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Repository: bids-standard/bids-starter-kit
Branch: main
Commit: 409a857932d3
Files: 91
Total size: 251.4 KB
Directory structure:
gitextract_ajxyoq0h/
├── .all-contributorsrc
├── .github/
│ └── workflows/
│ └── deploy_book.yml
├── .gitignore
├── LICENSE
├── Makefile
├── README.md
├── interactiveTreeVisualization/
│ └── epilepsyClassification2017/
│ ├── tree.html
│ ├── treeData.js
│ ├── treeFunctions.js
│ └── treeStyle.css
├── matlabCode/
│ ├── anat/
│ │ ├── createBIDS_T1w_json_full.m
│ │ ├── createBIDS_T1w_json_full_schma_based.m
│ │ └── createBIDS_T1w_json_short.m
│ ├── eeg-meg/
│ │ ├── createBIDS_meg_json_full.m
│ │ ├── createBIDS_meg_json_short.m
│ │ └── rename_brainvision_files.m
│ ├── fmap/
│ │ └── createBIDS_fmap_json.m
│ ├── func/
│ │ ├── createBIDS_bold_json_full.m
│ │ └── createBIDS_bold_json_short.m
│ ├── general/
│ │ ├── README.md
│ │ ├── bids_spreadsheet2participants.m
│ │ ├── createBIDS_dataset_description_json.m
│ │ ├── createBIDS_events_tsv_json_full.m
│ │ ├── createBIDS_participants_tsv.m
│ │ ├── createBIDS_samples_tsv.m
│ │ ├── input/
│ │ │ └── spreadsheet_to_convert.xlsx
│ │ └── tests/
│ │ ├── data/
│ │ │ ├── participants.json
│ │ │ └── participants.tsv
│ │ └── test_bids_spreadsheet2participants.m
│ ├── ieeg/
│ │ ├── createBIDS_channels_tsv.m
│ │ ├── createBIDS_coordsystem_json.m
│ │ ├── createBIDS_data_WriteBrainVisionWithFieldtrip.m
│ │ ├── createBIDS_electrodes_tsv.m
│ │ └── createBIDS_ieeg_json.m
│ ├── micr/
│ │ ├── createBIDS_micr_json_full.m
│ │ └── createBIDS_micr_json_short.m
│ ├── miss_hit.cfg
│ └── pet/
│ ├── createBIDS_blood_auto_tsv_and_json_short.m
│ ├── createBIDS_blood_manual_tsv_and_json_full.m
│ ├── createBIDS_blood_manual_tsv_and_json_short.m
│ ├── createBIDS_pet_json_full.m
│ └── createBIDS_pet_json_short.m
├── pythonCode/
│ ├── createBIDS_MP2RAGE_json.py
│ └── createBIDS_dataset_description_json.py
├── reports/
│ └── Google-2018-report.md
├── src/
│ ├── CONTRIBUTING.md
│ ├── _config.yml
│ ├── _toc.yml
│ ├── epilepsy_phenotype.rst
│ ├── index.md
│ ├── references.bib
│ └── tree.html
└── templates/
├── participants.json
├── participants.tsv
├── phenotype/
│ ├── EpilepsyClassification.tsv
│ └── EpilepsyClassification2017.json
├── samples.json
├── samples.tsv
├── sub-01/
│ └── ses-01/
│ ├── anat/
│ │ ├── sub-01_ses-01_acq-FullExample_run-01_T1w.json
│ │ └── sub-01_ses-01_acq-ShortExample_run-01_T1w.json
│ ├── eeg/
│ │ ├── sub-01_ses-01_task-FilterExample_eeg.json
│ │ ├── sub-01_ses-01_task-FullExample_eeg.json
│ │ ├── sub-01_ses-01_task-MinimalExample_eeg.json
│ │ └── sub-01_ses-01_task-ReferenceExample_eeg.json
│ ├── fmap/
│ │ ├── sub-01_ses-01_acq-Case1_run-01_phasediff.json
│ │ ├── sub-01_ses-01_acq-Case2_run-01_phase1.json
│ │ ├── sub-01_ses-01_acq-Case2_run-01_phase2.json
│ │ ├── sub-01_ses-01_acq-Case3_run-01_fieldmap.json
│ │ └── sub-01_ses-01_acq-Case4_dir-LR_run-01_epi.json
│ ├── func/
│ │ ├── sub-01_ses-01_task-FullExample_run-01_bold.json
│ │ ├── sub-01_ses-01_task-FullExample_run-01_events.json
│ │ ├── sub-01_ses-01_task-FullExample_run-01_events.tsv
│ │ └── sub-01_ses-01_task-ShortExample_run-01_bold.json
│ ├── ieeg/
│ │ ├── sub-01_ses-01_coordsystem.json
│ │ ├── sub-01_ses-01_electrodes.tsv
│ │ ├── sub-01_ses-01_task-LongExample_run-01_channels.tsv
│ │ └── sub-01_ses-01_task-LongExample_run-01_ieeg.json
│ ├── meg/
│ │ ├── sub-01_ses-01_task-FullExample_acq-CTF_run-1_proc-sss_meg.json
│ │ └── sub-01_ses-01_task-ShortExample_acq-CTF_run-1_proc-sss_meg.json
│ ├── micr/
│ │ ├── sub-01_ses-01_sample-01_acq-Full_stain-03_chunk-01_SEM.json
│ │ └── sub-01_ses-01_sample-01_acq-Short_stain-03_chunk-01_SEM.json
│ └── pet/
│ ├── sub-01_ses-01_recording-AutosamplerShortExample_blood.json
│ ├── sub-01_ses-01_recording-AutosamplerShortExample_blood.tsv
│ ├── sub-01_ses-01_recording-ManualFullExample_blood.json
│ ├── sub-01_ses-01_recording-ManualFullExample_blood.tsv
│ ├── sub-01_ses-01_recording-ManualShortExample_blood.json
│ ├── sub-01_ses-01_recording-ManualShortExample_blood.tsv
│ ├── sub-01_ses-01_task-FullExample_pet.json
│ └── sub-01_ses-01_task-ShortExample_pet.json
└── sub-epilepsy01/
└── ses-01/
└── ieeg/
├── sub-epilepsy01_ses-01_electrodes.json
└── sub-epilepsy01_ses-01_electrodes.tsv
================================================
FILE CONTENTS
================================================
================================================
FILE: .all-contributorsrc
================================================
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================================================
FILE: .github/workflows/deploy_book.yml
================================================
---
name: deploy-book
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
# Only run this when the master branch changes
on:
push:
branches:
- main
# This job installs dependencies, build the book, and pushes it to `gh-pages`
jobs:
deploy-book:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
with:
submodules: recursive
fetch-depth: 0
# Install dependencies
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.12'
- name: Install dependencies
run: pip install jupyter-book sphinx-reredirects
# Build the book
- name: Build the book
run: make book
# Push the book's HTML to github-pages
- name: GitHub Pages action
uses: peaceiris/actions-gh-pages@v4.0.0
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
publish_dir: src/_build/html
================================================
FILE: .gitignore
================================================
.vscode/
.DS_Store
src/_build
desktop.ini
.idea/
# -----------------------------------------------------------------------------#
## template MATLAB gitignore from
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# Compiled MEX binaries (all platforms)
*.mex*
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*.mltbx
# Generated helpsearch folders
helpsearch*/
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slprj/
sccprj/
# Matlab code generation folders
codegen/
# Simulink autosave extension
*.autosave
# Simulink cache files
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# Octave session info
octave-workspace
# -----------------------------------------------------------------------------#
## template python gitignore from
# https://github.com/github/gitignore/blob/main/Python.gitignore
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class
# C extensions
*.so
# Distribution / packaging
.Python
build/
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
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# Installer logs
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# Translations
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# Django stuff:
*.log
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instance/
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# Scrapy stuff:
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# Sphinx documentation
docs/_build/
# PyBuilder
.pybuilder/
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# For a library or package, you might want to ignore these files since the code is
# intended to run in multiple environments; otherwise, check them in:
# .python-version
# pipenv
# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
# However, in case of collaboration, if having platform-specific dependencies or dependencies
# having no cross-platform support, pipenv may install dependencies that don't work, or not
# install all needed dependencies.
#Pipfile.lock
# poetry
# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
# This is especially recommended for binary packages to ensure reproducibility, and is more
# commonly ignored for libraries.
# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
#poetry.lock
# PEP 582; used by e.g. github.com/David-OConnor/pyflow
__pypackages__/
# Celery stuff
celerybeat-schedule
celerybeat.pid
# SageMath parsed files
*.sage.py
# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/
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.spyderproject
.spyproject
# Rope project settings
.ropeproject
# mkdocs documentation
/site
# mypy
.mypy_cache/
.dmypy.json
dmypy.json
# Pyre type checker
.pyre/
# pytype static type analyzer
.pytype/
# Cython debug symbols
cython_debug/
# PyCharm
# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
# and can be added to the global gitignore or merged into this file. For a more nuclear
# option (not recommended) you can uncomment the following to ignore the entire idea folder.
#.idea/
================================================
FILE: LICENSE
================================================
Attribution 4.0 International
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================================================
FILE: Makefile
================================================
.PHONY: all clean
define BROWSER_PYSCRIPT
import os, webbrowser, sys
from urllib.request import pathname2url
webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
endef
export BROWSER_PYSCRIPT
define PRINT_HELP_PYSCRIPT
import re, sys
for line in sys.stdin:
match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line)
if match:
target, help = match.groups()
print("%-20s %s" % (target, help))
endef
export PRINT_HELP_PYSCRIPT
BROWSER := python -c "$$BROWSER_PYSCRIPT"
# Put it first so that "make" without argument is like "make help".
help:
@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
clean:
rm -fr src/_build/
book: clean ## build the book
jupyter-book build src
view: book ## view the book
$(BROWSER) $$PWD/src/_build/html/index.html
test: ## build the book and tests the links
jupyter-book build src --builder linkcheck
================================================
FILE: README.md
================================================
<!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
[](#contributors-)
<!-- ALL-CONTRIBUTORS-BADGE:END -->
# The Starter-kit has moved to the <a href="https://bids.neuroimaging.io/getting_started/" target="_blank">new BIDS website</a>.
