newline - data[4] = header_string + '\n' + data[4] = header_string + "\n" # re-write header.tex file with new header string - with open('header.tex', 'w') as file: + with open("header.tex", "w") as file: file.writelines(data) @@ -147,7 +152,7 @@ def remove_internal_links_reference(root_path): for file in files: links_to_remove = [] if file.endswith(".md"): - with open(os.path.join(root, file), 'r') as markdown: + with open(os.path.join(root, file), "r") as markdown: data = markdown.readlines() # first find, which links need to be remove by scanning the @@ -179,7 +184,7 @@ def remove_internal_links_reference(root_path): data[ind] = line # Now write the changed data back to file - with open(os.path.join(root, file), 'w') as markdown: + with open(os.path.join(root, file), "w") as markdown: markdown.writelines(data) @@ -209,19 +214,18 @@ def remove_internal_links_inline(root_path): for root, dirs, files in sorted(os.walk(root_path)): for file in files: if file.endswith(".md"): - with open(os.path.join(root, file), 'r') as markdown: + with open(os.path.join(root, file), "r") as markdown: data = markdown.readlines() for ind, line in enumerate(data): match = pattern_inline.search(line) if match: - line = re.sub(pattern_inline, - f" {match.groups()[1]}", line) + line = re.sub(pattern_inline, f" {match.groups()[1]}", line) data[ind] = line - with open(os.path.join(root, file), 'w') as markdown: + with open(os.path.join(root, file), "w") as markdown: markdown.writelines(data) @@ -240,13 +244,13 @@ def assert_no_multiline_links(root_path): remove_internal_links_reference remove_internal_links_inline """ - pattern = re.compile(r'(\s|^)+\[([^\]]+)$') + pattern = re.compile(r"(\s|^)+\[([^\]]+)$") problems = dict() for root, dirs, files in sorted(os.walk(root_path)): for file in files: if file.endswith(".md"): - with open(os.path.join(root, file), 'r') as markdown: + with open(os.path.join(root, file), "r") as markdown: data = markdown.readlines() code_context = False @@ -272,8 +276,10 @@ def assert_no_multiline_links(root_path): problems[file] = problems.get(file, []) + [(ind, line)] if len(problems) > 0: - msg = ("Found multiline markdown links! Please reformat as single" - " line links.\n\n") + msg = ( + "Found multiline markdown links! Please reformat as single" + " line links.\n\n" + ) msg += json.dumps(problems, indent=4) raise AssertionError(msg) @@ -284,12 +290,12 @@ def modify_changelog(): This modification makes sure that in the pdf build, changelog is a new chapter. """ - with open('src_copy/src/CHANGES.md', 'r') as file: + with open("src_copy/src/CHANGES.md", "r") as file: data = file.readlines() data[0] = "# Changelog" - with open('src_copy/src/CHANGES.md', 'w') as file: + with open("src_copy/src/CHANGES.md", "w") as file: file.writelines(data) @@ -306,15 +312,18 @@ def correct_table(table, offset=[0.0, 0.0], debug=False): table : list of list of str Table content extracted from the markdown file. offset : list of int - Offset that is used to adjust the correction of number of dashes in the first (offset[0]) and - second (offset[1]) columns by the number specified in percentage. Defaults to [0.0, 0.0]. + Offset that is used to adjust the correction of number of dashes + in the first (offset[0]) and + second (offset[1]) columns by the number specified in percentage. + Defaults to [0.0, 0.0]. debug : bool If True, print debugging information. Defaults to False. Returns ------- new_table : list of list of str - List of corrected lines of the input table with corrected number of dashes and aligned fences. + List of corrected lines of the input table + with corrected number of dashes and aligned fences. To be later joined with pipe characters (``|``). corrected : bool Whether or not the table was corrected. @@ -334,7 +343,7 @@ def correct_table(table, offset=[0.0, 0.0], debug=False): if not len(set([len(i) for i in nb_of_chars])) == 1: print(' - ERROR for current table ... "nb_of_chars" is misaligned, see:\n') print(nb_of_chars) - print('\n - Skipping formatting of this table.') + print("\n - Skipping formatting of this table.") corrected = False return table, corrected @@ -343,7 +352,8 @@ def correct_table(table, offset=[0.0, 0.0], debug=False): max_chars_in_cols = nb_of_chars_arr.max(axis=0) max_chars = max_chars_in_cols.max() - # Computes an equal number of dashes per column based on the maximal number of characters over the columns + # Computes an equal number of dashes per column based + # on the maximal number of characters over the columns nb_of_dashes = max_chars prop_of_dashes = 1.0 / nb_of_cols @@ -352,11 +362,17 @@ def correct_table(table, offset=[0.0, 0.0], debug=False): second_column_width = int(offset[1] * nb_of_dashes) + nb_of_dashes if debug: - print(' - Number of chars in table cells: {}'.format(max_chars_in_cols)) - print(' - Number of dashes (per column): {}'.format(nb_of_dashes)) - print(' - Proportion of dashes (per column): {}'.format(prop_of_dashes)) - print(' - Final number of chars in first column: {}'.format(first_column_width)) - print(' - Final number of chars in second column: {}'.format(second_column_width)) + print(" - Number of chars in table cells: {}".format(max_chars_in_cols)) + print(" - Number of dashes (per column): {}".format(nb_of_dashes)) + print(" - Proportion of dashes (per column): {}".format(prop_of_dashes)) + print( + " - Final number of chars in first column: {}".format(first_column_width) + ) + print( + " - Final number of chars in second column: {}".format( + second_column_width + ) + ) # Format the lines with correct number of dashes or whitespaces and # correct alignment of fences and populate the new table (A List of str) @@ -364,9 +380,9 @@ def correct_table(table, offset=[0.0, 0.0], debug=False): for i, row in enumerate(table): if i == 1: - str_format = ' {:-{align}{width}} ' + str_format = " {:-{align}{width}} " else: - str_format = ' {:{align}{width}} ' + str_format = " {:{align}{width}} " row_content = [] for j, elem in enumerate(row): @@ -381,20 +397,30 @@ def correct_table(table, offset=[0.0, 0.0], debug=False): row_content.append(elem) else: # Handles alignment descriptors in pipe tables - if '-:' in elem and ':-' in elem: - str_format = ' {:-{align}{width}}: ' - row_content.append(str_format.format(':-', align='<', width=(column_width))) - elif '-:' not in elem and ':-' in elem: - str_format = ' {:-{align}{width}} ' - row_content.append(str_format.format(':-', align='<', width=(column_width))) - elif '-:' in elem and ':-'not in elem: - str_format = ' {:-{align}{width}}: ' - row_content.append(str_format.format('-', align='<', width=(column_width))) - elif i == 1 and '-:' not in elem and ':-' not in elem: - str_format = ' {:-{align}{width}} ' - row_content.append(str_format.format('-', align='<', width=(column_width))) + if "-:" in elem and ":-" in elem: + str_format = " {:-{align}{width}}: " + row_content.append( + str_format.format(":-", align="<", width=(column_width)) + ) + elif "-:" not in elem and ":-" in elem: + str_format = " {:-{align}{width}} " + row_content.append( + str_format.format(":-", align="<", width=(column_width)) + ) + elif "-:" in elem and ":-" not in elem: + str_format = " {:-{align}{width}}: " + row_content.append( + str_format.format("-", align="<", width=(column_width)) + ) + elif i == 1 and "-:" not in elem and ":-" not in elem: + str_format = " {:-{align}{width}} " + row_content.append( + str_format.format("-", align="<", width=(column_width)) + ) else: - row_content.append(str_format.format(elem, align='<', width=(column_width))) + row_content.append( + str_format.format(elem, align="<", width=(column_width)) + ) new_table.append(row_content) @@ -405,13 +431,13 @@ def _contains_table_start(line, debug=False): """Check if line is start of a md table.""" is_table = False - nb_of_pipes = line.count('|') - nb_of_escaped_pipes = line.count(r'\|') + nb_of_pipes = line.count("|") + nb_of_escaped_pipes = line.count(r"\|") nb_of_pipes = nb_of_pipes - nb_of_escaped_pipes - nb_of_dashes = line.count('--') + nb_of_dashes = line.count("--") if debug: - print('Number of dashes / pipes : {} / {}'.format(nb_of_dashes, nb_of_pipes)) + print("Number of dashes / pipes : {} / {}".format(nb_of_dashes, nb_of_pipes)) if nb_of_pipes > 2 and nb_of_dashes > 2: is_table = True @@ -443,14 +469,14 @@ def correct_tables(root_path, debug=False): ---------- .. [1] https://stackoverflow.com/a/21107911/5201771 """ - exclude_files = ['index.md', '01-contributors.md'] + exclude_files = ["index.md", "01-contributors.md"] for root, dirs, files in sorted(os.walk(root_path)): for file in files: if file.endswith(".md") and file not in exclude_files: - print('Check tables in {}'.format(os.path.join(root, file))) + print("Check tables in {}".format(os.path.join(root, file))) # Load lines of the markdown file - with open(os.path.join(root, file), 'r') as f: + with open(os.path.join(root, file), "r") as f: content = f.readlines() table_mode = False @@ -470,11 +496,14 @@ def correct_tables(root_path, debug=False): # Keep track of the line number where the table starts start_line = line_nb - 1 - print(' * Detected table starting line {}'.format(start_line)) + print(" * Detected table starting line {}".format(start_line)) # Extract for each row (header and the one containing dashes) # the content of each column and strip to remove extra whitespace - header_row = [c.strip() for c in re.split(r'(?= start_line and i < end_line: - new_content.append('|'.join(table[count]) + ' \n') + new_content.append("|".join(table[count]) + " \n") count += 1 elif i == end_line: - new_content.append('|'.join(table[count]) + ' \n\n') + new_content.append("|".join(table[count]) + " \n\n") count += 1 if corrected: - print(' - Appended corrected table lines to the new markdown content') + print( + " - Appended corrected table lines to new markdown content" + ) else: new_content.append(line) line_nb += 1 # Overwrite with the new markdown content - with open(os.path.join(root, file), 'w') as f: + with open(os.path.join(root, file), "w") as f: f.writelines(new_content) @@ -547,25 +583,26 @@ def edit_titlepage(): """Add title and version number of the specification to the titlepage.""" title, version_number, build_date = extract_header_string() - with open('cover.tex', 'r') as file: + with open("cover.tex", "r") as file: data = file.readlines() - data[-1] = ("\\textsc{\\large " + version_number + "}" + - "\\\\[0.5cm]" + - "{\\large " + - build_date + - "}" + - "\\\\[2cm]" + - "\\vfill" + - "\\end{titlepage}") + data[-1] = ( + rf"\textsc{{\large {version_number}}}" + r"\\[0.5cm]" + rf"{{\large {build_date}}}" + r"\\[2cm]" + r"\vfill" + r"\end{titlepage}" + ) - with open('cover.tex', 'w') as file: + with open("cover.tex", "w") as file: file.writelines(data) class MockPage: pass + class MockFile: pass @@ -611,7 +648,7 @@ def process_macros(duplicated_src_dir_path): page = MockPage() page.file = mock_file - _Context__self = {"page": page} + _Context__self = {"page": page} # noqa: F841 # Replace code snippets in the text with their outputs matches = re.findall(re_code_snippets, contents) @@ -619,10 +656,7 @@ def process_macros(duplicated_src_dir_path): # Remove macro delimiters to get *just* the function call function_string = m.strip("{} ") # Replace prefix with module name - function_string = function_string.replace( - "MACROS___", - "macros." - ) + function_string = function_string.replace("MACROS___", "macros.") # switch "use_pipe" flag OFF to render examples if "make_filetree_example" in function_string: function_string = function_string.replace( @@ -643,38 +677,42 @@ def process_macros(duplicated_src_dir_path): fo.write(contents) -if __name__ == '__main__': +if __name__ == "__main__": - duplicated_src_dir_path = 'src_copy/src' + duplicated_src_dir_path = "src_copy/src" - # Step 1: make a copy of the src directory in the current directory + # make a copy of the src directory in the current directory copy_src() - # Step 2: run mkdocs macros embedded in markdown files + # run mkdocs macros embedded in markdown files process_macros(duplicated_src_dir_path) - # Step 3: copy BIDS_logo to images directory of the src_copy directory + # remove mkdocs admonition + remove_admonitions( + input_folder=duplicated_src_dir_path, output_folder=duplicated_src_dir_path + ) + + # copy BIDS_logo to images directory of the src_copy directory copy_bids_logo() - # Step 4: copy images from subdirectories of src_copy directory + # copy images from subdirectories of src_copy directory copy_images(duplicated_src_dir_path) - subprocess.call("mv src_copy/src/images/images/* src_copy/src/images/", - shell=True) + subprocess.call("mv src_copy/src/images/images/* src_copy/src/images/", shell=True) - # Step 5: extract the latest version number, date and title + # extract the latest version number, date and title extract_header_string() add_header() edit_titlepage() - # Step 6: modify changelog to be a level 1 heading to facilitate section + # modify changelog to be a level 1 heading to facilitate section # separation modify_changelog() - # Step 7: remove all internal links + # remove all internal links assert_no_multiline_links(duplicated_src_dir_path) remove_internal_links_inline(duplicated_src_dir_path) remove_internal_links_reference(duplicated_src_dir_path) - # Step 8: correct number of dashes and fences alignment for rendering tables in PDF + # correct number of dashes and fences alignment for rendering tables in PDF correct_tables(duplicated_src_dir_path) diff --git a/pdf_build_src/remove_admonitions.py b/pdf_build_src/remove_admonitions.py new file mode 100644 index 00000000..1942f8b5 --- /dev/null +++ b/pdf_build_src/remove_admonitions.py @@ -0,0 +1,64 @@ +"""Script to remove all mkdocs admonition from the markdown files in a directory. + +See the pdf_build_src/tests/data/input directory to see what admonitions look like. +""" + +from __future__ import annotations + +import shutil +from pathlib import Path + +INDENT = " " + +ADMONITION_DELIMITERS = ["!!!", "???", "???