## Contributors ✨
Thanks goes to these wonderful people
([emoji key](https://allcontributors.org/docs/en/emoji-key)):
<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
<!-- prettier-ignore-start -->
<!-- markdownlint-disable -->
<table>
<tr>
<td align="center"><a href="https://github.com/dorahermes"><img src="https://avatars1.githubusercontent.com/u/4977351?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Dora Hermes</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/commits?author=dorahermes" title="Code">💻</a> <a href="#content-dorahermes" title="Content">🖋</a> <a href="#ideas-dorahermes" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/bids-standard/bids-starter-kit/pulls?q=is%3Apr+reviewed-by%3Adorahermes" title="Reviewed Pull Requests">👀</a> <a href="#maintenance-dorahermes" title="Maintenance">🚧</a> <a href="https://github.com/bids-standard/bids-starter-kit/commits?author=dorahermes" title="Documentation">📖</a></td>
<td align="center"><a href="http://chrisgorgolewski.org"><img src="https://avatars2.githubusercontent.com/u/238759?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Chris Gorgolewski</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/pulls?q=is%3Apr+reviewed-by%3Achrisgorgo" title="Reviewed Pull Requests">👀</a> <a href="#maintenance-chrisgorgo" title="Maintenance">🚧</a> <a href="https://github.com/bids-standard/bids-starter-kit/issues?q=author%3Achrisgorgo" title="Bug reports">🐛</a></td>
<td align="center"><a href="http://chrisholdgraf.com"><img src="https://avatars1.githubusercontent.com/u/1839645?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Chris Holdgraf</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/pulls?q=is%3Apr+reviewed-by%3Acholdgraf" title="Reviewed Pull Requests">👀</a> <a href="#content-choldgraf" title="Content">🖋</a> <a href="#maintenance-choldgraf" title="Maintenance">🚧</a></td>
<td align="center"><a href="https://chrisgahnstrom.wordpress.com/"><img src="https://avatars1.githubusercontent.com/u/12600386?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Chris Gahnström</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/commits?author=cofficer" title="Code">💻</a> <a href="#content-cofficer" title="Content">🖋</a> <a href="#ideas-cofficer" title="Ideas, Planning, & Feedback">🤔</a></td>
<td align="center"><a href="http://emdupre.me"><img src="https://avatars3.githubusercontent.com/u/15017191?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Elizabeth DuPre</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/pulls?q=is%3Apr+reviewed-by%3Aemdupre" title="Reviewed Pull Requests">👀</a> <a href="#maintenance-emdupre" title="Maintenance">🚧</a> <a href="#ideas-emdupre" title="Ideas, Planning, & Feedback">🤔</a> <a href="#content-emdupre" title="Content">🖋</a> <a href="https://github.com/bids-standard/bids-starter-kit/commits?author=emdupre" title="Documentation">📖</a></td>
<td align="center"><a href="https://github.com/anushkab"><img src="https://avatars0.githubusercontent.com/u/20943511?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Utmost Happiness</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/commits?author=anushkab" title="Code">💻</a> <a href="#content-anushkab" title="Content">🖋</a> <a href="#ideas-anushkab" title="Ideas, Planning, & Feedback">🤔</a></td>
<td align="center"><a href="https://whitakerlab.github.io"><img src="https://avatars1.githubusercontent.com/u/3626306?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Kirstie Whitaker</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/pulls?q=is%3Apr+reviewed-by%3AKirstieJane" title="Reviewed Pull Requests">👀</a> <a href="#ideas-KirstieJane" title="Ideas, Planning, & Feedback">🤔</a> <a href="#maintenance-KirstieJane" title="Maintenance">🚧</a> <a href="#content-KirstieJane" title="Content">🖋</a> <a href="https://github.com/bids-standard/bids-starter-kit/commits?author=KirstieJane" title="Documentation">📖</a> <a href="https://github.com/bids-standard/bids-starter-kit/issues?q=author%3AKirstieJane" title="Bug reports">🐛</a></td>
</tr>
<tr>
<td align="center"><a href="https://github.com/Park-Patrick"><img src="https://avatars3.githubusercontent.com/u/12662110?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Patrick Park</b></sub></a><br /><a href="#ideas-Park-Patrick" title="Ideas, Planning, & Feedback">🤔</a> <a href="#content-Park-Patrick" title="Content">🖋</a> <a href="https://github.com/bids-standard/bids-starter-kit/pulls?q=is%3Apr+reviewed-by%3APark-Patrick" title="Reviewed Pull Requests">👀</a></td>
<td align="center"><a href="http://peerherholz.github.io"><img src="https://avatars0.githubusercontent.com/u/20129524?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Peer Herholz</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/commits?author=PeerHerholz" title="Code">💻</a></td>
<td align="center"><a href="http://www.sbirc.ed.ac.uk/cyril/"><img src="https://avatars2.githubusercontent.com/u/4772878?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Cyril Pernet</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/commits?author=CPernet" title="Code">💻</a></td>
<td align="center"><a href="https://www.stefanappelhoff.com"><img src="https://avatars1.githubusercontent.com/u/9084751?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Stefan Appelhoff</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/pulls?q=is%3Apr+reviewed-by%3Asappelhoff" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/bids-standard/bids-starter-kit/commits?author=sappelhoff" title="Code">💻</a> <a href="#content-sappelhoff" title="Content">🖋</a> <a href="#ideas-sappelhoff" title="Ideas, Planning, & Feedback">🤔</a></td>
<td align="center"><a href="https://ilkayisik.github.io"><img src="https://avatars1.githubusercontent.com/u/22478219?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Ilkay Isik</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/issues?q=author%3Ailkayisik" title="Bug reports">🐛</a></td>
<td align="center"><a href="https://teonbrooks.com"><img src="https://avatars1.githubusercontent.com/u/1578674?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Teon L Brooks</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/issues?q=author%3Ateonbrooks" title="Bug reports">🐛</a></td>
<td align="center"><a href="https://github.com/bayab"><img src="https://avatars0.githubusercontent.com/u/16117420?v=4?s=100" width="100px;" alt=""/><br /><sub><b>ayab</b></sub></a><br /><a href="#content-bayab" title="Content">🖋</a></td>
</tr>
<tr>
<td align="center"><a href="https://remi-gau.github.io/"><img src="https://avatars3.githubusercontent.com/u/6961185?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Remi Gau</b></sub></a><br /><a href="#content-Remi-Gau" title="Content">🖋</a></td>
<td align="center"><a href="https://github.com/JaapVanDerAar"><img src="https://avatars3.githubusercontent.com/u/32334327?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Jaap van der Aar</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/commits?author=JaapVanDerAar" title="Code">💻</a> <a href="#content-JaapVanDerAar" title="Content">🖋</a> <a href="#ideas-JaapVanDerAar" title="Ideas, Planning, & Feedback">🤔</a></td>
<td align="center"><a href="https://github.com/GiulioCastegnaro"><img src="https://avatars2.githubusercontent.com/u/45361920?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Giulio Castegnaro</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/commits?author=GiulioCastegnaro" title="Code">💻</a> <a href="#content-GiulioCastegnaro" title="Content">🖋</a> <a href="#ideas-GiulioCastegnaro" title="Ideas, Planning, & Feedback">🤔</a></td>
<td align="center"><a href="https://github.com/franklin-feingold"><img src="https://avatars1.githubusercontent.com/u/35307458?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Franklin Feingold</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/issues?q=author%3Afranklin-feingold" title="Bug reports">🐛</a> <a href="https://github.com/bids-standard/bids-starter-kit/pulls?q=is%3Apr+reviewed-by%3Afranklin-feingold" title="Reviewed Pull Requests">👀</a></td>
<td align="center"><a href="http://www.nisox.org"><img src="https://avatars3.githubusercontent.com/u/5155907?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Thomas Nichols</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/pulls?q=is%3Apr+reviewed-by%3Anicholst" title="Reviewed Pull Requests">👀</a></td>
<td align="center"><a href="https://github.com/pvdemael"><img src="https://avatars1.githubusercontent.com/u/37624277?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Pieter Vandemaele</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/issues?q=author%3Apvdemael" title="Bug reports">🐛</a></td>
<td align="center"><a href="https://github.com/gllmflndn"><img src="https://avatars0.githubusercontent.com/u/5950855?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Guillaume Flandin</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/pulls?q=is%3Apr+reviewed-by%3Agllmflndn" title="Reviewed Pull Requests">👀</a> <a href="#ideas-gllmflndn" title="Ideas, Planning, & Feedback">🤔</a></td>
</tr>
<tr>
<td align="center"><a href="https://github.com/robertoostenveld"><img src="https://avatars1.githubusercontent.com/u/899043?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Robert Oostenveld</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/issues?q=author%3Arobertoostenveld" title="Bug reports">🐛</a> <a href="https://github.com/bids-standard/bids-starter-kit/pulls?q=is%3Apr+reviewed-by%3Arobertoostenveld" title="Reviewed Pull Requests">👀</a> <a href="#ideas-robertoostenveld" title="Ideas, Planning, & Feedback">🤔</a></td>
<td align="center"><a href="https://github.com/HappyFacade"><img src="https://avatars0.githubusercontent.com/u/54226355?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Happy</b></sub></a><br /><a href="#content-HappyFacade" title="Content">🖋</a></td>