+"] + + +def remove_admonitions( + input_folder: str | Path, output_folder: str | Path, indent: str = None +): + + if indent is None: + indent = INDENT + + md_files = Path(input_folder).glob("**/*.md") + + for file in md_files: + + with open(file, "r", encoding="utf8") as f: + content = f.readlines() + + output_file = Path(output_folder) / file.relative_to(input_folder) + output_file.parent.mkdir(parents=True, exist_ok=True) + print(f"processing: {file}\n to: {output_file}") + + with open(output_file, "w", encoding="utf8") as f: + + is_admonition = False + counter = 0 + for line in content: + + if any(line.startswith(x) for x in ADMONITION_DELIMITERS): + is_admonition = True + counter = 0 + continue + + # skip first line after admonition + if is_admonition and counter == 0: + counter += 1 + continue + + if line != "\n" and not line.startswith(indent): + is_admonition = False + + if is_admonition: + line = line.lstrip(indent) + + f.write(line) + + +if __name__ == "__main__": + """If run as a script this will just run the main function on test data.""" + input_folder = Path(__file__).parent / "tests" / "data" / "input" + output_folder = Path(__file__).parent / "tests" / "data" / "output" + shutil.rmtree(output_folder) + remove_admonitions(input_folder, output_folder) diff --git a/pdf_build_src/test_remove_admonitions.py b/pdf_build_src/test_remove_admonitions.py new file mode 100644 index 00000000..e995e422 --- /dev/null +++ b/pdf_build_src/test_remove_admonitions.py @@ -0,0 +1,25 @@ +from pathlib import Path + +from remove_admonitions import remove_admonitions + + +def test_remove_admonitions(tmp_path): + input_folder = Path(__file__).parent / "tests" / "data" / "input" + expected_folder = Path(__file__).parent / "tests" / "data" / "expected" + + remove_admonitions(input_folder, tmp_path) + + generated_files = list(tmp_path.glob("**/*.md")) + + for file in generated_files: + + expected = expected_folder / file.relative_to(tmp_path) + + with open(expected, "r", encoding="utf8") as f: + expected_content = f.readlines() + + with open(file, "r", encoding="utf8") as f: + generated_content = f.readlines() + + for expected_line, generated_line in zip(expected_content, generated_content): + assert generated_line == expected_line diff --git a/pdf_build_src/tests/data/expected/README.md b/pdf_build_src/tests/data/expected/README.md new file mode 100644 index 00000000..37fadc29 --- /dev/null +++ b/pdf_build_src/tests/data/expected/README.md @@ -0,0 +1,32 @@ +# Test inputs + +This input directory contains data to use for testing the pdf build code of the BIDS specification. + +For example the following admonition should be removed by `pdf_build_src/remove_admonitions.py`. + +Lorem ipsum dolor sit amet, consectetur adipiscing elit. +Nulla et euismod nulla. +Curabitur feugiat, tortor non consequat finibus, justo purus auctor massa, +nec semper lorem quam in massa. + +The `expected` directory should contain the documents +as they should look like after processing. + +[Mkdocs admonitions](https://squidfunk.github.io/mkdocs-material/reference/admonitions/#inline-blocks-inline-end) +come in different type. In aaddtion of the classical admonitions show above you have also: + +Collapsible admonitions start with 3 questions marks (`???`). + +Collapsible admonitions that will be shown as expanded +start with 3 questions marks and a plus sign (`???+`). + + + +Let's see + +- [`UK biobank`](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb) +- foo bar [`UK biobank`](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb) + +More of the admonition + +And here we resume normal thing. diff --git a/pdf_build_src/tests/data/expected/modality-specific-files/magnetic-resonance-imaging-data.md b/pdf_build_src/tests/data/expected/modality-specific-files/magnetic-resonance-imaging-data.md new file mode 100644 index 00000000..d70af64a --- /dev/null +++ b/pdf_build_src/tests/data/expected/modality-specific-files/magnetic-resonance-imaging-data.md @@ -0,0 +1,8 @@ +# Magnetic Resonance Imaging + +## Common metadata fields + +Lorem ipsum dolor sit amet, consectetur adipiscing elit. +Nulla et euismod nulla. +Curabitur feugiat, tortor non consequat finibus, justo purus auctor massa, +nec semper lorem quam in massa. diff --git a/pdf_build_src/tests/data/input/README.md b/pdf_build_src/tests/data/input/README.md new file mode 100644 index 00000000..cab48172 --- /dev/null +++ b/pdf_build_src/tests/data/input/README.md @@ -0,0 +1,40 @@ +# Test inputs + +This input directory contains data to use for testing the pdf build code of the BIDS specification. + +For example the following admonition should be removed by `pdf_build_src/remove_admonitions.py`. + +!!! note + + Lorem ipsum dolor sit amet, consectetur adipiscing elit. + Nulla et euismod nulla. + Curabitur feugiat, tortor non consequat finibus, justo purus auctor massa, + nec semper lorem quam in massa. + +The `expected` directory should contain the documents +as they should look like after processing. + +[Mkdocs admonitions](https://squidfunk.github.io/mkdocs-material/reference/admonitions/#inline-blocks-inline-end) +come in different type. In aaddtion of the classical admonitions show above you have also: + +??? note "Collapsible admonitions" + + Collapsible admonitions start with 3 questions marks (`???`). + +???+ note "Expanded collapsible admonitions" + + Collapsible admonitions that will be shown as expanded + start with 3 questions marks and a plus sign (`???+`). + + + +!!! example "non ordered list should be handle propeler" + + Let's see + + - [`UK biobank`](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb) + - foo bar [`UK biobank`](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb) + + More of the admonition + +And here we resume normal thing. diff --git a/pdf_build_src/tests/data/input/modality-specific-files/magnetic-resonance-imaging-data.md b/pdf_build_src/tests/data/input/modality-specific-files/magnetic-resonance-imaging-data.md new file mode 100644 index 00000000..bfc1b850 --- /dev/null +++ b/pdf_build_src/tests/data/input/modality-specific-files/magnetic-resonance-imaging-data.md @@ -0,0 +1,10 @@ +# Magnetic Resonance Imaging + +## Common metadata fields + +!!! warning "foo bar" + + Lorem ipsum dolor sit amet, consectetur adipiscing elit. + Nulla et euismod nulla. + Curabitur feugiat, tortor non consequat finibus, justo purus auctor massa, + nec semper lorem quam in massa. diff --git a/readthedocs.yml b/readthedocs.yml index b5e50426..5611c595 100644 --- a/readthedocs.yml +++ b/readthedocs.yml @@ -2,11 +2,14 @@ version: 2 build: os: ubuntu-22.04 + apt_packages: + - jq tools: - python: "3.10" + python: "3.11" jobs: pre_build: - bst -v export --output src/schema.json + - tools/no-bad-schema-paths.sh src/schema.json # README.md might need fixing mkdocs: configuration: mkdocs.yml diff --git a/release_images/merge_commit.png b/release_images/merge_commit.png new file mode 100644 index 00000000..3df09bab Binary files /dev/null and b/release_images/merge_commit.png differ diff --git a/src/CHANGES.md b/src/CHANGES.md index 3963dce3..087368ff 100644 --- a/src/CHANGES.md +++ b/src/CHANGES.md @@ -1,7 +1,83 @@ # Changelog -## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD) - +## [v1.9.0](https://github.com/bids-standard/bids-specification/tree/v1.9.0) (2023-11-20) + +- \[FIX] mention phenotype dir in folder structure [#1644](https://github.com/bids-standard/bids-specification/pull/1644) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[ENH] add `ElectricalStimulation` and `\*Parameters` metadata to MEEG jsons [#1638](https://github.com/bids-standard/bids-specification/pull/1638) ([sappelhoff](https://github.com/sappelhoff)) +- \[FIX] years and degrees Units and unit to be singular to match the rest [#1631](https://github.com/bids-standard/bids-specification/pull/1631) ([yarikoptic](https://github.com/yarikoptic)) +- \[FIX] Hierarchical Event Descriptors (HED) page update [#1623](https://github.com/bids-standard/bids-specification/pull/1623) ([effigies](https://github.com/effigies)) +- \[ENH] Add `descriptions.tsv` file relating to the `desc-\` entity [#1613](https://github.com/bids-standard/bids-specification/pull/1613) ([CPernet](https://github.com/CPernet)) +- \[FIX] Do not require notch frequencies to be parsed as numbers, accommodating multiples [#1605](https://github.com/bids-standard/bids-specification/pull/1605) ([effigies](https://github.com/effigies)) +- \[ENH] Allow Levels field of column descriptions to be objects with TermURLs for each level [#1603](https://github.com/bids-standard/bids-specification/pull/1603) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[ENH] Add optional low_cutoff and high_cutoff columns for fnirs channels.tsv [#1597](https://github.com/bids-standard/bids-specification/pull/1597) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[FIX] Recommend SliceTiming if MRAcquisitionType is "2D" [#1594](https://github.com/bids-standard/bids-specification/pull/1594) ([tsalo](https://github.com/tsalo)) +- \[ENH] Add Level objects to channels.json for motion [#1591](https://github.com/bids-standard/bids-specification/pull/1591) ([effigies](https://github.com/effigies)) +- \[ENH] Add "chunk" entity to MRI datatype [#1586](https://github.com/bids-standard/bids-specification/pull/1586) ([valosekj](https://github.com/valosekj)) +- \[SCHEMA]\[ENH] Remove atlas entity and replace it with seg in prep of BEP038 [#1579](https://github.com/bids-standard/bids-specification/pull/1579) ([melanieganz](https://github.com/melanieganz)) +- \[FIX] Correct PDw suffix description [#1578](https://github.com/bids-standard/bids-specification/pull/1578) ([jeremie-fouquet](https://github.com/jeremie-fouquet)) +- \[FIX] improve longitudinal example [#1576](https://github.com/bids-standard/bids-specification/pull/1576) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[INFRA] Adds Kim Ray as maintainer. [#1571](https://github.com/bids-standard/bids-specification/pull/1571) ([arokem](https://github.com/arokem)) +- \[ENH] Allow for "echo" entity to be used with T1w and other nonparametric anatomical suffixes [#1570](https://github.com/bids-standard/bids-specification/pull/1570) ([yarikoptic](https://github.com/yarikoptic)) +- \[FIX] Update `templates` in modality-agnostic-files [#1564](https://github.com/bids-standard/bids-specification/pull/1564) ([sappelhoff](https://github.com/sappelhoff)) +- \[FIX] Clarify that electrodes.tsv is optional for MEG, for use with simultaneous (i)EEG [#1555](https://github.com/bids-standard/bids-specification/pull/1555) ([effigies](https://github.com/effigies)) +- \[ENH] Allow UNKNOWN and NONE ContrastBolusIngredients [#1547](https://github.com/bids-standard/bids-specification/pull/1547) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[FIX] Update links to BIDS examples [#1545](https://github.com/bids-standard/bids-specification/pull/1545) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[ENH] add schema in appendix [#1543](https://github.com/bids-standard/bids-specification/pull/1543) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[ENH] add "visual correction" and "head stabilization" metadata [#1539](https://github.com/bids-standard/bids-specification/pull/1539) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[ENH] Clarify meaning of raw vs derivative datasets [#1537](https://github.com/bids-standard/bids-specification/pull/1537) ([CPernet](https://github.com/CPernet)) +- \[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)) +- \[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)) +- ENH: Define channel column for events and Delimiter field for column descriptions [#1483](https://github.com/bids-standard/bids-specification/pull/1483) ([effigies](https://github.com/effigies)) +- \[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)) +- \[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)) +- \[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)) +- \[MISC] 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)) +- \[ENH] Add reference for ASL BEP [#1357](https://github.com/bids-standard/bids-specification/pull/1357) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[FIX] remove redundant entity definitions in behavioral page [#1356](https://github.com/bids-standard/bids-specification/pull/1356) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[FIX] add missing processing entity for MEG physio files and render physio filename templates for fNIRS [#1355](https://github.com/bids-standard/bids-specification/pull/1355) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[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-\` to structural MRI acquisitions [#1185](https://github.com/bids-standard/bids-specification/pull/1185) ([melanieganz](https://github.com/melanieganz)) +- \[INFRA] use tributors to list contributors and CITATION.cff for referencing [#1115](https://github.com/bids-standard/bids-specification/pull/1115) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[ENH] Extend BIDS for Motion data (BEP029) [#981](https://github.com/bids-standard/bids-specification/pull/981) ([JuliusWelzel](https://github.com/JuliusWelzel)) +- \[SCHEMA] Add full object definitions for valid values in schema [#919](https://github.com/bids-standard/bids-specification/pull/919) ([tsalo](https://github.com/tsalo)) + +## [v1.8.0](https://github.com/bids-standard/bids-specification/tree/v1.8.0) (2022-10-29) + +- \[FIX] Drop the functional and f for NIRS [#1325](https://github.com/bids-standard/bids-specification/pull/1325) ([rob-luke](https://github.com/rob-luke)) +- \[FIX]\[SCHEMA] Add conditionals for PET ReconMethod\* and ReconFilter [#1299](https://github.com/bids-standard/bids-specification/pull/1299) ([bendhouseart](https://github.com/bendhouseart)) +- \[ENH] use schema to mention which "top directories" are allowed [#1289](https://github.com/bids-standard/bids-specification/pull/1289) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[ENH] Add glossary links to all tables [#1268](https://github.com/bids-standard/bids-specification/pull/1268) ([tsalo](https://github.com/tsalo)) +- \[ENH] Remove redundant entity definitions on MRI page [#1265](https://github.com/bids-standard/bids-specification/pull/1265) ([tsalo](https://github.com/tsalo)) +- \[ENH] Standardize and organize entity descriptions [#1264](https://github.com/bids-standard/bids-specification/pull/1264) ([tsalo](https://github.com/tsalo)) +- \[ENH] Add filename template legend [#1259](https://github.com/bids-standard/bids-specification/pull/1259) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[MISC] Reorder appendices [#1256](https://github.com/bids-standard/bids-specification/pull/1256) ([tsalo](https://github.com/tsalo)) +- \[MISC] Clarify: FieldMap PE technique --> no SPM [#1253](https://github.com/bids-standard/bids-specification/pull/1253) ([CPernet](https://github.com/CPernet)) - \[MISC] Adding qMRI BIDS article reference (BEP001) [#1251](https://github.com/bids-standard/bids-specification/pull/1251) ([agahkarakuzu](https://github.com/agahkarakuzu)) - \[ENH] Link to filename element definitions in filename templates [#1228](https://github.com/bids-standard/bids-specification/pull/1228) ([tsalo](https://github.com/tsalo)) - \[MISC] Remove label format and inheritance principle redundancies in fMRI section [#1197](https://github.com/bids-standard/bids-specification/pull/1197) ([Remi-Gau](https://github.com/Remi-Gau)) @@ -11,6 +87,7 @@ - \[FIX] Discourage use of "sample" in events if sampling frequency is ambiguous, add guidelines for precision [#1140](https://github.com/bids-standard/bids-specification/pull/1140) ([sappelhoff](https://github.com/sappelhoff)) - \[FIX] Clarify MEG empty-room recommendations [#1125](https://github.com/bids-standard/bids-specification/pull/1125) ([robertoostenveld](https://github.com/robertoostenveld)) - \[FIX] clarify no blank and duplicated headers in TSV [#1116](https://github.com/bids-standard/bids-specification/pull/1116) ([sappelhoff](https://github.com/sappelhoff)) +- \[ENH] Added the specification for using HED libraries in BIDS [#1106](https://github.com/bids-standard/bids-specification/pull/1106) ([VisLab](https://github.com/VisLab)) - \[ENH] Microscopy: NGFF format support [#1104](https://github.com/bids-standard/bids-specification/pull/1104) ([TheChymera](https://github.com/TheChymera)) - \[ENH] Add Microscopy-BIDS citation [#1102](https://github.com/bids-standard/bids-specification/pull/1102) ([mariehbourget](https://github.com/mariehbourget)) - \[FIX] MEG link typo [#1100](https://github.com/bids-standard/bids-specification/pull/1100) ([xi](https://github.com/xi)) @@ -20,7 +97,6 @@ - \[ENH] State of the schema sprint [#1075](https://github.com/bids-standard/bids-specification/pull/1075) ([effigies](https://github.com/effigies)) - \[MISC] Preface each macro call with comment [#1052](https://github.com/bids-standard/bids-specification/pull/1052) ([Remi-Gau](https://github.com/Remi-Gau)) - \[ENH] allow for .png and .tif in eeg/ieeg/meg as allowed for micr [#1049](https://github.com/bids-standard/bids-specification/pull/1049) ([yarikoptic](https://github.com/yarikoptic)) -- \[SCHEMA] Add a new `file\_relative` format [#1046](https://github.com/bids-standard/bids-specification/pull/1046) ([tsalo](https://github.com/tsalo)) - \[FIX] typo in "rawdata" example [#1045](https://github.com/bids-standard/bids-specification/pull/1045) ([sappelhoff](https://github.com/sappelhoff)) - \[MISC] consistently use "directory" instead of "folder" as a term [#1044](https://github.com/bids-standard/bids-specification/pull/1044) ([sappelhoff](https://github.com/sappelhoff)) - \[MISC] Update CODEOWNERS [#1040](https://github.com/bids-standard/bids-specification/pull/1040) ([erdalkaraca](https://github.com/erdalkaraca)) @@ -35,12 +111,12 @@ - \[ENH] Introduce the atlas entity for derivatives data [#997](https://github.com/bids-standard/bids-specification/pull/997) ([sebastientourbier](https://github.com/sebastientourbier)) - \[ENH] Clearly define "entity" in common principles [#947](https://github.com/bids-standard/bids-specification/pull/947) ([Lestropie](https://github.com/Lestropie)) - \[ENH] Add BIDS URIs and deprecate relative paths, RawSources and (possibly unused) BasedOn [#918](https://github.com/bids-standard/bids-specification/pull/918) ([effigies](https://github.com/effigies)) +- \[ENH] BEP030: Functional Near-Infrared Spectroscopy [#802](https://github.com/bids-standard/bids-specification/pull/802) ([rob-luke](https://github.com/rob-luke)) - \[FIX] Clarify run entity to accommodate multiple imaging modalities [#760](https://github.com/bids-standard/bids-specification/pull/760) ([yarikoptic](https://github.com/yarikoptic)) ## [v1.7.0](https://github.com/bids-standard/bids-specification/tree/v1.7.0) (2022-02-15) - \[FIX] Use wikipedia for TIFF URL, adobe's page is 404ing now [#1007](https://github.com/bids-standard/bids-specification/pull/1007) ([yarikoptic](https://github.com/yarikoptic)) -- REL: v1.7.0 [#1004](https://github.com/bids-standard/bids-specification/pull/1004) ([franklin-feingold](https://github.com/franklin-feingold)) - \[FIX] update highlighting of examples, JSON keys and values, and TSV headers or values in the schema [#998](https://github.com/bids-standard/bids-specification/pull/998) ([Remi-Gau](https://github.com/Remi-Gau)) - \[MISC] minor wording and consistency improvements for channels.tsv in EEG, MEG, iEEG [#993](https://github.com/bids-standard/bids-specification/pull/993) ([sappelhoff](https://github.com/sappelhoff)) - \[FIX] typo: extra sentence in anat section [#991](https://github.com/bids-standard/bids-specification/pull/991) ([Remi-Gau](https://github.com/Remi-Gau)) @@ -48,9 +124,9 @@ - \[FIX] update definition acq_time for sessions.tsv [#986](https://github.com/bids-standard/bids-specification/pull/986) ([Remi-Gau](https://github.com/Remi-Gau)) - \[FIX] add microscopy to modalities in schema [#984](https://github.com/bids-standard/bids-specification/pull/984) ([Remi-Gau](https://github.com/Remi-Gau)) - \[MISC] update steering group composition [#976](https://github.com/bids-standard/bids-specification/pull/976) ([Remi-Gau](https://github.com/Remi-Gau)) -- customize footer on html spec [#975](https://github.com/bids-standard/bids-specification/pull/975) ([sappelhoff](https://github.com/sappelhoff)) +- \[MISC] customize footer on html spec [#975](https://github.com/bids-standard/bids-specification/pull/975) ([sappelhoff](https://github.com/sappelhoff)) - \[FIX] Update HED appendix to comply with current HED version [#970](https://github.com/bids-standard/bids-specification/pull/970) ([VisLab](https://github.com/VisLab)) -- ENH: Update B0Field metadata to accommodate single-blip fieldmaps [#968](https://github.com/bids-standard/bids-specification/pull/968) ([effigies](https://github.com/effigies)) +- \[ENH] Update B0Field metadata to accommodate single-blip fieldmaps [#968](https://github.com/bids-standard/bids-specification/pull/968) ([effigies](https://github.com/effigies)) - \[FIX] Reword front page [#958](https://github.com/bids-standard/bids-specification/pull/958) ([arokem](https://github.com/arokem)) - \[MISC] Update links to starter kit website [#957](https://github.com/bids-standard/bids-specification/pull/957) ([effigies](https://github.com/effigies)) - \[FIX] Entity table: Clarify meaning of empty cells [#955](https://github.com/bids-standard/bids-specification/pull/955) ([Lestropie](https://github.com/Lestropie)) @@ -80,14 +156,12 @@ - \[INFRA] jQuery 3.4.1 → 3.6.0 [#875](https://github.com/bids-standard/bids-specification/pull/875) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos)) - \[INFRA] Add "codespell" tool to CI checks to catch typos sooner [#873](https://github.com/bids-standard/bids-specification/pull/873) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos)) - \[INFRA] Several style fixes (Flake8) for Python code in the repo [#872](https://github.com/bids-standard/bids-specification/pull/872) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos)) -- \[FIX] Make subheadings consistent in 06-longitudinal-and-multi-site-studies.md [#870](https://github.com/bids-standard/bids-specification/pull/870) ([guiomar](https://github.com/guiomar)) - \[MISC] add Anthony as maintainer [#868](https://github.com/bids-standard/bids-specification/pull/868) ([Remi-Gau](https://github.com/Remi-Gau)) - \[MISC] add "forward slash" requirement for paths to common principles [#867](https://github.com/bids-standard/bids-specification/pull/867) ([sappelhoff](https://github.com/sappelhoff)) - \[ENH] Add "ScanRAS" as an accepted coordinate frame for ieeg [#866](https://github.com/bids-standard/bids-specification/pull/866) ([alexrockhill](https://github.com/alexrockhill)) - \[INFRA] Add .lgtm.yml file for better