<td align="center"><a href="https://www.linkedin.com/in/tal-pal-attia-201373b0/"><img src="https://avatars1.githubusercontent.com/u/24300712?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Tal Pal Attia</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/commits?author=tpatpa" title="Code">💻</a></td>
<td align="center"><a href="https://github.com/VisLab"><img src="https://avatars1.githubusercontent.com/u/1189050?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Kay Robbins</b></sub></a><br /><a href="#ideas-VisLab" title="Ideas, Planning, & Feedback">🤔</a> <a href="#content-VisLab" title="Content">🖋</a></td>
<td align="center"><a href="https://erasmus-synclab.nl/"><img src="https://avatars1.githubusercontent.com/u/41283173?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Eduard Klapwijk</b></sub></a><br /><a href="#ideas-eduardklap" title="Ideas, Planning, & Feedback">🤔</a></td>
<td align="center"><a href="https://github.com/DorienHuijser"><img src="https://avatars1.githubusercontent.com/u/58177697?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Dorien Huijser</b></sub></a><br /><a href="#ideas-DorienHuijser" title="Ideas, Planning, & Feedback">🤔</a></td>
<td align="center"><a href="http://cmn.nimh.nih.gov/dsst"><img src="https://avatars1.githubusercontent.com/u/10297203?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Arshitha Basavaraj</b></sub></a><br /><a href="#ideas-Arshitha" title="Ideas, Planning, & Feedback">🤔</a></td>
</tr>
<tr>
<td align="center"><a href="https://lennartwittkuhn.com"><img src="https://avatars0.githubusercontent.com/u/42233065?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Lennart Wittkuhn</b></sub></a><br /><a href="#ideas-lnnrtwttkhn" title="Ideas, Planning, & Feedback">🤔</a></td>
<td align="center"><a href="https://github.com/bendhouseart"><img src="https://avatars.githubusercontent.com/u/28850131?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Anthony Galassi</b></sub></a><br /><a href="#ideas-bendhouseart" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/bids-standard/bids-starter-kit/commits?author=bendhouseart" title="Code">💻</a></td>
<td align="center"><a href="http://DrMowinckels.io"><img src="https://avatars.githubusercontent.com/u/14014329?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Athanasia Monika Mowinckel</b></sub></a><br /><a href="#ideas-Athanasiamo" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/bids-standard/bids-starter-kit/commits?author=Athanasiamo" title="Code">💻</a></td>
<td align="center"><a href="https://github.com/yonestar"><img src="https://avatars.githubusercontent.com/u/4513934?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Yoni Ashar</b></sub></a><br /><a href="#ideas-yonestar" title="Ideas, Planning, & Feedback">🤔</a></td>
<td align="center"><a href="https://github.com/dkp"><img src="https://avatars.githubusercontent.com/u/965184?v=4?s=100" width="100px;" alt=""/><br /><sub><b>dkp</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/issues?q=author%3Adkp" title="Bug reports">🐛</a></td>
<td align="center"><a href="https://jdkent.github.io/"><img src="https://avatars.githubusercontent.com/u/12564882?v=4?s=100" width="100px;" alt=""/><br /><sub><b>James Kent</b></sub></a><br /><a href="#ideas-jdkent" title="Ideas, Planning, & Feedback">🤔</a></td>
<td align="center"><a href="https://github.com/cfxb"><img src="https://avatars.githubusercontent.com/u/39246257?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Chris Benjamin</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/commits?author=cfxb" title="Documentation">📖</a></td>
</tr>
<tr>
<td align="center"><a href="http://isla.st"><img src="https://avatars.githubusercontent.com/u/23707851?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Isla</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/commits?author=Islast" title="Documentation">📖</a></td>
<td align="center"><a href="https://github.com/effigies"><img src="https://avatars.githubusercontent.com/u/83442?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Chris Markiewicz</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/commits?author=effigies" title="Documentation">📖</a></td>
<td align="center"><a href="https://ankiitgupta7.github.io/"><img src="https://avatars.githubusercontent.com/u/25341569?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Ankit Gupta</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/commits?author=ankiitgupta7" title="Documentation">📖</a></td>
<td align="center"><a href="https://github.com/alexvonlautz"><img src="https://avatars.githubusercontent.com/u/44004062?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Alex von Lautz</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/commits?author=alexvonlautz" title="Documentation">📖</a></td>
<td align="center"><a href="https://github.com/AlexandreHutton"><img src="https://avatars.githubusercontent.com/u/50920802?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Alexandre Hutton</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/commits?author=AlexandreHutton" title="Documentation">📖</a></td>
<td align="center"><a href="http://Abrren_Chen"><img src="https://avatars.githubusercontent.com/u/54808990?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Abrren Chen</b></sub></a><br /><a href="#maintenance-AbrrenC" title="Maintenance">🚧</a></td>
<td align="center"><a href="http://gabrielabs.com"><img src="https://avatars.githubusercontent.com/u/21208915?v=4?s=100" width="100px;" alt=""/><br /><sub><b>Gabriel Silveira</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/issues?q=author%3AGabomfim" title="Bug reports">🐛</a> <a href="https://github.com/bids-standard/bids-starter-kit/commits?author=Gabomfim" title="Code">💻</a></td>
</tr>
<tr>
<td align="center"><a href="http://1nathanliang.github.io"><img src="https://avatars.githubusercontent.com/u/36468637?v=4?s=100" width="100px;" alt=""/><br /><sub><b>nathan liang</b></sub></a><br /><a href="https://github.com/bids-standard/bids-starter-kit/issues?q=author%3A1nathanliang" title="Bug reports">🐛</a></td>
</tr>
</table>
<!-- markdownlint-restore -->
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<!-- ALL-CONTRIBUTORS-LIST:END -->
This project follows the
[all-contributors](https://github.com/all-contributors/all-contributors)
specification. Contributions of any kind welcome!
================================================
FILE: interactiveTreeVisualization/epilepsyClassification2017/tree.html
================================================
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>ILAE classification of the epilepsies Tree</title>
<link rel="stylesheet" href="./treeStyle.css">
</head>
<header>
<h1 align="center">ILAE classification of the epilepsies Tree</h1>
<p align="center">Scheffer, I. E., Berkovic, S., Capovilla, G., Connolly, M. B., French, J., Guilhoto, L., ... &
Nordli, D. R. (2017). ILAE classification of the epilepsies: position paper of the ILAE Commission for
Classification and Terminology. Epilepsia, 58(4), 512-521.</p>
<p align="center">
<button class="button" onclick="expandAll()">Expand All</button>
<button class="button" onclick="collapseAll()">Collapse All</button>
</p>
</header>
<body>
<!-- load the d3.js library -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.17/d3.min.js"></script>
<!-- load tree data -->
<script src="./treeData.js"></script>
<!-- load tree functions -->
<script src="./treeFunctions.js"></script>
</body>
<footer>
</footer>
</html>
<!--
References:
Scheffer, I. E., Berkovic, S., Capovilla, G., Connolly, M. B., French, J., Guilhoto, L., ... & Nordli, D. R. (2017). ILAE classification of the epilepsies: position paper of the ILAE Commission for Classification and Terminology. Epilepsia, 58(4), 512-521.
https://onlinelibrary.wiley.com/doi/full/10.1111/epi.13709
Simple d3.js tree diagram -
https://bl.ocks.org/d3noob/8323795
Interactive d3.js tree diagram -
https://bl.ocks.org/d3noob/8375092
Export SVG D3 visualization to PNG or JPEG -
http://bl.ocks.org/Rokotyan/0556f8facbaf344507cdc45dc3622177
d3-hierarchy -
https://github.com/d3/d3-hierarchy/blob/v1.1.8/README.md#tree
-->
================================================
FILE: interactiveTreeVisualization/epilepsyClassification2017/treeData.js
================================================
var treeData = [{
"name": "Epilepsy Classification",
"parent": "null",
"_children": [
// ****** Seizure Type ******
{
"name": "Seizure Type",
"parent": "Epilepsy Classification",
"_children": [
// *** Generalised ***
{
"name": "Generalised",
"parent": "Seizure Type",
"_children": [{
"name": "Motor",
"parent": "Generalised",
"_children": [{
"name": "Generalized tonic-clonic and variants",
"parent": "Motor"
},
{
"name": "Generalized tonic",
"parent": "Motor"
},
{
"name": "Generalized atonic",
"parent": "Motor"
},
{
"name": "Myoclonic",
"parent": "Motor"
},
{
"name": "Myoclonic-atonic",
"parent": "Motor"
},
{
"name": "Epileptic spasms",
"parent": "Motor"
}
]
},
{
"name": "Non-motor",
"parent": "Generalised",
"_children": [{
"name": "Typical Absence",
"parent": "Non-motor"
}, {
"name": "Atypical Absence",
"parent": "Non-motor"
}, {
"name": "Myoclonic absence",
"parent": "Non-motor"
}, {
"name": "Absence with eyelid myoclonia",
"parent": "Non-motor"
}]
}
]
},
// *** Focal ***
{
"name": "Focal",
"parent": "Seizure Type",
"_children": [{
"name": "Awareness",
"parent": "Focal",
"_children": [{
"name": "Aware",
"parent": "Awareness",
}, {
"name": "Impaired Awareness",
"parent": "Awareness",
}]
},
{
"name": "Motor",
"parent": "Focal",
"_children": [{
"name": "Focal clonic seizure",
"parent": "Motor"
},
{
"name": "Focal tonic seizure",
"parent": "Motor"
},
{
"name": "Focal motor seizure with dystonia",
"parent": "Motor"
},
{
"name": "Focal myoclonic seizure",
"parent": "Motor"
},
{
"name": "Focal atonic seizure",
"parent": "Motor"
},
{
"name": "Focal motor seizure with paresis/paralysis",
"parent": "Motor"
},
{
"name": "Focal epileptic spasms",
"parent": "Motor"
},
{
"name": "Focal hyperkinetic seizure",
"parent": "Motor"
},
{
"name": "Focal automatism seizure",
"parent": "Motor"
},
{