usage of LGTM CI tool [#865](https://github.com/bids-standard/bids-specification/pull/865) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos)) - \[FIX] update physio bids name in longitudinal study page examples [#863](https://github.com/bids-standard/bids-specification/pull/863) ([Remi-Gau](https://github.com/Remi-Gau)) - \[INFRA] Enforce consistent line endings via .gitattributes [#861](https://github.com/bids-standard/bids-specification/pull/861) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos)) -- \[INFRA] dos2unix [#859](https://github.com/bids-standard/bids-specification/pull/859) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos)) - \[FIX] Clarify case collision intolerance as a file naming principle [#858](https://github.com/bids-standard/bids-specification/pull/858) ([yarikoptic](https://github.com/yarikoptic)) - \[INFRA] LGTM recommendation: Unused local variable [#853](https://github.com/bids-standard/bids-specification/pull/853) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos)) - \[INFRA] LGTM warning: Variable defined multiple times [#851](https://github.com/bids-standard/bids-specification/pull/851) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos)) @@ -102,7 +176,6 @@ - \[SCHEMA] Add TSV column files [#827](https://github.com/bids-standard/bids-specification/pull/827) ([tsalo](https://github.com/tsalo)) - \[ENH] add metadata to PET calibration factor: "DoseCalibrationFactor" [#825](https://github.com/bids-standard/bids-specification/pull/825) ([CPernet](https://github.com/CPernet)) - \[FIX] correct file location of scans.tsv file in example [#824](https://github.com/bids-standard/bids-specification/pull/824) ([ghisvail](https://github.com/ghisvail)) -- \[FIX] Add missing closing parenthesis in 02-common-principle.md [#822](https://github.com/bids-standard/bids-specification/pull/822) ([sebastientourbier](https://github.com/sebastientourbier)) - \[MISC] update available datatypes in specification [#819](https://github.com/bids-standard/bids-specification/pull/819) ([sappelhoff](https://github.com/sappelhoff)) - \[FIX] document required column order MEG, EEG, iEEG, PET, and fix typo iEEG [#818](https://github.com/bids-standard/bids-specification/pull/818) ([sappelhoff](https://github.com/sappelhoff)) - \[ENH] BEP031 - New columns to participants.tsv file [#816](https://github.com/bids-standard/bids-specification/pull/816) ([mariehbourget](https://github.com/mariehbourget)) @@ -136,7 +209,6 @@ ## [v1.6.0](https://github.com/bids-standard/bids-specification/tree/v1.6.0) (2021-04-22) - \[FIX] Typos discovered by codespell [#784](https://github.com/bids-standard/bids-specification/pull/784) ([yarikoptic](https://github.com/yarikoptic)) -- REL: v1.6.0 [#776](https://github.com/bids-standard/bids-specification/pull/776) ([effigies](https://github.com/effigies)) - \[FIX] Rename "Unit" metadata to "Units" for consistency with existing fields [#773](https://github.com/bids-standard/bids-specification/pull/773) ([effigies](https://github.com/effigies)) - \[FIX] typo in pet: institution -> institutional [#771](https://github.com/bids-standard/bids-specification/pull/771) ([sappelhoff](https://github.com/sappelhoff)) - \[INFRA] install git in linkchecker job [#767](https://github.com/bids-standard/bids-specification/pull/767) ([sappelhoff](https://github.com/sappelhoff)) @@ -156,7 +228,6 @@ ## [v1.5.0](https://github.com/bids-standard/bids-specification/tree/v1.5.0) (2021-02-23) - \[MISC] Updated TotalAcquiredVolumes into TotalAcquiredPairs [#742](https://github.com/bids-standard/bids-specification/pull/742) ([effigies](https://github.com/effigies)) -- REL: v1.5.0 [#736](https://github.com/bids-standard/bids-specification/pull/736) ([franklin-feingold](https://github.com/franklin-feingold)) - \[SCHEMA] Update qMRI fieldmap schema [#728](https://github.com/bids-standard/bids-specification/pull/728) ([effigies](https://github.com/effigies)) - \[FIX] Add deprecated anatomical MRI suffixes back into schema [#725](https://github.com/bids-standard/bids-specification/pull/725) ([tsalo](https://github.com/tsalo)) - \[FIX] Correct schema irregularities for func datatype [#724](https://github.com/bids-standard/bids-specification/pull/724) ([tsalo](https://github.com/tsalo)) @@ -171,7 +242,7 @@ - \[ENH] BEP001 - qMRI maps and some additional metadata [#690](https://github.com/bids-standard/bids-specification/pull/690) ([agahkarakuzu](https://github.com/agahkarakuzu)) - \[ENH] BEP001 - Entity-linked file collections [#688](https://github.com/bids-standard/bids-specification/pull/688) ([effigies](https://github.com/effigies)) - \[ENH] BEP001 - New entities: inv & mt [#681](https://github.com/bids-standard/bids-specification/pull/681) ([agahkarakuzu](https://github.com/agahkarakuzu)) -- \[DOC] add contributing guidelines to add figures in the specs [#679](https://github.com/bids-standard/bids-specification/pull/679) ([Remi-Gau](https://github.com/Remi-Gau)) +- \[MISC] add contributing guidelines to add figures in the specs [#679](https://github.com/bids-standard/bids-specification/pull/679) ([Remi-Gau](https://github.com/Remi-Gau)) - \[MISC] use RFC 2119 language in legend of the "volume timing" table [#678](https://github.com/bids-standard/bids-specification/pull/678) ([Remi-Gau](https://github.com/Remi-Gau)) - \[FIX] Add OPTIONAL acq entity to channels.tsv, events.tsv to match electrophysiological acquisitions [#677](https://github.com/bids-standard/bids-specification/pull/677) ([sappelhoff](https://github.com/sappelhoff)) - \[MISC] Update all links to use HTTPS whenever possible. [#676](https://github.com/bids-standard/bids-specification/pull/676) ([gllmflndn](https://github.com/gllmflndn)) @@ -196,7 +267,6 @@ - \[INFRA] minor robustness enhancements to pdf build shell script [#642](https://github.com/bids-standard/bids-specification/pull/642) ([yarikoptic](https://github.com/yarikoptic)) - \[FIX] consistent CoordinateSystem fields for ephys [#641](https://github.com/bids-standard/bids-specification/pull/641) ([sappelhoff](https://github.com/sappelhoff)) -- REL: v1.4.1 [#640](https://github.com/bids-standard/bids-specification/pull/640) ([franklin-feingold](https://github.com/franklin-feingold)) - \[INFRA] set up github action to detect latin phrases [#636](https://github.com/bids-standard/bids-specification/pull/636) ([Remi-Gau](https://github.com/Remi-Gau)) - \[ENH] Add a definition for "deprecation" [#634](https://github.com/bids-standard/bids-specification/pull/634) ([sappelhoff](https://github.com/sappelhoff)) - \[MISC] consolidate BIDS citations in introduction [#630](https://github.com/bids-standard/bids-specification/pull/630) ([sappelhoff](https://github.com/sappelhoff)) @@ -241,7 +311,6 @@ - \[INFRA] add copyright holder to license. [#521](https://github.com/bids-standard/bids-specification/pull/521) ([sappelhoff](https://github.com/sappelhoff)) - \[FIX] clarify XXXCoord\* in the coordinate systems appendix [#520](https://github.com/bids-standard/bids-specification/pull/520) ([sappelhoff](https://github.com/sappelhoff)) - \[ENH] Update `beh/` specification to contrast with any neural recordings [#515](https://github.com/bids-standard/bids-specification/pull/515) ([effigies](https://github.com/effigies)) -- \[FIX] 'segmentation' spelling in 05-derivatives/03-imaging.md [#514](https://github.com/bids-standard/bids-specification/pull/514) ([rwblair](https://github.com/rwblair)) - \[FIX] restructure and clarify \*\_physio/\*\_stim section [#513](https://github.com/bids-standard/bids-specification/pull/513) ([sappelhoff](https://github.com/sappelhoff)) - \[FIX] clarify file formats in EEG, iEEG [#511](https://github.com/bids-standard/bids-specification/pull/511) ([sappelhoff](https://github.com/sappelhoff)) - \[FIX] Add links and release dates to pre GH changelog, fix formatting [#509](https://github.com/bids-standard/bids-specification/pull/509) ([sappelhoff](https://github.com/sappelhoff)) @@ -255,7 +324,6 @@ ## [v1.4.0](https://github.com/bids-standard/bids-specification/tree/v1.4.0) (2020-06-11) -- REL: v1.4.0 [#496](https://github.com/bids-standard/bids-specification/pull/496) ([franklin-feingold](https://github.com/franklin-feingold)) - \[FIX] Clarify language on unsetting a key/value pair [#495](https://github.com/bids-standard/bids-specification/pull/495) ([nicholst](https://github.com/nicholst)) - \[ENH] optionally allow LICENSE file [#483](https://github.com/bids-standard/bids-specification/pull/483) ([sappelhoff](https://github.com/sappelhoff)) - \[INFRA] linkchecker - ignore github pull and tree URLs [#477](https://github.com/bids-standard/bids-specification/pull/477) ([yarikoptic](https://github.com/yarikoptic)) @@ -269,7 +337,6 @@ - \[FIX] Add reference to PDF on front page of specification [#452](https://github.com/bids-standard/bids-specification/pull/452) ([nicholst](https://github.com/nicholst)) - \[INFRA] Add conditional for link-checking releases [#451](https://github.com/bids-standard/bids-specification/pull/451) ([franklin-feingold](https://github.com/franklin-feingold)) - \[FIX] unordered list formatting in BEP018 [#449](https://github.com/bids-standard/bids-specification/pull/449) ([sappelhoff](https://github.com/sappelhoff)) -- REL: 1.3.1-dev [#448](https://github.com/bids-standard/bids-specification/pull/448) ([franklin-feingold](https://github.com/franklin-feingold)) - \[FIX] fix inconsistencies for task label between sections [#446](https://github.com/bids-standard/bids-specification/pull/446) ([Remi-Gau](https://github.com/Remi-Gau)) - \[FIX] update DECISION-MAKING.md document with new governance [#441](https://github.com/bids-standard/bids-specification/pull/441) ([sappelhoff](https://github.com/sappelhoff)) - \[ENH] BEP 003: Common Derivatives [#265](https://github.com/bids-standard/bids-specification/pull/265) ([effigies](https://github.com/effigies)) @@ -282,7 +349,6 @@ - \[FIX] Clarify snake_case+CamelCase in TSV+JSON [#442](https://github.com/bids-standard/bids-specification/pull/442) ([sappelhoff](https://github.com/sappelhoff)) - \[FIX] Eliminate web/online-specific language [#437](https://github.com/bids-standard/bids-specification/pull/437) ([nicholst](https://github.com/nicholst)) - \[INFRA] ensure build_docs_pdf CircleCI job runs last [#436](https://github.com/bids-standard/bids-specification/pull/436) ([sappelhoff](https://github.com/sappelhoff)) -- REL: v1.3.0 [#435](https://github.com/bids-standard/bids-specification/pull/435) ([franklin-feingold](https://github.com/franklin-feingold)) - \[INFRA] Add issue templates for GitHub [#434](https://github.com/bids-standard/bids-specification/pull/434) ([sappelhoff](https://github.com/sappelhoff)) - \[INFRA] Get latest PDF build from CircleCI artifacts [#433](https://github.com/bids-standard/bids-specification/pull/433) ([sappelhoff](https://github.com/sappelhoff)) - \[INFRA] Update release protocol [#432](https://github.com/bids-standard/bids-specification/pull/432) ([franklin-feingold](https://github.com/franklin-feingold)) @@ -292,7 +358,6 @@ - \[FIX] Unify section titles and table-of-contents entries [#422](https://github.com/bids-standard/bids-specification/pull/422) ([nicholst](https://github.com/nicholst)) - \[INFRA] add # before heading in CHANGES [#419](https://github.com/bids-standard/bids-specification/pull/419) ([sappelhoff](https://github.com/sappelhoff)) - \[INFRA] fix heading of auto changelog to be a markdown header [#417](https://github.com/bids-standard/bids-specification/pull/417) ([sappelhoff](https://github.com/sappelhoff)) -- REL: 1.3.0-dev [#413](https://github.com/bids-standard/bids-specification/pull/413) ([franklin-feingold](https://github.com/franklin-feingold)) - \[ENH] Add OPTIONAL EthicsApprovals field to dataset description [#412](https://github.com/bids-standard/bids-specification/pull/412) ([effigies](https://github.com/effigies)) - \[ENH] BEP 018 - Genetic Information [#395](https://github.com/bids-standard/bids-specification/pull/395) ([effigies](https://github.com/effigies)) @@ -300,7 +365,6 @@ - \[FIX] improve wording on data dictionaries [#410](https://github.com/bids-standard/bids-specification/pull/410) ([sappelhoff](https://github.com/sappelhoff)) - \[MISC] update contributions by CPernet [#409](https://github.com/bids-standard/bids-specification/pull/409) ([CPernet](https://github.com/CPernet)) -- REL: v1.2.2 [#405](https://github.com/bids-standard/bids-specification/pull/405) ([franklin-feingold](https://github.com/franklin-feingold)) - \[MISC] Add Sébastien Tourbier to contributors [#394](https://github.com/bids-standard/bids-specification/pull/394) ([sebastientourbier](https://github.com/sebastientourbier)) - \[FIX] consistent units description between EEG/MEG/iEEG. Clarify (derived) SI units + prefixes [#391](https://github.com/bids-standard/bids-specification/pull/391) ([sappelhoff](https://github.com/sappelhoff)) - \[MISC] moved list of extension proposals to the main BIDS website [#389](https://github.com/bids-standard/bids-specification/pull/389) ([robertoostenveld](https://github.com/robertoostenveld)) @@ -317,7 +381,7 @@ - \[FIX] Clarify channels.tsv is RECOMMENDED consistently across ephys [#347](https://github.com/bids-standard/bids-specification/pull/347) ([sappelhoff](https://github.com/sappelhoff)) - \[FIX] Typo fix (contract -> contrast) in events documentation [#346](https://github.com/bids-standard/bids-specification/pull/346) ([snastase](https://github.com/snastase)) - \[MISC] rm TOC.md - seems no longer pertinent/used [#341](https://github.com/bids-standard/bids-specification/pull/341) ([yarikoptic](https://github.com/yarikoptic)) -- \[MISC] Move the PR template to a separate folder and improve contents [#338](https://github.com/bids-standard/bids-specification/pull/338) ([jhlegarreta](https://github.com/jhlegarreta)) +- \[MISC] Move the PR template to a separate directory and improve contents [#338](https://github.com/bids-standard/bids-specification/pull/338) ([jhlegarreta](https://github.com/jhlegarreta)) - \[INFRA] Find npm requirements file in Circle [#336](https://github.com/bids-standard/bids-specification/pull/336) ([franklin-feingold](https://github.com/franklin-feingold)) - \[ENH] Clarify phenotypic and assessment data in new section [#331](https://github.com/bids-standard/bids-specification/pull/331) ([sappelhoff](https://github.com/sappelhoff)) - \[MISC] add information about continuous integration checks to PR template [#330](https://github.com/bids-standard/bids-specification/pull/330) ([sappelhoff](https://github.com/sappelhoff)) @@ -331,7 +395,6 @@ - \[FIX] Add CBV and phase to Entity table [#312](https://github.com/bids-standard/bids-specification/pull/312) ([tsalo](https://github.com/tsalo)) - \[FIX] Normalization of template-generated standard spaces [#306](https://github.com/bids-standard/bids-specification/pull/306) ([oesteban](https://github.com/oesteban)) - \[ENH] Release protocol notes [#304](https://github.com/bids-standard/bids-specification/pull/304) ([franklin-feingold](https://github.com/franklin-feingold)) -- REL: 1.3.0-dev [#303](https://github.com/bids-standard/bids-specification/pull/303) ([franklin-feingold](https://github.com/franklin-feingold)) - \[INFRA] Adding contributor appendix sentence to PR template [#299](https://github.com/bids-standard/bids-specification/pull/299) ([franklin-feingold](https://github.com/franklin-feingold)) - \[ENH] Added discontinuous datatype for EEG and iEEG [#286](https://github.com/bids-standard/bids-specification/pull/286) ([wouterpotters](https://github.com/wouterpotters)) - \[FIX] Clarify paragraph about custom data types [#264](https://github.com/bids-standard/bids-specification/pull/264) ([effigies](https://github.com/effigies)) @@ -341,7 +404,6 @@ - \[FIX] repair link in anatomical MRI table [#297](https://github.com/bids-standard/bids-specification/pull/297) ([sappelhoff](https://github.com/sappelhoff)) - \[ENH] Clarify requirements in Release Protocol [#294](https://github.com/bids-standard/bids-specification/pull/294) ([franklin-feingold](https://github.com/franklin-feingold)) - \[INFRA] Use linkchecker (from a dedicated docker image) to check all URLs [#293](https://github.com/bids-standard/bids-specification/pull/293) ([yarikoptic](https://github.com/yarikoptic)) -- REL: v1.2.1 [#291](https://github.com/bids-standard/bids-specification/pull/291) ([franklin-feingold](https://github.com/franklin-feingold)) - \[ENH] Adding Contributors and updating contributions [#284](https://github.com/bids-standard/bids-specification/pull/284) ([franklin-feingold](https://github.com/franklin-feingold)) - \[MISC] update Code of Conduct contact [#281](https://github.com/bids-standard/bids-specification/pull/281) ([franklin-feingold](https://github.com/franklin-feingold)) - \[ENH] Update contributing guide and README to make discussion forums easy to find [#279](https://github.com/bids-standard/bids-specification/pull/279) ([emdupre](https://github.com/emdupre)) @@ -362,7 +424,6 @@ - \[MISC] Document BEPs that are not active anymore, but have not been merged [#240](https://github.com/bids-standard/bids-specification/pull/240) ([sappelhoff](https://github.com/sappelhoff)) - \[FIX] remove ManufacturersAmplifierModelName (again) [#236](https://github.com/bids-standard/bids-specification/pull/236) ([robertoostenveld](https://github.com/robertoostenveld)) - \[INFRA] Update release protocol [#235](https://github.com/bids-standard/bids-specification/pull/235) ([effigies](https://github.com/effigies)) -- REL: 1.3.0-dev [#234](https://github.com/bids-standard/bids-specification/pull/234) ([effigies](https://github.com/effigies)) - \[INFRA] Enable version panel for quickly finding previous versions [#232](https://github.com/bids-standard/bids-specification/pull/232) ([effigies](https://github.com/effigies)) - \[FIX] Clarify Appendix II: The list of licenses only lists examples [#222](https://github.com/bids-standard/bids-specification/pull/222) ([sappelhoff](https://github.com/sappelhoff)) - \[FIX] Trivial column header fix [#220](https://github.com/bids-standard/bids-specification/pull/220) ([nicholst](https://github.com/nicholst)) @@ -394,7 +455,6 @@ ## [v1.2.0](https://github.com/bids-standard/bids-specification/tree/v1.2.0) (2019-03-04) -- REL: v1.2.0 [#161](https://github.com/bids-standard/bids-specification/pull/161) ([chrisgorgo](https://github.com/chrisgorgo)) - \[MISC] Adding Dimitri Papadopoulos Orfanos to the list of contributors [#157](https://github.com/bids-standard/bids-specification/pull/157) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos)) - \[FIX] use "specification" not "protocol" to refer to BIDS [#156](https://github.com/bids-standard/bids-specification/pull/156) ([yarikoptic](https://github.com/yarikoptic)) - \[FIX] Fix example misalignment [#155](https://github.com/bids-standard/bids-specification/pull/155) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos)) @@ -412,8 +472,6 @@ ## [v1.1.2](https://github.com/bids-standard/bids-specification/tree/v1.1.2) (2019-01-10) -- REL: v.1.1.2 [#121](https://github.com/bids-standard/bids-specification/pull/121) ([chrisgorgo](https://github.com/chrisgorgo)) -- \[MISC] Update 01-contributors.md [#120](https://github.com/bids-standard/bids-specification/pull/120) ([oesteban](https://github.com/oesteban)) - \[ENH] Global fields in data dictionaries [#117](https://github.com/bids-standard/bids-specification/pull/117) ([chrisgorgo](https://github.com/chrisgorgo)) - \[MISC] Propose BEP026 MER [#116](https://github.com/bids-standard/bids-specification/pull/116) ([greydongilmore](https://github.com/greydongilmore)) - \[FIX] Remove duplicate entries in MEG table [#113](https://github.com/bids-standard/bids-specification/pull/113) ([franklin-feingold](https://github.com/franklin-feingold)) @@ -427,10 +485,8 @@ - \[MISC] Change BEP numbers to include MRS [#94](https://github.com/bids-standard/bids-specification/pull/94) ([Hboni](https://github.com/Hboni)) - \[FIX] harmonize and thus shorten templates etc [#93](https://github.com/bids-standard/bids-specification/pull/93) ([yarikoptic](https://github.com/yarikoptic)) - \[MISC] put links and some text into README [#91](https://github.com/bids-standard/bids-specification/pull/91) ([sappelhoff](https://github.com/sappelhoff)) -- \[MISC] Add extension proposal in 01-introduction.md [#88](https://github.com/bids-standard/bids-specification/pull/88) ([Hboni](https://github.com/Hboni)) - \[FIX] additional table to recap 'volume acquisition timing' [#87](https://github.com/bids-standard/bids-specification/pull/87) ([Remi-Gau](https://github.com/Remi-Gau)) - \[FIX] Small typo in "scanning sequence" DICOM Tag [#84](https://github.com/bids-standard/bids-specification/pull/84) ([Remi-Gau](https://github.com/Remi-Gau)) -- \[MISC] Update 01-contributors.md [#83](https://github.com/bids-standard/bids-specification/pull/83) ([teonbrooks](https://github.com/teonbrooks)) - \[ENH] Added CBV contrast [#82](https://github.com/bids-standard/bids-specification/pull/82) ([TheChymera](https://github.com/TheChymera)) - \[MISC] Add CC-BY 4.0 license [#81](https://github.com/bids-standard/bids-specification/pull/81) ([KirstieJane](https://github.com/KirstieJane)) - \[INFRA] Fix Travis break [#80](https://github.com/bids-standard/bids-specification/pull/80) ([franklin-feingold](https://github.com/franklin-feingold)) @@ -440,11 +496,10 @@ - \[MISC] Updated my contributions [#75](https://github.com/bids-standard/bids-specification/pull/75) ([nicholst](https://github.com/nicholst)) - \[FIX] update HED appendix [#74](https://github.com/bids-standard/bids-specification/pull/74) ([sappelhoff](https://github.com/sappelhoff)) - \[FIX] unicode: replace greek mu and omega by micro and ohm signs [#73](https://github.com/bids-standard/bids-specification/pull/73) ([sappelhoff](https://github.com/sappelhoff)) -- \[MISC] Update 01-contributors.md [#72](https://github.com/bids-standard/bids-specification/pull/72) ([francopestilli](https://github.com/francopestilli)) - \[ENH] add `ce-\` for fmri data [#70](https://github.com/bids-standard/bids-specification/pull/70) ([dasturge](https://github.com/dasturge)) - \[INFRA] pin pip version [#68](https://github.com/bids-standard/bids-specification/pull/68) ([chrisgorgo](https://github.com/chrisgorgo)) - \[MISC] Fix link in index [#46](https://github.com/bids-standard/bids-specification/pull/46) ([chrisgorgo](https://github.com/chrisgorgo)) -- \[MISC] edit contributing guide [#44](https://github.com/bids-standard/bids-specification/pull/44) ([Park-Patrick](https://github.com/Park-Patrick)) +- \[MISC] edit contributing guide [#44](https://github.com/bids-standard/bids-specification/pull/44) ([patrick-g-h](https://github.com/patrick-g-h)) - \[INFRA] Mkdocs configuration and RTD setup [#42](https://github.com/bids-standard/bids-specification/pull/42) ([choldgraf](https://github.com/choldgraf)) - \[MISC] Move definitions, compulsory, and raw/derivatives sections to principles [#40](https://github.com/bids-standard/bids-specification/pull/40) ([chrisgorgo](https://github.com/chrisgorgo)) - \[MISC] Remove duplicate section [#39](https://github.com/bids-standard/bids-specification/pull/39) ([chrisgorgo](https://github.com/chrisgorgo)) @@ -478,30 +533,30 @@ - Added support for MEG data (merged BEP008). - Added `SequenceName` field. -- Added support for describing events with Hierarchical Event Descriptors: [4.3 Task events](04-modality-specific-files/05-task-events.md). -- Added `VolumeTiming` and `AcquisitionDuration` fields: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data). +- Added support for describing events with Hierarchical Event Descriptors: [4.3 Task events](modality-specific-files/task-events.md). +- Added `VolumeTiming` and `AcquisitionDuration` fields: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data). - Added `DwellTime` field. ## [1.0.2](https://doi.org/10.5281/zenodo.3759801) (2017-07-18) -- Added support for high resolution (anatomical) T2star images: [4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data). -- Added support for multiple defacing masks: [4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data). -- Added optional key and metadata field for contrast enhanced structural scans: [4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data). -- Added `DelayTime` field: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data). -- Added support for multi echo BOLD data: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data). +- Added support for high