"name": "Focal motor seizure with dysarthria / anarthria",
"parent": "Motor"
},
{
"name": "Focal motor seizure with negative myoclonus",
"parent": "Motor"
},
{
"name": "Focal motor seizure with version",
"parent": "Motor"
},
{
"name": "Focal bilateral motor seizure",
"parent": "Motor"
}
]
},
{
"name": "Non-motor",
"parent": "Focal",
"_children": [{
"name": "Focal sensory seizure",
"parent": "Non-motor",
"_children": [{
"name": "Focal somatosensory seizure",
"parent": "Focal sensory seizure"
}, {
"name": "Focal sensory visual seizure",
"parent": "Focal sensory seizure"
}, {
"name": "Focal sensory auditory seizure",
"parent": "Focal sensory seizure"
}, {
"name": "Focal sensory olfactory seizure",
"parent": "Focal sensory seizure"
}, {
"name": "Focal sensory gustatory seizure",
"parent": "Focal sensory seizure"
}, {
"name": "Focal sensory vestibular seizure",
"parent": "Focal sensory seizure"
}, {
"name": "Focal sensory seizure with hot-cold sensations",
"parent": "Focal sensory seizure"
}, {
"name": "Focal sensory seizure with cephalic sensation",
"parent": "Focal sensory seizure"
}]
},
{
"name": "Focal cognitive seizure",
"parent": "Non-motor",
"_children": [{
"name": "Focal cognitive seizure with expressive dysphasia / aphasia",
"parent": "Focal cognitive seizure"
}, {
"name": "Focal cognitive seizure with anomia",
"parent": "Focal cognitive seizure"
}, {
"name": "Focal cognitive seizure with receptive dysphasia / aphasia",
"parent": "Focal cognitive seizure"
}, {
"name": "Focal cognitive seizure with auditory agnosia",
"parent": "Focal cognitive seizure"
}, {
"name": "Focal cognitive seizure with conduction dysphasia / aphasia",
"parent": "Focal cognitive seizure"
}, {
"name": "Focal cognitive seizure with dyslexia / alexia",
"parent": "Focal cognitive seizure"
}, {
"name": "Focal cognitive seizure with memory impairment",
"parent": "Focal cognitive seizure"
}, {
"name": "Focal cognitive seizure with deja vu / jamais vu",
"parent": "Focal cognitive seizure"
}, {
"name": "Focal cognitive seizure with hallucination",
"parent": "Focal cognitive seizure"
}, {
"name": "Focal cognitive seizure with illusion",
"parent": "Focal cognitive seizure"
}, {
"name": "Focal cognitive seizure with dissociation",
"parent": "Focal cognitive seizure"
}, {
"name": "Focal cognitive seizure with forced thinking",
"parent": "Focal cognitive seizure"
}, {
"name": "Focal cognitive seizure with dyscalculia / acalculia",
"parent": "Focal cognitive seizure"
}, {
"name": "Focal cognitive seizure with dysgraphia/agraphia",
"parent": "Focal cognitive seizure"
}, {
"name": "Focal cognitive seizure with left-right confusion",
"parent": "Focal cognitive seizure"
}, {
"name": "Focal cognitive seizure with neglect",
"parent": "Focal cognitive seizure"
}]
},
{
"name": "Focal emotional seizure",
"parent": "Non-motor",
"_children": [{
"name": "Focal emotional seizure with fear/anxiety/panic",
"parent": "Focal emotional seizure"
}, {
"name": "Focal emotional seizure with laughing (gelastic)",
"parent": "Focal emotional seizure"
}, {
"name": "Focal emotional seizure with crying (dacrystic)",
"parent": "Focal emotional seizure"
}, {
"name": "Focal emotional seizure with pleasure",
"parent": "Focal emotional seizure"
}, {
"name": "Focal emotional seizure with anger",
"parent": "Focal emotional seizure"
}]
},
{
"name": "Focal autonomic seizure",
"parent": "Non-motor",
"_children": [{
"name": "Focal autonomic seizure with palpitations / tachycardia / bradycardia / asystole",
"parent": "Focal autonomic seizure"
}, {
"name": "Focal autonomic seizure with epigastric sensation",
"parent": "Focal autonomic seizure"
}, {
"name": "Focal autonomic seizure with pallor / flushing",
"parent": "Focal autonomic seizure"
}, {
"name": "Focal autonomic seizure with hypoventilation / hyperventilation / altered respiration",
"parent": "Focal autonomic seizure"
}, {
"name": "Focal autonomic seizure with piloerection",
"parent": "Focal autonomic seizure"
}, {
"name": "Focal autonomic seizure with erection",
"parent": "Focal autonomic seizure"
}, {
"name": "Focal autonomic seizure with urge to urinate / defecate",
"parent": "Focal autonomic seizure"
}, {
"name": "Focal autonomic seizure with lacrimation",
"parent": "Focal autonomic seizure"
}, {
"name": "Focal autonomic seizure with pupillary dilation / constriction",
"parent": "Focal autonomic seizure"
}]
},
{
"name": "Focal behavioural arrest seizure",
"parent": "Non-motor",
"_children": [{
"name": "Focal behavioural arrest seizure",
"parent": "Focal behavioural arrest seizure"
}]
}
]
},
{
"name": "Focal to bilateral tonic-clonic seizure",
"parent": "Focal",
"_children": [{
"name": "Focal to bilateral tonic-clonic seizure",
"parent": "Focal to bilateral tonic-clonic seizure"
}]
}
]
},
// *** Unknown ***
{
"name": "Unknown",
"parent": "Seizure Type",
"_children": [{
"name": "Motor",
"parent": "Focal",
"_children": [{
"name": "Tonic–clonic",
"parent": "Motor"
},
{
"name": "Epileptic spasms",
"parent": "Motor"
}
]
},
{
"name": "Non-motor",
"parent": "Focal",
"_children": [{
"name": "Behaviour arrest",
"parent": "Non-motor"
}, {
"name": "Unclassified",
"parent": "Non-motor"
}]
}
]
}
]
},
// ****** Epilepsy Type ******
{
"name": "Epilepsy Type",
"parent": "Epilepsy Classification",
"_children": [{
"name": "Generalised Epilepsy",
"parent": "Epilepsy Type"
}, {
"name": "Focal Epilepsy",
"parent": "Epilepsy Type"
}, {
"name": "Combined generalised and focal Epilepsy",
"parent": "Epilepsy Type"
}, {
"name": "Unknown Epilepsy",
"parent": "Epilepsy Type"
}]
},
// ****** Epilepsy Syndrome ******
{
"name": "Epilepsy Syndrome",
"parent": "Epilepsy Classification",
"_children": [{
"name": "Neonatal/Infantile",
"parent": "Epilepsy Syndrome",
"_children": [{
"name": "Self-limited neonatal seizures and Self-limited familial neonatal epilepsy",
"parent": "Neonatal/Infantile"
}, {
"name": "Self limited familial and non-familial infantile epilepsy",
"parent": "Neonatal/Infantile"
}, {
"name": "Early myoclonic encephalopathy",
"parent": "Neonatal/Infantile"
}, {
"name": "Ohtahara syndrome",
"parent": "Neonatal/Infantile"
}, {
"name": "West syndrome",
"parent": "Neonatal/Infantile"
}, {
"name": "Dravet syndrome",
"parent": "Neonatal/Infantile"
}, {
"name": "Myoclonic epilepsy in infancy",
"parent": "Neonatal/Infantile"
}, {
"name": "Epilepsy of infancy with migrating focal seizures",
"parent": "Neonatal/Infantile"
}, {
"name": "Myoclonic encephalopathy in non-progressive disorders",
"parent": "Neonatal/Infantile"
}, {
"name": "Febrile seizures plus, genetic epilepsy with febrile seizures plus",
"parent": "Neonatal/Infantile"
}]
}, {
"name": "Childhood",
"parent": "Epilepsy Syndrome",
"_children": [{
"name": "Epilepsy with myoclonic-atonic seizures",
"parent": "Childhood"
}, {
"name": "Epilepsy with eyelid myoclonias",
"parent": "Childhood"
}, {
"name": "Lennox-Gastaut syndrome",
"parent": "Childhood"
}, {
"name": "Childhood absence epilepsy",
"parent": "Childhood"
}, {
"name": "Epilepsy with myoclonic absences",
"parent": "Childhood"
}, {
"name": "Panayiotopoulos syndrome",
"parent": "Childhood"
}, {
"name": "Childhood occipital epilepsy (Gastaut type)",
"parent": "Childhood"
}, {
"name": "Photosensitive occipital lobe epilepsy",
"parent": "Childhood"
}, {
"name": "Childhood epilepsy with centrotemporal spikes",
"parent": "Childhood"
}, {
"name": "Atypical childhood epilepsy with centrotemporal spikes",
"parent": "Childhood"
}, {
"name": "Epileptic encephalopathy with continuous spike-and-wave during sleep",
"parent": "Childhood"
}, {
"name": "Landau-Kleffner syndrome",
"parent": "Childhood"
}, {
"name": "Autosomal dominant nocturnal frontal lobe epilepsy",
"parent": "Childhood"
}]
}, {
"name": "Adolescent/Adult",
"parent": "Epilepsy Syndrome",
"_children": [{
"name": "Juvenile absence epilepsy",
"parent": "Adolescent/Adult"
}, {
"name": "Juvenile myoclonic epilepsy",
"parent": "Adolescent/Adult"
}, {
"name": "Epilepsy with generalized tonic-clonic seizures alone",
"parent": "Adolescent/Adult"
}, {
"name": "Autosomal dominant epilepsy with auditory features",
"parent": "Adolescent/Adult"
}, {
"name": "Other familial temporal lobe epilepsies",
"parent": "Adolescent/Adult"
}]
}, {
"name": "Any Age",
"parent": "Epilepsy Syndrome",
"_children": [{
"name": "Familial focal epilepsy with variable foci",
"parent": "Any Age"
},
{
"name": "Reflex epilepsies",
"parent": "Any Age"
}, {
"name": "Progressive myoclonus epilepsies",
"parent": "Any Age"
}
]
}]
},
// ****** Etiology ******
{
"name": "Etiology",
"parent": "Epilepsy Classification",
"_children": [{
"name": "Genetic Etiology",
"parent": "Etiology",
"_children": [{
"name": "Chromosomal abnormalities",
"parent": "Genetic Etiology"
}, {
"name": "Gene abnormalities",
"parent": "Genetic Etiology"
}]
}, {
"name": "Structural Etiology",
"parent": "Etiology",
"_children": [{
"name": "Malformations of cortical development",
"parent": "Structural Etiology"
}, {
"name": "Vascular malformations",
"parent": "Structural Etiology"
}, {
"name": "Hippocampal sclerosis",
"parent": "Structural Etiology"
}, {
"name": "Hypoxic-ischemic structural abnormalities",
"parent": "Structural Etiology"
}, {
"name": "Traumatic Brain Injury",
"parent": "Structural Etiology"
}, {
"name": "Tumors",
"parent": "Structural Etiology"
}, {
"name": "Porencephalic cyst",
"parent": "Structural Etiology"
}]
}, {
"name": "Metabolic Etiology",
"parent": "Etiology",
"_children": [{
"name": "Biotinidase and holocarboxylase synthase deficiency",
"parent": "Metabolic Etiology"
}, {
"name": "Cerebral folate deficiency",
"parent": "Metabolic Etiology"
}, {
"name": "Creatine disorders",
"parent": "Metabolic Etiology"
}, {
"name": "Folinic acid responsive seizures",
"parent": "Metabolic Etiology"
}, {
"name": "Glucose transporter 1 (GLUT1) deficiency",
"parent": "Metabolic Etiology"
}, {
"name": "Mitochondrial disorders",
"parent": "Metabolic Etiology"
}, {
"name": "Peroxisomal Disorders",
"parent": "Metabolic Etiology"
}, {
"name": "Pyridoxine dependent epilepsy/PNPO deficiency",