resolution (anatomical) T2star images: [4.1 Anatomy imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#anatomy-imaging-data). +- Added support for multiple defacing masks: [4.1 Anatomy imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#anatomy-imaging-data). +- Added optional key and metadata field for contrast enhanced structural scans: [4.1 Anatomy imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#anatomy-imaging-data). +- Added `DelayTime` field: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data). +- Added support for multi echo BOLD data: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data). ## [1.0.1](https://doi.org/10.5281/zenodo.3759788) (2017-03-13) -- Added `InstitutionName` field: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data). -- Added `InstitutionAddress` field: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data). -- Added `DeviceSerialNumber` field: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data). -- Added `NumberOfVolumesDiscardedByUser` and `NumberOfVolumesDiscardedByScanner` field: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data). -- Added `TotalReadoutTime to` functional images metadata list: [4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data). +- Added `InstitutionName` field: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data). +- Added `InstitutionAddress` field: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data). +- Added `DeviceSerialNumber` field: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data). +- Added `NumberOfVolumesDiscardedByUser` and `NumberOfVolumesDiscardedByScanner` field: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data). +- Added `TotalReadoutTime to` functional images metadata list: [4.1 Task (including resting state) imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data). ## 1.0.1-rc1 -- Added T1 Rho maps: [4.1 Anatomy imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data). -- Added support for phenotypic information split into multiple files: [3.2 Participant key file](03-modality-agnostic-files.md#participants-file). +- Added T1 Rho maps: [4.1 Anatomy imaging data](modality-specific-files/magnetic-resonance-imaging-data.md#anatomy-imaging-data). +- Added support for phenotypic information split into multiple files: [3.2 Participant key file](modality-agnostic-files.md#participants-file). - Added recommendations for multi site datasets. - Added `SoftwareVersions`. - Added `run-` to the phase encoding maps. Improved the description. diff --git a/src/appendices/arterial-spin-labeling.md b/src/appendices/arterial-spin-labeling.md index 35b77238..4d1253ea 100644 --- a/src/appendices/arterial-spin-labeling.md +++ b/src/appendices/arterial-spin-labeling.md @@ -73,7 +73,7 @@ Y. Suzuki and [OSIPI Task force 4.1: ASL lexicon milestone 1](https://osipi.gith ### (P)CASL sequence -![PCASL](../04-modality-specific-files/images/asl_pcasl_sequence.png) +![PCASL](../modality-specific-files/images/asl_pcasl_sequence.png) For (P)CASL, specifying the `LabelingDuration` and the `PostLabelingDelay` is required. The `LabelingDuration` is defined as the total duration of the labeling pulse train in seconds. @@ -89,7 +89,7 @@ whereas in case of `CASL`,the recommended `CASLType` field describes if a separa ### (P)CASL Labeling Pulses -![PCASL Labeling Pulses](../04-modality-specific-files/images/asl_pcasl_labeling_pulses.png) +![PCASL Labeling Pulses](../modality-specific-files/images/asl_pcasl_labeling_pulses.png) Several recommended metadata fields describe the labeling pulses of the labeling pulse train in PCASL. The `LabelingPulseAverageGradient` and the `LabelingPulseMaximumGradient` are the average labeling gradient @@ -101,7 +101,7 @@ and the delay between the peaks of the individual labeling pulses in millisecond ### PASL sequence -![PASL without Bolus Cut-off](../04-modality-specific-files/images/asl_pasl_boluscutoff_false.png) +![PASL without Bolus Cut-off](../modality-specific-files/images/asl_pasl_boluscutoff_false.png) For PASL, specifying the `PostLabelingDelay` is required. `PostLabelingDelay` is the time, in seconds, from the middle of the labeling pulse until the middle of @@ -109,7 +109,7 @@ the excitation pulse applied to the imaging slab (for 3D acquisition) or first s Additionally, the `BolusCutOffFlag` field is required, which is a boolean indicating if a bolus cut-off technique has been applied. -![PASL QUIPSSII](../04-modality-specific-files/images/asl_pasl_boluscutoff_true_quipssII.png) +![PASL QUIPSSII](../modality-specific-files/images/asl_pasl_boluscutoff_true_quipssII.png) When `BolusCutOffFlag` is set true for `PASL`, two additional metadata fields are required: `BolusCutOffTechnique` and `BolusCutOffDelay`. @@ -117,7 +117,7 @@ In this example, the `BolusCutOffTechnique`, which is the name of the technique is QUIPSS-II consisting of only one bolus cut-off pulse. The `BolusCutOffDelay` is therefore a number, representing the duration between the end of the labeling and the start of the bolus cut-off saturation pulse, in seconds. -![PASL Q2TIPS](../04-modality-specific-files/images/asl_pasl_boluscutoff_true_q2tips.png) +![PASL Q2TIPS](../modality-specific-files/images/asl_pasl_boluscutoff_true_q2tips.png) In this example, the `BolusCutOffTechnique` applied is Q2TIPS, consisting of multiple bolus cut-off pulses. In this case, only the duration of the first and last pulse should be specified in `BolusCutOffDelay`. @@ -127,4 +127,4 @@ In this case, only the duration of the first and last pulse should be specified The specification includes a dependency table, describing metadata field dependencies for ASL. This flowchart is intended to further clarify that table. -![ASL Flowchart](../04-modality-specific-files/images/asl_flowchart.png) +![ASL Flowchart](../modality-specific-files/images/asl_flowchart.png) diff --git a/src/appendices/contributors.md b/src/appendices/contributors.md index 03698ed5..2ffab474 100644 --- a/src/appendices/contributors.md +++ b/src/appendices/contributors.md @@ -3,300 +3,365 @@ Legend (source: ) -| **Emoji** | **Represents** | -| --------- | --------------------------------------------------------------------------------- | -| 💬 | Answering Questions (on the mailing list, NeuroStars, GitHub, or in person, etc.) | -| 🐛 | Bug reports | -| 📝 | Blogposts | -| 💻 | Code | -| 🖋 | Content (separate from Blogposts, for example Website news) | -| 📖 | Documentation and specification | -| 🔣 | Data (example datasets) | -| 🎨 | Design | -| 💡 | Examples (for example datasets, use `Data`) | -| 📋 | Event Organizers | -| 💵 | Financial Support | -| 🔍 | Funding/Grant Finders | -| 🤔 | Ideas & Planning | -| 🚇 | Infrastructure (hosting, build-tools, etc.) | -| 🚧 | Maintenance of the BIDS standard | -| 🧑‍🏫 | Mentoring new contributors | -| 🔌 | Plugin/utility libraries | -| 📆 | Project management | -| 👀 | Reviewed Pull Requests | -| 🔧 | Tools | -| 🌍 | Translation | -| ⚠️ | Tests | -| ✅ | Tutorials | -| 📢 | Talks | -| 📓 | User testing (of new features, tools, etc.) | -| 📹 | Videos | +| **Emoji** | **Represents** | +| --------- | -------------------------------------------------------------------------------------- | +| 💬 | Answering Questions (on the mailing list, NeuroStars, GitHub, in person, or otherwise) | +| 🐛 | Bug reports | +| 📝 | Blogposts | +| 💻 | Code | +| 🖋 | Content (separate from Blogposts, for example Website news) | +| 📖 | Documentation and specification | +| 🔣 | Data (example datasets) | +| 🎨 | Design | +| 💡 | Examples (for example datasets, use `Data`) | +| 📋 | Event Organizers | +| 💵 | Financial Support | +| 🔍 | Funding/Grant Finders | +| 🤔 | Ideas & Planning | +| 🚇 | Infrastructure (hosting, build-tools, and so on) | +| 🚧 | Maintenance of the BIDS standard | +| 🧑‍🏫 | Mentoring new contributors | +| 🔌 | Plugin/utility libraries | +| 📆 | Project management | +| 👀 | Reviewed Pull Requests | +| 🔧 | Tools | +| 🌍 | Translation | +| ⚠️ | Tests | +| ✅ | Tutorials | +| 📢 | Talks | +| 📓 | User testing (of new features, tools, and so on) | +| 📹 | Videos | The following individuals have contributed to the Brain Imaging Data Structure ecosystem (in alphabetical order). If you contributed to the BIDS ecosystem and your name is not listed, please add it. -- Eric Achten 📖🔣📓 -- Azeez Adebimpe 📖 -- Rémi Adon 📖 -- Fidel Alfaro Almagro 💬📖💡🔌 -- David Alsop 📖 -- Stefan Appelhoff 📖💬🤔🐛💡💻👀⚠️📢✅🔧🔌📝🚧🔣 -- Yoni Ashar 📖 -- Tal Pal Attia 📖 -- Tibor Auer 💬📖💡🔧📢🐛🤔 -- Sylvain Baillet 📖🔍 -- Shashank Bansal 📖 -- Arshitha Basavaraj 📖🚇💻 -- Leandro Beltrachini 📖 -- Chris Benjamin 📖 -- Timo Berg 📖 -- Étienne Bergeron 🔣💻 -- Suyash Bhogawar 📖💡⚠️🔧💬 -- Stephan Bickel 📖 -- Ulrike Bingel 📖 -- Ethan Blackwood 👀📖 -- David Boas 📖 -- Elizabeth Bock 📖💡 -- Hugo Boniface 📖 -- Kristofer Bouchard 📖 -- Mathieu Boudreau 💬🤔📢 -- Marie-Hélène Bourget 📖🔣💻🤔 -- Eric Bridgeford 📖🔧 -- Teon L. Brooks 📖💻⚠️💬👀🤔🔧🐛📢 -- Christian Büchel 📖 -- Vince D. Calhoun 📖 -- Giulio Castegnaro 📖 -- Marco Castellaro 💬🐛💻📖💡⚠️📢🚇 -- Filippo Maria Castelli 📖🔣 -- Michael Chappell 📖🔣📆 -- Gang Chen 📖 -- William Clarke 📖 -- Patricia Clement 💬🐛💻📖🔣💡📋🤔📆⚠️📢 -- Helena Cockx 📖 -- Alexander L. Cohen 🐛💻📖💬 -- Julien Cohen-Adad 📖🔣🤔 -- R. Cameron Craddock 📖📢 -- Martin Craig 🔣 -- Sasha D'Ambrosio 📖 -- Samir Das 📖 -- Olivier David 📖 -- Orrin Devinsky 📖 -- Gilles de Hollander 📖 -- Alejandro de la Vega 🐛💻⚠️ -- Arnaud Delorme 📖💡 -- John Detre 📖 -- Benjamin Dichter 📖 -- Erin W. Dickie 📖🤔👀📢💬 -- Timo Dickscheid 📖 -- Dejan Draschkow 📖 -- Eugene P. Duff 📖 -- Elizabeth DuPre 📖💡🔍🤔💬 -- Joke Durnez 📖🔧💻 -- Eric Earl 📖💬🐛🚧🔧🤔 -- Anders Eklund 📖📢💻 -- Sara Elgayar 📖 -- Oscar Esteban 📖🔧🤔💬💻 -- Franklin W. Feingold 📋📝✅💬🤔🎨📢👀🚇🖋📆 -- Guillaume Flandin 📖💻 -- Adeen Flinker 📖 -- Alexandru Foias 📖🔣 -- Brett L. Foster 📖 -- Ana Fouto 📓 -- Benjamin Gagl 📖 -- Chris Gahnström 📖 -- Anthony Galassi 📖 -- Giuseppe Gallitto 📖 -- Melanie Ganz-Benjaminsen 📖🔣💻🤔📆🔍📢 -- Samuel Garcia 🤔👀📖 -- Remi Gau 📖💻💬📢🐛💻🚇👀🔧🤔 -- James Gholam 📖 -- Satrajit S. Ghosh 📖💻 -- Ashley G. Gillman 📖 -- Greydon Gilmore 📖 -- Tristan Glatard 📖💻 -- Mathias Goncalves 💻🔧📢 -- Krzysztof J. Gorgolewski 📖💻💬🤔🔍📢📝💡🔌 -- Alexandre Gramfort 📖💡 -- Klara Gregorova 📖 -- Jeffrey S. Grethe 💬🐛✅📢 -- Iris Groen 📖 -- David Groppe 📖 -- Sören Grothkopp 📖 -- Aysegul Gunduz 📖 -- Matthias Günther 📖 -- Yaroslav O. Halchenko 📖📢🔧💬🐛 -- Liberty Hamilton 📖 -- Tom Hampshire 📖 -- Daniel A. Handwerker 📖 -- Michael Hanke 📖🤔🔧🐛📢 -- Michael P. Harms 📖⚠️🔧 -- Soichi Hayashi 📖🔧🐛 -- Richard N. Henson 📖 -- Peer Herholz 💬📖👀🔧✅📢 -- Dora Hermes 📖💻✅🔍🤔 -- Luis Hernandez-Garcia 📖📓 -- Katja Heuer 🔧 -- Dorien Huijser 📖 -- Alexandre Hutton 📖 -- Richard Höchenberger 📖 -- Chris Holdgraf 📖🤔 -- Christopher J. Honey 📖 -- Andrew Hoopes 📖 -- Christian Horea 📖 -- Jean-Christophe Houde 📖 -- Maria de la Iglesia 📖 -- Ilkay Isik 📖 -- Hamish Innes-Brown 📖 -- International Neuroinformatics Coordinating Facility 💵📋 -- Andrew Jahn 📓 -- Andrew Janke 📖💻 -- Mainak Jas 📖💻 -- Sein Jeung 📖 -- Alexander Jones 💻🐛 -- Tamás Józsa 📓 -- Jakub Kaczmarzyk 📖🔧🚇 -- Lee Kamentsky 📖 -- Agah Karakuzu 💬📖🔣🤔 -- David Keator 📖 -- James Kent 💬💻 -- Ali Khan 📖 -- Gregory Kiar 📖💻🎨🔧 -- Balint Kincses 📖 -- Thomas Kirk 📖 -- Robert Knight 📖 -- Joost Kuijer 📖 -- Jean-Philippe Lachaux 📖 -- Marc Lalancette 📖 -- Pamela LaMontagne 📖💡 -- Kevin Larcher 💬 -- Jonathan C. Lau 📖 -- Laura and John Arnold Foundation 💵 -- Alexander von Lautz 📖 -- Alberto Lazari 📖 -- Kangjoo Lee 📖 -- Christopher Lee-Messer 📖 -- Jon Haitz Legarreta 💻📖 -- Dan Levitas 📖 -- Adam Li 📖💻 -- Xiangrui Li 📖💻 -- Ilona Lipp 📖 -- Vladimir Litvak 📖 -- Hanzhang Lu 📖 -- Robert Luke 📖 -- Brian N. Lundstrom 📖 -- Dan Lurie 🤔📖🔧🔌💻💬 -- Camille Maumet 📖 -- Christopher J. Markiewicz 💬🐛💻📖🎨💡🤔🔌👀🔧📢🔣📋🚧 -- Giacomo Mazzamuto 📖🔣 -- David McAlpine 📖 -- Manuel Mercier 📖🤔 -- Mark Mikkelsen 📖 -- Kai J. Miller 📖 -- Markus Morawski 📖 -- Clara Moreau 📖 -- Jeremy Moreau 📖💡 -- Zachary Michael 📖 -- Ezequiel Mikulan 📖💻 -- Michael P. Milham 💡🔍 -- Jeanette Mumford 📖 -- Athanasia Monika Mowinckel 📖 -- Henk Mutsaerts 💬🐛💻📖💡📋🤔📆📢📓 -- Manjari Narayan 📖 -- National Institute of Mental Health 💵 -- Mikael Naveau 🐛 -- B. Nolan Nichols 📖 -- Thomas E. Nichols 📖📢🔧👀🚧 -- Dylan Nielson 📖💻🔧 -- Aki Nikolaidis 📖 -- Gustav Nilsonne 📖 -- Guiomar Niso 🤔🎨🔍👀📋📝🔧🐛💻🔣✅💬📖💡📢 -- Martin Noergaard 📖🔣💻🤔📢 -- Michael P. Notter 💬📝✅📢📖 -- Jeffrey G. Ojemann 📖 -- Thomas Okell 📖 -- Aaron Oliver-Taylor 