"parent": "Metabolic Etiology"
}]
}, {
"name": "Immune Etiology",
"parent": "Etiology",
"_children": [{
"name": "Rasmussen syndrome",
"parent": "Immune Etiology"
}, {
"name": "Antibody mediated etiologies",
"parent": "Immune Etiology"
}]
}, {
"name": "Infectious Etiology",
"parent": "Etiology",
"_children": [{
"name": "Bacterial Meningitis",
"parent": "Infectious Etiology"
}, {
"name": "Cerebral Malaria",
"parent": "Infectious Etiology"
}, {
"name": "Cerebral Toxoplasmosis",
"parent": "Infectious Etiology"
}, {
"name": "CMV",
"parent": "Infectious Etiology"
}, {
"name": "HIV",
"parent": "Infectious Etiology"
}, {
"name": "Neurocysticercosis",
"parent": "Infectious Etiology"
}, {
"name": "Tuberculosis",
"parent": "Infectious Etiology"
}, {
"name": "Viral Encephalitis",
"parent": "Infectious Etiology"
}, {
"name": "Other infections",
"parent": "Infectious Etiology"
}]
}, {
"name": "Unknown Etiology",
"parent": "Etiology",
"_children": [{
"name": "Febrile infection related epilepsy syndrome (FIRES)",
"parent": "Unknown Etiology"
}]
}]
}
]
}];
================================================
FILE: interactiveTreeVisualization/epilepsyClassification2017/treeFunctions.js
================================================
// ************** Generate the tree diagram *****************
var margin = {
top: 50,
right: 150,
bottom: 50,
left: 150
},
width = 2 * window.innerWidth - margin.right - margin.left,
height = 4 * window.innerHeight - margin.top - margin.bottom;
var i = 0,
duration = 750,
root;
var tree = d3.layout.tree()
.separation(function (a, b) {
if (a.depth > 0) {
depth = a.depth
} else {
depth = 1
}
return (a.parent === b.parent ? 2 : 3) / depth;
})
.size([height, width]);
//var tree = d3.layout.tree()
// .size([height, width]);
var diagonal = d3.svg.diagonal()
.projection(function (d) {
return [d.y, d.x];
});
var svg0 = d3.select("body").append("svg")
.attr("width", width + margin.right + margin.left)
.attr("height", height + margin.top + margin.bottom)
.attr("style", "background-color:white")
svg = svg0.append("g")
.attr("transform", "translate(" + margin.left + "," + margin.top + ")");
root = treeData[0];
root.x0 = height / 2;
root.y0 = 0;
update(root);
d3.select(self.frameElement).style("height", "500px");
// ************** functions to update the tree diagram *****************
function update(source) {
var levelWidth = [1];
var childCount = function (level, n) {
if (n.children && n.children.length > 0) {
if (levelWidth.length <= level + 1) levelWidth.push(0);
levelWidth[level + 1] += n.children.length;
n.children.forEach(function (d) {
childCount(level + 1, d);
});
}
};
childCount(0, root);
var newHeight = d3.max(levelWidth) * 50; // 50 pixels per line
tree = tree.size([newHeight, width]);
// Compute the new tree layout.
var nodes = tree.nodes(root).reverse(),
links = tree.links(nodes);
// Normalize for fixed-depth.
nodes.forEach(function (d) {
d.y = d.depth * 350;
});
// Update the nodes…
var node = svg.selectAll("g.node")
.data(nodes, function (d) {
return d.id || (d.id = ++i);
});
// Enter any new nodes at the parent's previous position.
var nodeEnter = node.enter().append("g")
.attr("class", "node")
.attr("transform", function (d) {
return "translate(" + source.y0 + "," + source.x0 + ")";
})
.on("click", click);
nodeEnter.append("circle")
.attr("r", 1e-6)
.style("fill", function (d) {
return d._children ? "lightsteelblue" : "#fff";
});
nodeEnter.append("text")
.attr("x", function (d) {
return d.children || d._children ? -13 : 13;
})
.attr("dy", ".35em")
.attr("text-anchor", function (d) {
return d.children || d._children ? "end" : "start";
})
.text(function (d) {
return d.name;
})
.style("fill-opacity", 1e-6);
// Transition nodes to their new position.
var nodeUpdate = node.transition()
.duration(duration)
.attr("transform", function (d) {
return "translate(" + d.y + "," + d.x + ")";
});
nodeUpdate.select("circle")
.attr("r", 10)
.style("fill", function (d) {
return d._children ? "lightsteelblue" : "#fff";
});
nodeUpdate.select("text")
.style("fill-opacity", 1);
// Transition exiting nodes to the parent's new position.
var nodeExit = node.exit().transition()
.duration(duration)
.attr("transform", function (d) {
return "translate(" + source.y + "," + source.x + ")";
})
.remove();
nodeExit.select("circle")
.attr("r", 1e-6);
nodeExit.select("text")
.style("fill-opacity", 1e-6);
// Update the links…
var link = svg.selectAll("path.link")
.data(links, function (d) {
return d.target.id;
});
// Enter any new links at the parent's previous position.
link.enter().insert("path", "g")
.attr("class", "link")
.attr("d", function (d) {
var o = {
x: source.x0,
y: source.y0
};
return diagonal({
source: o,
target: o
});
})
// Transition links to their new position.
link.transition()
.duration(duration)
.attr("d", diagonal);
// Transition exiting nodes to the parent's new position.
link.exit().transition()
.duration(duration)
.attr("d", function (d) {
var o = {
x: source.x,
y: source.y
};
return diagonal({
source: o,
target: o
});
})
.remove();
// Stash the old positions for transition.
nodes.forEach(function (d) {
d.x0 = d.x;
d.y0 = d.y;
});
}
// Toggle children on click.
function click(d) {
if (d.children) {
d._children = d.children;
d.children = null;
} else {
d.children = d._children;
d._children = null;
}
update(d);
}
function expand(d) {
var children = (d.children) ? d.children : d._children;
if (d._children) {
d.children = d._children;
d._children = null;
}
if (children)
children.forEach(expand);
}
function collapse(d) {
if (d.children) {
d._children = d.children;
d._children.forEach(collapse);
d.children = null;
}
}
function expandAll() {
expand(root);
update(root);
}
function collapseAll() {
root.children.forEach(collapse);
collapse(root);
update(root);
}
// ************** functions to save the tree diagram *****************
// Set-up the export button
d3.select('#saveButton').on('click', function () {
var svgString = getSVGString(svg0.node());
svgString2Image(svgString, 1 * width, 1 * height, 'png', save); // passes Blob and filesize String to the callback
function save(dataBlob, filesize) {
saveAs(dataBlob, 'D3 vis exported to PNG.png'); // FileSaver.js function
}
});
// Below are the functions that handle actual exporting:
// getSVGString ( svgNode ) and svgString2Image( svgString, width, height, format, callback )
function getSVGString(svgNode) {
svgNode.setAttribute('xlink', 'http://www.w3.org/1999/xlink');
var cssStyleText = getCSSStyles(svgNode);
appendCSS(cssStyleText, svgNode);
var serializer = new XMLSerializer();
var svgString = serializer.serializeToString(svgNode);
svgString = svgString.replace(/(\w+)?:?xlink=/g, 'xmlns:xlink='); // Fix root xlink without namespace
svgString = svgString.replace(/NS\d+:href/g, 'xlink:href'); // Safari NS namespace fix
return svgString;
function getCSSStyles(parentElement) {
var selectorTextArr = [];
// Add Parent element Id and Classes to the list
selectorTextArr.push('#' + parentElement.id);
for (var c = 0; c < parentElement.classList.length; c++)
if (!contains('.' + parentElement.classList[c], selectorTextArr))
selectorTextArr.push('.' + parentElement.classList[c]);
// Add Children element Ids and Classes to the list
var nodes = parentElement.getElementsByTagName("*");
for (var i = 0; i < nodes.length; i++) {
var id = nodes[i].id;
if (!contains('#' + id, selectorTextArr))
selectorTextArr.push('#' + id);
var classes = nodes[i].classList;
for (var c = 0; c < classes.length; c++)
if (!contains('.' + classes[c], selectorTextArr))
selectorTextArr.push('.' + classes[c]);
}
// Extract CSS Rules
var extractedCSSText = "";
for (var i = 0; i < document.styleSheets.length; i++) {
var s = document.styleSheets[i];
try {
if (!s.cssRules) continue;
} catch (e) {
if (e.name !== 'SecurityError') throw e; // for Firefox
continue;
}
var cssRules = s.cssRules;
for (var r = 0; r < cssRules.length; r++) {
if (contains(cssRules[r].selectorText, selectorTextArr))
extractedCSSText += cssRules[r].cssText;
}
}
return extractedCSSText;
function contains(str, arr) {
return arr.indexOf(str) === -1 ? false : true;
}
}
function appendCSS(cssText, element) {
var styleElement = document.createElement("style");
styleElement.setAttribute("type", "text/css");
styleElement.innerHTML = cssText;
var refNode = element.hasChildNodes() ? element.children[0] : null;
element.insertBefore(styleElement, refNode);
}
}
function svgString2Image(svgString, width, height, format, callback) {
var format = format ? format : 'png';
var imgsrc = 'data:image/svg+xml;base64,' + btoa(unescape(encodeURIComponent(svgString))); // Convert SVG string to data URL
var canvas = document.createElement("canvas");
var context = canvas.getContext("2d");
canvas.width = width;
canvas.height = height;
var image = new Image();
image.onload = function () {
context.clearRect(0, 0, width, height);
context.drawImage(image, 0, 0, width, height);
canvas.toBlob(function (blob) {
var filesize = Math.round(blob.length / 1024) + ' KB';
if (callback) callback(blob, filesize);
});
};
image.src = imgsrc;
}
================================================
FILE: interactiveTreeVisualization/epilepsyClassification2017/treeStyle.css
================================================
.node {
cursor: pointer;
}
.node circle {
fill: #fff;
stroke: steelblue;
stroke-width: 3px;
}
.node text {
font: 12px sans-serif;
}
.link {
fill: none;
stroke: #ccc;
stroke-width: 3px;
}
.button {
background-color: #ccc;
color: black;
border: none;
padding: 15px 32px;
border-radius: 8px;
text-align: center;
text-decoration: none;
display: inline-block;
font-size: 14px;
transition-duration: 0.4s;
cursor: pointer;
}
.button:hover {
background-color:steelblue;
}
================================================
FILE: matlabCode/anat/createBIDS_T1w_json_full.m
================================================
% Template Matlab script to create a BIDS compatible file:
%
% sub-01_ses-01_run-01_acq-FullExample_T1w.json
%
% This example lists only the REQUIRED, RECOMMENDED and OPTIONAL fields.