📖 -- Hernando Ombao 📖 -- Robert Oostenveld 📖🔧📢💡✅⚠️🤔💬🐛📝💻🖋🔣🎨📋🚇👀📓📹 -- Dimitri Papadopoulos Orfanos 📖💡🤔💬 -- Felipe Orihuela-Espina 📖 -- Eduard Ort 📖 -- Patrick Park 📖💡💬 -- Maurice Pasternak 📓 -- Chloé Pasturel 📖 -- Dianne Patterson 📖 -- John Pellman 📖 -- Cyril Pernet 💬📝📖🎨💡📋🤔📢 -- Franco Pestilli 📖💻🎨💡🤔👀🔧📋🔍🚇 -- Jan Petr 💬🐛💻📖🔣💡📋🤔📆⚠️📢 -- Natalia Petridou 📖 -- Dmitry Petrov 📖💻 -- Christophe Phillips 📖 -- Gio Piantoni 📖 -- Andrea Pigorini 📖 -- Russell A. Poldrack 📖🔍📢 -- Jean-Baptiste Poline 📖📢🤔🎨 -- Luca Pollonini 📖 -- Wouter V. Potters 📖 -- Nader Pouratian 📖 -- Pradeep Reddy Raamana 💻🔧 -- Vasudev Raguram 💻🎨📖🔧 -- Nick F. Ramsey 📖 -- Travis Riddle 📖🔧🐛 -- Pierre Rioux 📖 -- Petra Ritter 📖 -- Kay Robbins 💻📖🐛 -- Alex Rockhill 📖🔧 -- Ariel Rokem 📖 -- Chris Rorden 📖💻 -- Jose Manuel Saborit 📖 -- Taylor Salo 💬📖🔌 -- Matt Sanderson 📖💻 -- Gunnar Schaefer 📖 -- Michael Schirner 📖 -- Jan-Mathijs Schoffelen 📖 -- Graham Searle 📖 -- Parul Sethi 📖🔧⚠️💻 -- Maureen J Shader 📖 -- Robert E. Smith 💻📖 -- Vanessa Sochat 📖 -- Tamas Spisak 📖 -- Julia Sprenger 📖 -- Isla Staden 📖 -- Arjen Stolk 📖 -- Nicole C. Swann 📖 -- Filip Szczepankiewicz 📖 -- Martin Szinte 📖 -- François Tadel 📖🔌💡 -- Sylvain Takerkart 📖 -- Bertrand Thirion 📖 -- David Thomas 📖🔣 -- Roberto Toro 🔧 -- Sébastien Tourbier 🤔👀📢🐛💻📖 -- Paule-Joanne Toussaint 📖 -- Nicholas Traut 📖🔧💻 -- William Triplett 📖 -- Jessica A. Turner 📖 -- Pieter Vandemaele 📖💻 -- Max A. van den Boom 💻👀📖 -- Wietske van der Zwaag 🔣💬 -- Matthias Van Osch 📖 -- Gaël Varoquaux 📖 -- Jaap von der Aar 📖 -- Sjoerd Vos 📖 -- Bradley Voytek 📖 -- Tor Wager 📖 -- Adina S. Wagner 🎨 -- Lennart Walger 📖 -- Brian A. Wandell 📖 -- Hao Ting Wang 📖🐛 -- Yuan Wang 💻 -- Julius Welzel 📖 -- Joseph Wexler 📖💡 -- Kirstie Whitaker 📖💡🔍🤔📢💬 -- Martin Wilson 📖 -- Jonathan Winawer 📖 -- Lennart Wittkuhn 📖 -- Joseph Woods 📖 -- Tal Yarkoni 💻📖🤔🔍🔌👀📢🐛🎨 -- Lyuba Zehl 📖 + + +| name | contributions | +| ---------------------------------------------------- | -------------------------------------- | +| Aaron Oliver-Taylor | 📖 | +| Adam Li | 📖💻 | +| Adam Thomas | 📖 | +| Adeen Flinker | 📖 | +| Adina S. Wagner | 🎨💻 | +| Agah Karakuzu | 💬📖🔣🤔💻 | +| Aki Nikolaidis | 📖 | +| Alberto Lazari | 📖 | +| Alejandro de la Vega | 🐛💻⚠️ | +| Alessio Giacomel | 📖 | +| Alex Rockhill | 📖🔧💻 | +| Alexander Jones | 💻🐛 | +| Alexander L. Cohen | 🐛💻📖💬 | +| Alexander von Lautz | 📖 | +| Alexandre Gramfort | 📖💡 | +| Alexandre Hutton | 📖 | +| Alexandre Routier | 📖 | +| Alexandru Foias | 📖🔣 | +| Ali Khan | 📖 | +| Alizee Wickenheiser | 🔧 | +| Ana Fouto | 📓 | +| Anders Eklund | 📖📢💻 | +| Andrea Pigorini | 📖 | +| Andrew Hoopes | 📖 | +| Andrew Jahn | 📓 | +| Andrew Janke | 📖💻 | +| Anibal Sólon | 💻🐛 | +| Anthony Galassi | 📖💻 | +| Ariel Rokem | 📖💻 | +| Arjen Stolk | 📖 | +| Arnaud Delorme | 📖💡🤔 | +| Arnaud Marcoux | 📖 | +| Arshitha Basavaraj | 📖🚇💻 | +| Ashley G. Gillman | 📖 | +| Athanasia Monika Mowinckel | 📖 | +| Aysegul Gunduz | 📖 | +| Azeez Adebimpe | 📖 | +| B. Nolan Nichols | 📖 | +| Balint Kincses | 📖 | +| Benjamin Beasley | 📖 | +| Benjamin Dichter | 📖 | +| Benjamin Gagl | 📖 | +| Bertrand Thirion | 📖 | +| Bradley Voytek | 📖 | +| Brett L. Foster | 📖 | +| Brian A. Wandell | 📖 | +| Brian N. Lundstrom | 📖 | +| Camille Maumet | 📖 | +| Carlo Miniussi | 📖 | +| Cecile Madjar | 🔣🔧 | +| Chloé Pasturel | 📖 | +| Chris Benjamin | 📖 | +| Chris Gahnström | 📖 | +| Chris Holdgraf | 📖🤔💻 | +| Chris J. Gorgolewski | 📖💻💬🤔🔍📢📝💡🔌 | +| Chris Rorden | 📖💻 | +| Christian Büchel | 📖 | +| Christian Horea | 💻📖 | +| Christine Rogers | 🔣📖🤔🚇🔧 | +| Christophe Phillips | 📖 | +| Christopher J. Honey | 📖 | +| Christopher J. Markiewicz | 💬🐛💻📖🎨💡🤔🔌👀🔧📢🔣📋🚧 | +| Christopher Lee-Messer | 📖 | +| Clara Moreau | 📖 | +| Clint Hansen | 📖🤔 | +| Cyril Pernet | 💬📝📖🎨💡📋🤔📢 | +| Cyrus Eierud | 📖 | +| D. Sturgeon | 💻 | +| Dan Levitas | 📖 | +| Dan Lurie | 🤔📖🔧🔌💻💬 | +| Daniel A. Handwerker | 📖 | +| David Alsop | 📖 | +| David Boas | 📖 | +| David Groppe | 📖 | +| David Keator | 📖 | +| David McAlpine | 📖 | +| David Thomas | 📖🔣 | +| Dejan Draschkow | 📖 | +| Dianne Patterson | 📖 | +| Dimitri Papadopoulos Orfanos | 📖💡🤔💬💻 | +| Dmitry Petrov | 📖💻 | +| Dora Hermes | 📖💻✅🔍🤔 | +| Dorien Huijser | 📖 | +| Douglas N. Greve | 📖 | +| Duncan Macleod | 📖🚇 | +| Dung Truong | 📖💻🔧🤔 | +| Dylan Nielson | 📖💻🔧 | +| Eduard Ort | 📖💻 | +| Eleonora Marcantoni | 📖 | +| Elizabeth Bock | 📖💡 | +| Elizabeth DuPre | 📖💡🔍🤔💬💻 | +| Elke Warmerdam | 🔣📖 | +| Erdal Karaca | 💻 | +| Eric A. Earl | 📖💬🐛🚧🔧🤔💻 | +| Eric Achten | 📖🔣📓 | +| Eric Bridgeford | 📖🔧 | +| Erin W. Dickie | 📖🤔👀📢💬💻 | +| Ethan Blackwood | 👀📖 | +| Eugene P. Duff | 📖 | +| Ezequiel Mikulan | 📖💻 | +| Felipe Orihuela-Espina | 📖 | +| Fidel Alfaro Almagro | 💬📖💡🔌 | +| Filip Szczepankiewicz | 📖 | +| Filippo Maria Castelli | 📖🔣 | +| Franco Pestilli | 📖💻🎨💡🤔👀🔧📋🔍🚇📢 | +| Franklin W. Feingold | 📋📝✅💬🤔🎨📢👀🚇🖋️📆💻 | +| François Tadel | 📖🔌💡 | +| Gaia Rizzo | 📖 | +| Gang Chen | 📖 | +| Gaël Varoquaux | 📖 | +| Ghislain Vaillant | 💻 | +| Giacomo Bertazzoli | 📖 | +| Giacomo Guidali | 📖 | +| Giacomo Mazzamuto | 📖🔣 | +| Gilles de Hollander | 📖 | +| Gio Piantoni | 📖 | +| Gitte M. Knudsen | 📖 | +| Giulio Castegnaro | 📖 | +| Giuseppe Gallitto | 📖 | +| Graham Searle | 📖 | +| Granville J. Matheson | 📖 | +| Gregory Kiar | 📖💻🎨🔧 | +| Gregory Noack | 📖💻⚠️ | +| Greydon Gilmore | 📖💻 | +| Guillaume Flandin | 📖💻 | +| Gunnar Schaefer | 📖 | +| Gustav Nilsonne | 📖 | +| Hamish Innes-Brown | 📖 | +| Hanne D. Hansen | 📖 | +| Hanzhang Lu | 📖 | +| Hao-Ting Wang | 📖🐛 | +| Helena Cockx | 📖🤔💬 | +| Henk Mutsaerts | 💬🐛💻📖💡📋🤔📆📢📓 | +| Hernando Ombao | 📖 | +| Hugo Boniface | 📖💻 | +| Ilkay Isik | 📖 | +| Ilona Lipp | 📖 | +| International Neuroinformatics Coordinating Facility | 💵📋 | +| Iris Groen | 📖 | +| Isla Staden | 📖 | +| Jaap von der Aar | 📖 | +| Jakub Kaczmarzyk | 📖🔧🚇 | +| James Gholam | 📖 | +| James Kent | 💬💻 | +| Jan Mathijs Schoffelen | 📖 | +| Jan Petr | 💬🐛💻📖🔣💡📋🤔📆⚠️📢 | +| Jan-Mathijs Schoffelen | 📖 | +| Jean-Baptiste Poline | 📖📢🤔🎨💻 | +| Jean-Christophe Houde | 📖💻 | +| Jean-Dominique Gallezot | 📖 | +| Jean-Philippe Lachaux | 📖 | +| Jeanette Mumford | 📖 | +| Jefferson Casimir | 🔧 | +| Jeffrey G. Ojemann | 📖 | +| Jeffrey S. Grethe | 💬🐛✅📢💻 | +| JegouA | 💻 | +| Jelle Dalenberg | 📖 | +| Jeremy Moreau | 📖💡 | +| Jessica A. Turner | 📖 | +| Jochem Rieger | 📖 | +| John Detre | 📖 | +| John Pellman | 📖 | +| John T. Wodder | 💻 | +| Joke Durnez | 📖🔧💻 | +| Jon Haitz Legarreta Gorroño | 💻📖 | +| Jonathan C. Lau | 📖 | +| Jonathan Winawer | 📖 | +| Joost Kuijer | 📖 | +| Jose Manuel Saborit | 📖 | +| Joseph Wexler | 📖💡 | +| Joseph Woods | 📖 | +| Julia Guiomar Niso Galán | 🤔🎨🔍👀📋📝🔧🐛💻🔣✅💬📖💡📢 | +| Julia Sprenger | 📖 | +| Julien Cohen-Adad | 📖🔣🤔 | +| Julius Welzel | 📖💡🐛💻🔣🤔💬📓 | +| Kai J. Miller | 📖 | +| Kangjoo Lee | 📖 | +| Katja Heuer | 🔧 | +| Kay Robbins | 💻📖🐛 | +| Kevin Larcher | 💬 | +| Kimberly Ray | 📖📋🤔📆 | +| Kirstie Whitaker | 📖💡🔍🤔📢💬💻 | +| Klara Gregorova | 📖 | +| Klaus Gramann | 📖🤔 | +| Kris Thielemans | 📖 | +| Kristofer Bouchard | 📖 | +| Kurt Schilling | 📖 | +| Laetitia Fesselier | 🔧 | +| Laura and John Arnold Foundation | 💵 | +| Leandro Beltrachini | 📖 | +| Lee Kamentsky | 📖 | +| Lennart Walger | 📖 | +| Lennart Wittkuhn | 📖 | +| Liberty Hamilton | 📖 | +| Luca Pollonini | 📖 | +| Luis Hernandez-Garcia | 📖📓 | +| Luke J. Edwards | 📖💬 | +| Lyuba Zehl | 📖 | +| Mainak Jas | 📖💻 | +| Manjari Narayan | 📖 | +| Manuel Mercier | 📖🤔 | +| Maqsood Yaqub | 📖 | +| Marc Lalancette | 📖💻 | +| Marco Castellaro | 💬🐛💻📖💡⚠️📢🚇 | +| Maria de la Iglesia | 📖 | +| Marie-Hélène Bourget | 📖🔣💻🤔 | +| Mark Mikkelsen | 📖 | +| Markus Morawski | 📖 | +| Marta Bortoletto | 📖 | +| Martin Craig | 🔣 | +| Martin Noergaard | 📖🔣💻🤔📢 | +| Martin Szinte | 📖 | +| Martin Wilson | 📖 | +| Martina Bulgari | 📖 | +| Mateusz Pawlik | 📖🐛🤔🚧👀 | +| Mathias Goncalves | 💻🔧📢 | +| Mathieu Boudreau | 💬🤔📢 | +| Matt Sanderson | 📖💻 | +| Matteo Tonietto | 📖 | +| Matthias Günther | 📖 | +| Matthias Van Osch | 📖 | +| Maureen J Shader | 📖 | +| Maurice Pasternak | 📓 | +| Max A. van den Boom | 💻👀📖🐛 | +| Melanie Ganz-Benjaminsen | 📖🔣💻🤔📆🔍📢 | +| Michael Chappell | 📖🔣📆 | +| Michael Hanke | 📖🤔🔧🐛📢 | +| Michael P. Harms | 📖⚠️🔧 | +| Michael P. Milham | 💡🔍 | +| Michael P. Notter | 💬📝✅📢📖 | +| Michael Schirner | 📖 | +| Mikaël Naveau | 🐛 | +| Nader Pouratian | 📖 | +| Natalia Petridou | 📖 | +| National Institute of Mental Health | 💵 | +| Nell Hardcastle | 💻📖🤔🚇👀💬 | +| Nicholas Traut | 📖🔧💻 | +| Nick F. Ramsey | 📖 | +| Nicole C. Swann | 📖 | +| Nima Bigdely Shamlo | 📖 | +| Olivier David | 📖 | +| Orrin Devinsky | 📖 | +| Oscar Esteban | 📖🔧🤔💬💻 | +| Pamela LaMontagne | 📖💡 | +| Parul Sethi | 📖🔧⚠️💻 | +| Patricia Clement | 💬🐛💻📖🔣💡📋🤔📆⚠️📢 | +| Patrick Park | 📖💡💬💻 | +| Paule-Joanne Toussaint | 📖 | +| Peer Herholz | 💬📖👀🔧✅📢 | +| Petra Ritter | 📖 | +| Pierre Rioux | 📖 | +| Pieter Vandemaele | 📖💻 | +| Pradeep Reddy Raamana | 💻🔧 | +| R. Cameron Craddock | 📖📢 | +| Remi Gau | 📖💻💬📢🐛💻🚇👀🔧🤔 | +| Richard Höchenberger | 📖💻 | +| Richard N. Henson | 📖 | +| Robert B. Innis | 📖 | +| Robert E. Smith | 💻📖 | +| Robert Knight | 📖 | +| Robert Luke | 💻 | +| Robert Oostenveld | 📖🔧📢💡✅⚠️🤔💬🐛📝💻🖋️🔣🎨📋🚇👀📓📹 | +| Roberto Toro | 🔧 | +| Rohan Goyal | 📖 | +| Ross W. Blair | 💻 | +| Russell A. Poldrack | 📖🔍📢 | +| Rémi Adon | 📖 | +| Samir Das | 📖 | +| Samuel Garcia | 🤔👀📖 | +| Samuel Nastase | 💻 | +| Sara Elgayar | 📖 | +| Sasha D'Ambrosio | 📖 | +| Satrajit S. Ghosh | 📖💻 | +| Scott Makeig | 📖 | +| Sein Jeung | 📖💡🐛💻🔣🤔💬🔧📓 | +| Shashank Bansal | 📖 | +| Sjoerd B. Vos | 📖 | +| Soichi Hayashi | 📖🔧🐛 | +| Stefan Appelhoff | 📖💬🤔🐛💡💻👀⚠️📢✅🔧🔌📝🚧🔣 | +| Stephan Bickel | 📖 | +| Steven Meisler | 🐛💻💬🔧📓 | +| Suyash Bhogawar | 📖💡⚠️🔧💬 | +| Sylvain Baillet | 📖🔍 | +| Sylvain Takerkart | 📖 | +| Sébastien Tourbier | 🤔👀📢🐛💻📖 | +| Sören Grothkopp | 📖🔣📓 | +| Tal Pal Attia | 📖 | +| Tal Yarkoni | 💻📖🤔🔍🔌👀📢🐛🎨 | +| Tamas Spisak | 📖 | +| Tamás Józsa | 📓 | +| Taylor Salo | 💬📖🔌💻 | +| Teon L. Brooks | 📖💻⚠️💬👀🤔🔧🐛📢 | +| Thomas E. Nichols | 📖📢🔧👀🚧💻 | +| Thomas Funck | 📖 | +| Thomas Kirk | 📖 | +| Thomas Okell | 📖 | +| Tibor Auer | 💬📖💡🔧📢🐛🤔 | +| Timo Dickscheid | 📖 | +| Timotheus Berg | 📖🤔📓 | +| Tobey Betthauser | 📖 | +| Tobias Bengfort | 💻 | +| Tom Hampshire | 📖 | +| Tor Wager | 📖 | +| Travis Riddle | 📖🔧🐛 | +| Tristan Glatard | 📖💻 | +| Tyler Collins | 🔣🔧 | +| Ulrike Bingel | 📖 | +| Vanessa Sochat | 📖 | +| Vasudev Raguram | 💻🎨📖🔧 | +| Vince D. Calhoun | 📖 | +| Vittorio Iacovella | 📖 | +| Vladimir Litvak | 📖 | +| Wietske van der Zwaag | 🔣💬 | +| William Clarke | 📖 | +| William Triplett | 📖 | +| Wouter V. Potters | 💻📖 | +| Xiangrui Li | 📖💻 | +| Yaroslav O. Halchenko | 📖📢🔧💬🐛💻🔣🔍🤔🔌👀📓🚇 | +| Yoni Ashar | 📖 | +| Yuan Wang | 💻 | +| Zachary Michael | 📖 | +| ezemikulan | 💻 | +| josator2 | 💻 | +| monkeyman192 | 💻 | +| Étienne Bergeron | 🔣💻 | diff --git a/src/appendices/coordinate-systems.md b/src/appendices/coordinate-systems.md index 91273835..c5b44207 100644 --- a/src/appendices/coordinate-systems.md +++ b/src/appendices/coordinate-systems.md @@ -86,7 +86,7 @@ of restricted keywords for MEG, EEG, or iEEG, please open a new issue on the Note that the short descriptions below may not capture all details. For detailed descriptions of the coordinate systems below, please see the -[FieldTrip webpage](https://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined). +[FieldTrip webpage](https://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined/). ### Commonly used anatomical landmarks in MEG, EEG, and iEEG research @@ -195,25 +195,25 @@ Unless specified explicitly in the sidecar file in the ### Standard template identifiers -| **Coordinate System** | **Description** | **Used by** | **Reference** | -| ---------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------ | ---------------------------------------------------------------------------------------------------------------------------------- | -| ICBM452AirSpace | Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" with "linear transforms of the subjects into the atlas space using a 12-parameter affine transformation" | | [https://www.loni.usc.edu/research/atlases](http://web.archive.org/web/20220802122857/https://www.loni.usc.edu/research/atlases) | -| ICBM452Warp5Space | Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" "based on a 5th order polynomial transformation into the atlas space" | | [https://www.loni.usc.edu/research/atlases](http://web.archive.org/web/20220802122857/https://www.loni.usc.edu/research/atlases) | -| IXI549Space | Reference space defined by the average of the "549 (...) subjects