% When adding additional metadata please use CamelCase
% Writing json files relies on the JSONio library
% https://github.com/bids-standard/bids-matlab
%
% Make sure it is in the matab/octave path
try
bids.bids_matlab_version;
catch
warning('%s\n%s\n%s\n%s', ...
'Writing the JSON file seems to have failed.', ...
'Make sure that the following library is in the matlab/octave path:', ...
'https://github.com/bids-standard/bids-matlab');
end
%%
clear;
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project = 'templates';
sub_label = '01';
ses_label = '01';
run_label = '01';
% The OPTIONAL acq-<label> key/value pair corresponds to a custom label
% the user MAY use to distinguish a different set of parameters used for
% acquiring the same modality.
acq_label = 'FullExample';
name_spec.modality = 'anat';
name_spec.suffix = 'T1w';
name_spec.ext = '.json';
name_spec.entities = struct('ses', ses_label, ...
'acq', acq_label, ...
'run', run_label, ...
'sub', sub_label);
% using the 'use_schema', true
% ensures that the entities will be in the correct order
bids_file = bids.File(name_spec, 'use_schema', true);
% Contrust the fullpath version of the filename
json_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.filename);
%%
% Assign the fields in the Matlab structure that can be saved as a json.
% all REQUIRED /RECOMMENDED /OPTIONAL metadata fields for Magnetic Resonance Imaging data
%% Adding metadata
% to get the definition of each metadata,
% you can use the bids.Schema class from bids matlab
% For example
schema = bids.Schema;
def = schema.get_definition('TaskName');
fprintf(def.description);
%% Scanner Hardware metadata fields
json.Manufacturer = ' ';
json.ManufacturersModelName = ' ';
json.MagneticFieldStrength = ' ';
json.DeviceSerialNumber = ' ';
json.StationName = ' ';
json.SoftwareVersions = ' ';
json.HardcopyDeviceSoftwareVersion = ' ';
l;
json.ReceiveCoilName = ' ';
json.ReceiveCoilActiveElements = ' ';
json.GradientSetType = ' ';
json.MRTransmitCoilSequence = ' ';
json.MatrixCoilMode = ' ';
json.CoilCombinationMethod = ' ';
%% Sequence Specifics metadata fields
json.PulseSequenceType = ' ';
json.ScanningSequence = ' ';
json.SequenceVariant = ' ';
json.ScanOptions = ' ';
json.SequenceName = ' ';
json.PulseSequenceDetails = ' ';
json.NonlinearGradientCorrection = ' ';
%% In-Plane Spatial Encoding metadata fields
json.NumberShots = ' ';
json.ParallelReductionFactorInPlane = ' ';
json.ParallelAcquisitionTechnique = ' ';
json.PartialFourier = ' ';
json.PartialFourierDirection = ' ';
json.WaterFatShift = ' ';
json.EchoTrainLength = ' ';
%% Timing Parameters metadata fields
json.EchoTime = ' ';
json.InversionTime = ' ';
json.SliceEncodingDirection = ' ';
json.DwellTime = ' ';
%% RF & Contrast metadata field
json.FlipAngle = ' ';
%% Slice Acceleration metadata field
json.MultibandAccelerationFactor = ' ';
%% Anatomical landmarks metadata fields
json.AnatomicalLandmarkCoordinates = ' ';
%% Institution information metadata fields
json.InstitutionName = ' ';
json.InstitutionAddress = ' ';
json.InstitutionalDepartmentName = ' ';
%% Write JSON
% Make sure the directory exists
bids.util.mkdir(fileparts(json_name));
bids.util.jsonencode(json_name, json);
================================================
FILE: matlabCode/anat/createBIDS_T1w_json_full_schma_based.m
================================================
% Similar to "createBIDS_T1w_json_full.m"
% but relies on the BIDS schema to get a more updated version
% of the list of metadata
% This is work in progress but should become most useful when the BIDS
% shcema is updated to include what are the required fields a given suffix
%%
clear;
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project = 'templates';
sub_label = '01';
ses_label = '01';
run_label = '01';
% The OPTIONAL acq-<label> key/value pair corresponds to a custom label
% the user MAY use to distinguish a different set of parameters used for
% acquiring the same modality.
acq_label = 'SchemaBased';
name_spec.modality = 'anat';
name_spec.suffix = 'T1w';
name_spec.ext = '.json';
name_spec.entities = struct('sub', sub_label, ...
'ses', ses_label, ...
'acq', acq_label, ...
'run', run_label);
% using the 'use_schema', true
% ensures that the entities will be in the correct order
bids_file = bids.File(name_spec, 'use_schema', true);
% Contrust the fullpath version of the filename
anat_json_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.filename);
% Make sure the directory exists
bids.util.mkdir(fileparts(anat_json_name));
%%
% Assign the fields in the Matlab structure that can be saved as a json.
% all REQUIRED /RECOMMENDED /OPTIONAL metadata fields for Magnetic Resonance Imaging data
fprintf(1, '\n');
anat_json = struct();
schema = bids.Schema;
mri_fields = fieldnames(schema.content.rules.sidecars.mri);
for i = 1:numel(mri_fields)
this_field = schema.content.rules.sidecars.mri.(mri_fields{i});
mri_subfields = fieldnames(this_field.fields);
for j = 1:numel(mri_subfields)
this_subfield = this_field.fields.(mri_subfields{j});
if ischar(this_subfield) && strcmp(this_subfield, 'recommended')
fprintf(1, '%s\n', mri_subfields{j});
this_field.fields;
anat_json.(mri_subfields{j}) = ' ';
end
end
end
%% Write JSON
% bids.util.jsonencode(anat_json_name, anat_json);
fprintf(1, '\n');
================================================
FILE: matlabCode/anat/createBIDS_T1w_json_short.m
================================================
% Template Matlab script to create a BIDS compatible file:
%
% sub-01_ses-01_acq-ShortExample_run-01_T1w.json
%
% This example lists only the REQUIRED fields.
% When adding additional metadata please use CamelCase
% Writing json files relies on the JSONio library
% https://github.com/bids-standard/bids-matlab
%
% Make sure it is in the matab/octave path
try
bids.bids_matlab_version;
catch
warning('%s\n%s\n%s\n%s', ...
'Writing the JSON file seems to have failed.', ...
'Make sure that the following library is in the matlab/octave path:', ...
'https://github.com/bids-standard/bids-matlab');
end
%%
clear;
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project = 'templates';
sub_label = '01';
ses_label = '01';
run_label = '01';
% The OPTIONAL acq-<label> key/value pair corresponds to a custom label
% the user MAY use to distinguish a different set of parameters used for
% acquiring the same modality.
acq_label = 'ShortExample';
name_spec.modality = 'anat';
name_spec.suffix = 'T1w';
name_spec.ext = '.json';
name_spec.entities = struct('sub', sub_label, ...
'ses', ses_label, ...
'acq', acq_label, ...
'run', run_label);
% using the 'use_schema', true
% ensures that the entities will be in the correct order
bids_file = bids.File(name_spec, 'use_schema', true);
% Contrust the fullpath version of the filename
json_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.filename);
% Make sure the directory exists
bids.util.mkdir(fileparts(json_name));
%%
% Assign the fields in the Matlab structure that can be saved as a json.
% all REQUIRED /RECOMMENDED /OPTIONAL metadata fields for Magnetic Resonance Imaging data
%% Adding metadata
% to get the definition of each metadata,
% you can use the bids.Schema class from bids matlab
% For example
schema = bids.Schema;
def = schema.get_definition('TaskName');
fprintf(def.description);
%% In-Plane Spatial Encoding metadata fields
json.PhaseEncodingDirection = ' ';
json.EffectiveEchoSpacing = ' ';
json.TotalReadoutTime = ' ';
%% Timing Parameters metadata fields
json.EchoTime = ' ';
%% Write JSON
bids.util.jsonencode(json_name, json);
================================================
FILE: matlabCode/eeg-meg/createBIDS_meg_json_full.m
================================================
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Create JSON using MATLAB for MEG BIDS:
%
% This template is for MEG data of any kind,
% including but not limited to task-based, resting-state, and noise recordings.
%
% If multiple Tasks were performed within a single Run,
% the task description can be set to "task-multitask".
%
% The _meg.json SHOULD contain details on the Tasks.
%
% Some manufacturers data storage
% conventions use folders which contain data files of various nature:
% for example: CTF's .ds format, or 4D/BTi.
%
% Please refer to Appendix VI for examples from a selection of MEG manufacturers
%
% By @Cofficer, Created 9/03/2018
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Writing json files relies on the JSONio library
% https://github.com/bids-standard/bids-matlab
%
% Make sure it is in the matab/octave path
try
bids.bids_matlab_version;
catch
warning('%s\n%s\n%s\n%s', ...
'Writing the JSON file seems to have failed.', ...
'Make sure that the following library is in the matlab/octave path:', ...
'https://github.com/bids-standard/bids-matlab');
end
clear;
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project = 'templates';
sub_label = '01';
ses_label = '01';
task_label = 'FullExample';
acq_label = 'CTF';
run_label = '1';
% A "proc" (processed) label has been added, especially useful for files coming from Maxfilter
% (for example: sss, tsss, trans, quat, mc, etc.)
proc_label = 'sss';
name_spec.modality = 'meg';
name_spec.suffix = 'meg';
name_spec.ext = '.json';
name_spec.entities = struct('sub', sub_label, ...
'acq', acq_label, ...
'ses', ses_label, ...
'task', task_label, ...
'run', run_label, ...
'proc', proc_label);
% using the 'use_schema', true
% ensures that the entities will be in the correct order
bids_file = bids.File(name_spec, 'use_schema', true);
% Contrust the fullpath version of the filename
json_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.filename);
%% Adding metadata
% Assign the fields in the Matlab structure that can be saved as a json.
% The following fields must be defined:
% to get the definition of each metadata,
% you can use the bids.Schema class from bids matlab
% For example
schema = bids.Schema;
def = schema.get_definition('TaskName');
fprintf(def.description);
json.TaskName = task_label;
json.InstitutionName = '';
json.InstitutionAddress = '';
json.Manufacturer = '';
json.ManufacturersModelName = '';
json.SoftwareVersions = '';
json.TaskDescription = '';
json.Instructions = '';
json.CogPOID = 'http://www.cogpo.org/ontologies/CogPOver1.owl#FIXME';
json.DeviceSerialNumber = '';
%%
% The following MEG specific fields must also be defined:
json.SamplingFrequency = '';
json.PowerLineFrequency = '';
json.DewarPosition = '';
json.SoftwareFilters = '';
json.DigitizedLandmarks = '';
json.DigitizedHeadPoints = '';
%%
% The following fields should be present for MEG:
json.MEGChannelCount = [];
json.MEGREFChannelCount = [];
json.EEGChannelCount = [];
json.ECOGChannelCount = [];
json.SEEGChannelCount = [];
json.EOGChannelCount = [];
json.ECGChannelCount = [];
json.EMGChannelCount = [];
json.MiscChannelCount = [];
json.TriggerChannelCount = [];
json.RecordingDuration = [];
json.RecordingType = '';
json.EpochLength = '';
json.ContinuousHeadLocalization = '';
json.HeadCoilFrequency = [];
json.MaxMovement = '';
json.SubjectArtefactDescription = '';
json.AssociatedEmptyRoom = '';
%%
% Specific EEG fields if recorded with MEG
% SHOULD be present:
json.EEGSamplingFrequency = [];
json.EEGPlacementScheme = '';
json.ManufacturersAmplifierModelName = '';
json.EEGReference = '';
%% Write JSON
% Make sure the directory exists
bids.util.mkdir(fileparts(json_name));
bids.util.jsonencode(json_name, json);
================================================
FILE: matlabCode/eeg-meg/createBIDS_meg_json_short.m
================================================
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Create JSON using MATLAB for MEG BIDS:
%
% This template is for MEG data of any kind, including but not limited to task-based,
% resting-state, and noise recordings.
%
% If multiple Tasks were performed within a single Run,
% the task description can be set to "task-multitask".
%
% The _meg.json SHOULD contain details on the Tasks.
%
% Some manufacturers data storage conventions use folders
% which contain data files of various nature:
% for example: CTF's .ds format, or 4D/BTi.
%
% Please refer to Appendix VI for examples from a selection of MEG manufacturers
%
% By Cofficer, Created 14/03/2018
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Writing json files relies on the JSONio library
% https://github.com/bids-standard/bids-matlab
%
% Make sure it is in the matab/octave path
try
bids.bids_matlab_version;
catch
warning('%s\n%s\n%s\n%s', ...
'Writing the JSON file seems to have failed.', ...
'Make sure that the following library is in the matlab/octave path:', ...
'https://github.com/bids-standard/bids-matlab');
end
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project = 'templates';
sub_label = '01';
ses_label = '01';
task_label = 'ShortExample';
acq_label = 'CTF';
run_label = '1';
% A "proc" (processed) label has been added, especially useful for files coming from Maxfilter
% (for example: sss, tsss, trans, quat, mc, etc.)
proc_label = 'sss';
name_spec.modality = 'meg';
name_spec.suffix = 'meg';
name_spec.ext = '.json';
name_spec.entities = struct('sub', sub_label, ...
'acq', acq_label, ...
'ses', ses_label, ...
'task', task_label, ...
'run', run_label, ...
'proc', proc_label);
% using the 'use_schema', true
% ensures that the entities will be in the correct order
bids_file = bids.File(name_spec, 'use_schema', true);
% Contrust the fullpath version of the filename
json_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.filename);
%% Adding metadata
% Assign the fields in the Matlab structure that can be saved as a json.
% The following fields must be defined:
% to get the definition of each metadata,
% you can use the bids.Schema class from bids matlab
% For example
schema = bids.Schema;
def = schema.get_definition('TaskName');
fprintf(def.description);
%%
json.TaskName = task_label;
%%
json.SamplingFrequency = [];
json.PowerLineFrequency = [];
json.DewarPosition = '';
json.SoftwareFilters = '';
json.DigitizedLandmarks = '';
json.DigitizedHeadPoints = '';
%% Write JSON
% Make sure the directory exists
bids.util.mkdir(fileparts(json_name));
bids.util.jsonencode(json_name, json);
================================================
FILE: matlabCode/eeg-meg/rename_brainvision_files.m
================================================
function rename_brainvision_files(varargin)
% RENAME_BRAINVISION_FILES renames a BrainVision EEG dataset, which consists of a vhdr header
% file, vmrk marker file and a data file that usually has the extension dat, eeg or seg.
%
% Use as
% rename_brainvision_files(oldname, newname, 'rmf', 'on')
% where both the old and the new filename should be strings corresponding to the
% header file, for instance: including the vhdr extension.
% 'rmf' option indicates to remove old files and can be turned 'on' of 'off' (default)
%
% See also http://www.fieldtriptoolbox.org/ and https://sccn.ucsd.edu/wiki/EEGLAB for
% open source software to process BrainVision EEG data.
%
% Robert Oostenveld https://gist.github.com/robertoostenveld/e31637a777c514bf1e86272e1092316e
% Cyril Pernet - fixed few bugs here and there https://gist.github.com/CPernet/e037df46e064ca83a49fb4c595d4566a
%% deal with inputs
rmf = 'off'; % by default do not delete files
if nargin >= 3
if strcmpi(varargin{3}, 'rmf')
if nargin == 3
disp('no value associated to the remove file option, assuming off');
else
rmf = varargin{4};
end
else
error(['unrecognized option argument ''' varargin{3} '''']);
end
end
oldheaderfile = varargin{1};
newheaderfile = varargin{2};
clear varargin;
% determine whether the file extensions should be in lower or upper case
if ~isempty(regexp(newheaderfile, 'VHDR$', 'once'))
switchcase = @upper;
else
switchcase = @lower;
end
% determine the filename without extension
[~, f, ~] = fileparts(newheaderfile);
%% do the renaming
% deal with the header file
assert(exist(oldheaderfile, 'file') ~= 0, 'the file %s does not exists', oldheaderfile);
assert(exist(newheaderfile, 'file') == 0, 'the file %s already exists', newheaderfile);
fid1 = fopen(oldheaderfile, 'r'); % read old
fid2 = fopen(newheaderfile, 'w'); % write new
while ~feof(fid1)
line = fgetl(fid1);
if ~isempty(regexp(line, '^MarkerFile', 'once'))
[~, rem] = strtok(line, '=');
oldmarkerfile = rem(2:end);
[~, ~, x] = fileparts(oldmarkerfile);
newmarkerfile = [f switchcase(x)];
line = sprintf('MarkerFile=%s', newmarkerfile);
elseif ~isempty(regexp(line, '^DataFile', 'once'))
[~, rem] = strtok(line, '=');
olddatafile = rem(2:end);
[~, ~, x] = fileparts(olddatafile);
newdatafile = [f switchcase(x)];
line = sprintf('DataFile=%s', newdatafile);
end
fprintf(fid2, '%s\r\n', line);
end
fclose(fid1);
fclose(fid2);
% deal with the marker file
if exist(oldmarkerfile, 'file') == 0
[~, ~, ext] = fileparts(oldmarkerfile);
[~, ff, ~] = fileparts(oldheaderfile); % re-reading as sometimes weird names comes up
if exist([ff ext], 'file')
oldmarkerfile = [ff ext];
else
error('the file %s does not exists', oldmarkerfile);
end
end
assert(exist(newmarkerfile, 'file') == 0, 'the file %s already exists', newmarkerfile);
fid1 = fopen(oldmarkerfile, 'r');
fid2 = fopen(newmarkerfile, 'w');
while ~feof(fid1)
line = fgetl(fid1);
if ~isempty(regexp(line, '^HeaderFile', 'once'))
[~, rem] = strtok(line, '=');
oldheaderfile = rem(2:end);
[~, ~, x] = fileparts(oldheaderfile);
newheaderfile = [f switchcase(x)];
line = sprintf('HeaderFile=%s', newheaderfile);
elseif ~isempty(regexp(line, '^DataFile', 'once'))
[~, rem] = strtok(line, '=');
olddatafile = rem(2:end);
[~, ~, x] = fileparts(olddatafile);
newdatafile = [f switchcase(x)];
line = sprintf('DataFile=%s', newdatafile);
end
fprintf(fid2, '%s\r\n', line);
end
fclose(fid1);
fclose(fid2);
% deal with the data file
if exist(olddatafile, 'file') == 0
[~, ~, ext] = fileparts(olddatafile);
[~, ff, ~] = fileparts(oldheaderfile); % re-reading as sometimes weird names comes up
if exist([ff ext], 'file')
olddatafile = [ff ext];
else
error('the file %s does not exists', oldmarkerfile);
end
end
assert(exist(newdatafile, 'file') == 0, 'the file %s already exists', newdatafile);
status = copyfile(olddatafile, newdatafile);
if ~status
error('failed to copy data from %s to %s', olddatafile, newdatafile);
end
%% delete old files *try* in case of user restriction
if strcmpi(rmf, 'on')
try
delete(oldheaderfile);
end
try
delete(oldmarkerfile);
end
try
delete(olddatafile);
end
end
================================================
FILE: matlabCode/fmap/createBIDS_fmap_json.m
================================================
%% Template Matlab script to create an BIDS compatible _fmap.json file
% There are different cases, see BIDS spec 1.0.2 paragraph 8.9
% This example lists all required and optional fields.