from the IXI dataset" linearly transformed to ICBM MNI 452. | SPM12 | [https://brain-development.org/](https://brain-development.org/) | -| fsaverage | The `fsaverage` is a **dual template** providing both volumetric and surface coordinates references. The volumetric template corresponds to a FreeSurfer variant of `MNI305` space. The `fsaverage` atlas also defines a surface reference system (formerly described as fsaverage\[3\|4\|5\|6\|sym\]). | Freesurfer | | -| fsaverageSym | The `fsaverage` is a **dual template** providing both volumetric and surface coordinates references. The volumetric template corresponds to a FreeSurfer variant of `MNI305` space. The `fsaverageSym` atlas also defines a symmetric surface reference system (formerly described as `fsaveragesym`). | Freesurfer | | -| fsLR | The `fsLR` is a **dual template** providing both volumetric and surface coordinates references. The volumetric template corresponds to `MNI152NLin6Asym`. Surface templates are given at several sampling densities: 164k (used by HCP pipelines for 3T and 7T anatomical analysis), 59k (used by HCP pipelines for 7T MRI bold and DWI analysis), 32k (used by HCP pipelines for 3T MRI bold and DWI analysis), or 4k (used by HCP pipelines for MEG analysis) fsaverage_LR surface reconstructed from the T1w image. | Freesurfer | | -| MNIColin27 | Average of 27 T1 scans of a single subject | SPM96 | [https://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres](https://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres) | -| MNI152Lin | Also known as ICBM (version with linear coregistration) | SPM99 to SPM8 | [https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin](https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin) | -| MNI152NLin2009\[a-c\]\[Sym\|Asym\] | Also known as ICBM (non-linear coregistration with 40 iterations, released in 2009). It comes in either three different flavours each in symmetric or asymmetric version. | DARTEL toolbox in SPM12b | [https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009](https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009) | -| MNI152NLin6Sym | Also known as symmetric ICBM 6th generation (non-linear coregistration). | FSL | [https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6](https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6) | -| MNI152NLin6ASym | A variation of `MNI152NLin6Sym` built by A. Janke that is released as the _MNI template_ of FSL. Volumetric templates included with [HCP-Pipelines](https://github.com/Washington-University/HCPpipelines/tree/master/global/templates) correspond to this template too. | HCP-Pipelines | [doi:10.1016/j.neuroimage.2012.01.024](https://doi.org/10.1016/j.neuroimage.2012.01.024) | -| MNI305 | Also known as avg305. | | | -| NIHPD | Pediatric templates generated from the NIHPD sample. Available for different age groups (4.5–18.5 y.o., 4.5–8.5 y.o., 7–11 y.o., 7.5–13.5 y.o., 10–14 y.o., 13–18.5 y.o. This template also comes in either -symmetric or -asymmetric flavor. | | [https://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1](https://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1) | -| OASIS30AntsOASISAnts | | | [https://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436](https://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436) | -| OASIS30Atropos | | | [https://mindboggle.info/data.html](https://mindboggle.info/data.html) | -| Talairach | Piecewise linear scaling of the brain is implemented as described in TT88. | | [http://talairach.org/](http://talairach.org/) | -| UNCInfant | Infant Brain Atlases from Neonates to 1- and 2-year-olds. | | [https://www.nitrc.org/projects/pediatricatlas](https://www.nitrc.org/projects/pediatricatlas) | +| **Coordinate System** | **Description** | **Used by** | **Reference** | +| ---------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------- | +| ICBM452AirSpace | Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" with "linear transforms of the subjects into the atlas space using a 12-parameter affine transformation" | | [https://www.loni.usc.edu/research/atlases](https://www.loni.usc.edu/research/atlases) | +| ICBM452Warp5Space | Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" "based on a 5th order polynomial transformation into the atlas space" | | [https://www.loni.usc.edu/research/atlases](https://www.loni.usc.edu/research/atlases) | +| IXI549Space | Reference space defined by the average of the "549 (...) subjects from the IXI dataset" linearly transformed to ICBM MNI 452. | SPM12 | [https://brain-development.org/](https://brain-development.org/) | +| fsaverage | The `fsaverage` is a **dual template** providing both volumetric and surface coordinates references. The volumetric template corresponds to a FreeSurfer variant of `MNI305` space. The `fsaverage` atlas also defines a surface reference system (formerly described as fsaverage\[3\|4\|5\|6\|sym\]). | Freesurfer | | +| fsaverageSym | The `fsaverage` is a **dual template** providing both volumetric and surface coordinates references. The volumetric template corresponds to a FreeSurfer variant of `MNI305` space. The `fsaverageSym` atlas also defines a symmetric surface reference system (formerly described as `fsaveragesym`). | Freesurfer | | +| fsLR | The `fsLR` is a **dual template** providing both volumetric and surface coordinates references. The volumetric template corresponds to `MNI152NLin6Asym`. Surface templates are given at several sampling densities: 164k (used by HCP pipelines for 3T and 7T anatomical analysis), 59k (used by HCP pipelines for 7T MRI bold and DWI analysis), 32k (used by HCP pipelines for 3T MRI bold and DWI analysis), or 4k (used by HCP pipelines for MEG analysis) fsaverage_LR surface reconstructed from the T1w image. | Freesurfer | | +| MNIColin27 | Average of 27 T1 scans of a single subject | SPM96 | [https://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres](https://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres) | +| MNI152Lin | Also known as ICBM (version with linear coregistration) | SPM99 to SPM8 | [https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin](https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin) | +| MNI152NLin2009\[a-c\]\[Sym\|Asym\] | Also known as ICBM (non-linear coregistration with 40 iterations, released in 2009). It comes in either three different flavors each in symmetric or asymmetric version. | DARTEL toolbox in SPM12b | [https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009](https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009) | +| MNI152NLin6Sym | Also known as symmetric ICBM 6th generation (non-linear coregistration). | FSL | [https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6](https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6) | +| MNI152NLin6ASym | A variation of `MNI152NLin6Sym` built by A. Janke that is released as the _MNI template_ of FSL. Volumetric templates included with [HCP-Pipelines](https://github.com/Washington-University/HCPpipelines/tree/master/global/templates) correspond to this template too. | HCP-Pipelines | [doi:10.1016/j.neuroimage.2012.01.024](https://doi.org/10.1016/j.neuroimage.2012.01.024) | +| MNI305 | Also known as avg305. | | | +| NIHPD | Pediatric templates generated from the NIHPD sample. Available for different age groups (4.5–18.5 y.o., 4.5–8.5 y.o., 7–11 y.o., 7.5–13.5 y.o., 10–14 y.o., 13–18.5 y.o. This template also comes in either -symmetric or -asymmetric flavor. | | [https://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1](https://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1) | +| OASIS30AntsOASISAnts | | | [https://figshare.com/articles/dataset/ANTs_ANTsR_Brain_Templates/915436](https://figshare.com/articles/dataset/ANTs_ANTsR_Brain_Templates/915436) | +| OASIS30Atropos | | | [https://mindboggle.info/data.html](https://mindboggle.info/data.html) | +| Talairach | Piecewise linear scaling of the brain is implemented as described in TT88. | | [http://talairach.org/](http://talairach.org/) | +| UNCInfant | Infant Brain Atlases from Neonates to 1- and 2-year-olds. | | [https://www.nitrc.org/projects/pediatricatlas](https://www.nitrc.org/projects/pediatricatlas) | The following template identifiers are retained for backwards compatibility of BIDS implementations. @@ -221,7 +221,7 @@ However, their use is [DEPRECATED][deprecated]. | **Coordinate System** | **Description** | **RECOMMENDED alternative identifier** | | ----------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------- | -| fsaverage\[3\|4\|5\|6\|sym\] | Images were sampled to the FreeSurfer surface reconstructed from the subject’s T1w image, and registered to an fsaverage template | fsaverage\[Sym\] | +| fsaverage\[3\|4\|5\|6\|sym\] | Images were sampled to the FreeSurfer surface reconstructed from the subject's T1w image, and registered to an fsaverage template | fsaverage\[Sym\] | | UNCInfant\[0\|1\|2\]V\[21\|22\|23\] | Infant Brain Atlases from Neonates to 1- and 2-year-olds. [https://www.nitrc.org/projects/pediatricatlas](https://www.nitrc.org/projects/pediatricatlas) | UNCInfant | ### Nonstandard coordinate system identifiers @@ -249,6 +249,6 @@ Please note that `space-scanner` SHOULD NOT be used, it is mentioned in this spe -[common file level metadata fields]: ../05-derivatives/02-common-data-types.md#common-file-level-metadata-fields +[common file level metadata fields]: ../derivatives/common-data-types.md#common-file-level-metadata-fields -[deprecated]: ../02-common-principles.md#definitions +[deprecated]: ../common-principles.md#definitions diff --git a/src/appendices/cross-modality-correspondence.md b/src/appendices/cross-modality-correspondence.md index f77598d1..c71a1c73 100644 --- a/src/appendices/cross-modality-correspondence.md +++ b/src/appendices/cross-modality-correspondence.md @@ -7,7 +7,7 @@ please pay specific attention to the format the MR images are in. It is important to note whether the MR images have been unwarped in order to correct for gradient non-linearities, indicated by the `NonlinearGradientCorrection` metadata field -(see [Magnetic Resonance Imaging Data - Sequence Specifics](../04-modality-specific-files/01-magnetic-resonance-imaging-data.md#sequence-specifics)). +(see [Magnetic Resonance Imaging Data - Sequence Specifics](../modality-specific-files/magnetic-resonance-imaging-data.md#sequence-specifics)). The reason for this is that the MRI needs to be corrected for nonlinear gradients in order to fit the accompanying PET scans for co-registration (Knudsen et al. 2020, [doi:10.1177/0271678X20905433](https://doi.org/10.1177/0271678X20905433); diff --git a/src/appendices/entities.md b/src/appendices/entities.md index 06101ce0..2cdd8385 100644 --- a/src/appendices/entities.md +++ b/src/appendices/entities.md @@ -1,10 +1,10 @@ # Entities -This section compiles the entities (key-value pairs within file names) described throughout this -specification, and describes each. +This section compiles the entities (key-value pairs within filenames) +described throughout this specification, and describes each. A general introduction to entities is given in the section on -[filename structure](../02-common-principles.md#file-name-structure). +[filename structure](../common-principles.md#filenames). The ordering of entities, and whether each is OPTIONAL, REQUIRED, or MUST NOT be specified for a given file type, is specified in the [Entity Table](entity-table.md). diff --git a/src/appendices/entity-table.md b/src/appendices/entity-table.md index f07c6998..4dff2dcf 100644 --- a/src/appendices/entity-table.md +++ b/src/appendices/entity-table.md @@ -1,7 +1,8 @@ # Entity table -This section compiles the entities (key-value pairs within file names) described throughout this -specification, and establishes a common order within a filename. +This section compiles the entities (key-value pairs within filenames) +described throughout this specification, +and establishes a common order within a filename. For example, if a file has an acquisition and reconstruction label, the acquisition entity must precede the reconstruction entity. REQUIRED and OPTIONAL entities for a given file type are denoted; @@ -10,7 +11,7 @@ Entity formats indicate whether the value is alphanumeric (`