% When adding additional metadata please use CamelCase
%
% DHermes, 2017
% Writing json files relies on the JSONio library
% https://github.com/bids-standard/bids-matlab
%
% Make sure it is in the matab/octave path
try
bids.bids_matlab_version;
catch
warning('%s\n%s\n%s\n%s', ...
'Writing the JSON file seems to have failed.', ...
'Make sure that the following library is in the matlab/octave path:', ...
'https://github.com/bids-standard/bids-matlab');
end
%% Case 1: Phase difference image and at least one magnitude image
clear;
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project = 'templates';
sub_label = '01';
ses_label = '01';
acq_label = 'Case1';
run_label = '01';
name_spec.modality = 'fmap';
name_spec.suffix = 'phasediff';
name_spec.ext = '.json';
name_spec.entities = struct('sub', sub_label, ...
'ses', ses_label, ...
'acq', acq_label, ...
'run', run_label);
% using the 'use_schema', true
% ensures that the entities will be in the correct order
bids_file = bids.File(name_spec, 'use_schema', true);
% Contrust the fullpath version of the filename
json_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.filename);
%% Adding metadata
% to get the definition of each metadata,
% you can use the bids.Schema class from bids matlab
% For example
schema = bids.Schema;
def = schema.get_definition('TaskName');
fprintf(def.description);
json.EchoTime1 = '';
json.EchoTime2 = '';
json.IntendedFor = {'sub-01/ses-01/func/...'
'sub-01/ses-01/func/...'};
% Write JSON
% Make sure the directory exists
bids.util.mkdir(fileparts(json_name));
bids.util.jsonencode(json_name, json);
%% Case 2: Two phase images and two magnitude images
clear;
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project = 'templates';
sub_label = '01';
ses_label = '01';
acq_label = 'Case2';
run_label = '01';
name_spec.modality = 'fmap';
name_spec.suffix = 'phase1';
name_spec.ext = '.json';
name_spec.entities = struct('sub', sub_label, ...
'ses', ses_label, ...
'acq', acq_label, ...
'run', run_label);
% using the 'use_schema', true
% ensures that the entities will be in the correct order
bids_file = bids.File(name_spec, 'use_schema', true);
% Contrust the fullpath version of the filename
fmap1_json_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.filename);
name_spec.suffix = 'phase2';
bids_file = bids.File(name_spec, 'use_schema', true);
fmap2_json_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.filename);
%% Adding metadata
% to get the definition of each metadata,
% you can use the bids.Schema class from bids matlab
% For example
schema = bids.Schema;
def = schema.get_definition('TaskName');
fprintf(def.description);
fmap1_json.EchoTime = '';
fmap1_json.IntendedFor = {'sub-01/ses-01/func/...'
'sub-01/ses-01/func/...'};
fmap2_json.EchoTime = '';
fmap2_json.IntendedFor = {'sub-01/ses-01/func/...'
'sub-01/ses-01/func/...'};
% Write JSON
% Make sure the directory exists
bids.util.mkdir(fileparts(fmap1_json_name));
bids.util.jsonencode(fmap1_json_name, fmap1_json);
bids.util.jsonencode(fmap2_json_name, fmap2_json);
%% Case 3: A single, real fieldmap image (showing the field inhomogeneity in each voxel)
clear;
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project = 'templates';
sub_label = '01';
ses_label = '01';
acq_label = 'Case3';
run_label = '01';
name_spec.modality = 'fmap';
name_spec.suffix = 'fieldmap';
name_spec.ext = '.json';
name_spec.entities = struct('sub', sub_label, ...
'ses', ses_label, ...
'acq', acq_label, ...
'run', run_label);
% using the 'use_schema', true
% ensures that the entities will be in the correct order
bids_file = bids.File(name_spec, 'use_schema', true);
% Contrust the fullpath version of the filename
json_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.filename);
%% Adding metadata
% to get the definition of each metadata,
% you can use the bids.Schema class from bids matlab
% For example
schema = bids.Schema;
def = schema.get_definition('TaskName');
fprintf(def.description);
json.Units = '';
json.IntendedFor = {'sub-01/ses-01/func/...'
'sub-01/ses-01/func/...'};
% Write JSON
% Make sure the directory exists
bids.util.mkdir(fileparts(json_name));
bids.util.jsonencode(json_name, json);
%% Case 4: Multiple phase encoded directions (topup)
clear;
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project = 'templates';
sub_label = '01';
ses_label = '01';
acq_label = 'Case4';
run_label = '01';
% dir_label value can be set to arbitrary alphanumeric
% label ([a-zA-Z0-9]+ for example "LR" or "AP") that can help users to
% distinguish between different files, but should not be used to infer any
% scanning parameters (such as phase encoding directions) of the corresponding sequence.
dir_label = 'LR';
name_spec.modality = 'fmap';
name_spec.suffix = 'epi';
name_spec.ext = '.json';
name_spec.entities = struct('sub', sub_label, ...
'ses', ses_label, ...
'acq', acq_label, ...
'run', run_label, ...
'dir', dir_label);
% using the 'use_schema', true
% ensures that the entities will be in the correct order
bids_file = bids.File(name_spec, 'use_schema', true);
% Contrust the fullpath version of the filename
json_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.filename);
%% Adding metadata
% to get the definition of each metadata,
% you can use the bids.Schema class from bids matlab
% For example
schema = bids.Schema;
def = schema.get_definition('TaskName');
fprintf(def.description);
json.PhaseEncodingDirection = '';
json.TotalReadoutTime = '';
json.IntendedFor = {'sub-01/ses-01/func/...'
'sub-01/ses-01/func/...'};
% Write JSON
% Make sure the directory exists
bids.util.mkdir(fileparts(json_name));
bids.util.jsonencode(json_name, json);
================================================
FILE: matlabCode/func/createBIDS_bold_json_full.m
================================================
%% Template Matlab script to create an BIDS compatible _bold.json file
% This example lists all required and optional fields.
% When adding additional metadata please use CamelCase
% Use version of DICOM ontology terms whenever possible.
%
% DHermes, 2017
% Writing json files relies on the JSONio library
% https://github.com/bids-standard/bids-matlab
%
% Make sure it is in the matab/octave path
try
bids.bids_matlab_version;
catch
warning('%s\n%s\n%s\n%s', ...
'Writing the JSON file seems to have failed.', ...
'Make sure that the following library is in the matlab/octave path:', ...
'https://github.com/bids-standard/bids-matlab');
end
%%
clear;
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project = 'templates';
sub_label = '01';
ses_label = '01';
task_label = 'FullExample';
run_label = '01';
name_spec.modality = 'func';
name_spec.suffix = 'bold';
name_spec.ext = '.json';
name_spec.entities = struct('sub', sub_label, ...
'ses', ses_label, ...
'task', task_label, ...
'run', run_label);
% using the 'use_schema', true
% ensures that the entities will be in the correct order
bids_file = bids.File(name_spec, 'use_schema', true);
% Contrust the fullpath version of the filename
json_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.filename);
%% Adding metadata
% to get the definition of each metadata,
% you can use the bids.Schema class from bids matlab
% For example
schema = bids.Schema;
def = schema.get_definition('TaskName');
fprintf(def.description);
%% Required fields
json.TaskName = 'FullExample';
json.RepetitionTime = [];
%% Required fields if using a fieldmap
json.PhaseEncodingDirection = '';
json.EffectiveEchoSpacing = [];
json.EchoTime = [];
%% Recommended fields:
%% Scanner Hardware metadata fields
json.Manufacturer = '';
json.ManufacturersModelName = '';
json.MagneticFieldStrength = [];
json.DeviceSerialNumber = '';
json.StationName = ' ';
json.SoftwareVersions = ' ';
json.HardcopyDeviceSoftwareVersion = '';
json.ReceiveCoilName = ' ';
json.ReceiveCoilActiveElements = '';
json.GradientSetType = '';
json.MRTransmitCoilSequence = '';
json.MatrixCoilMode = '';
json.CoilCombinationMethod = '';
%% Sequence Specifics metadata fields
json.PulseSequenceType = '';
json.ScanningSequence = '';
json.SequenceVariant = '';
json.ScanOptions = '';
json.SequenceName = '';
json.PulseSequenceDetails = '';
json.NonlinearGradientCorrection = '';
%% In-Plane Spatial Encoding metadata fields
json.NumberShots = [];
json.ParallelReductionFactorInPlane = '';
json.ParallelAcquisitionTechnique = '';
json.PartialFourier = '';
json.PartialFourierDirection = '';
json.WaterFatShift = '';
json.EchoTrainLength = '';
%% Timing Parameters metadata fields
json.InversionTime = [];
json.SliceEncodingDirection = '';
json.DwellTime = [];
json.TotalReadoutTime = [];
json.DelayAfterTrigger = [];
json.NumberOfVolumesDiscardedByScanner = [];
json.NumberOfVolumesDiscardedByUser = [];
%% RF & Contrast metadata field
json.FlipAngle = [];
%% Slice Acceleration metadata field
json.MultibandAccelerationFactor = [];
%% Task metadata field
json.Instructions = '';
json.TaskDescription = '';
json.CogAtlasID = 'https://www.cognitiveatlas.org/FIXME';
json.CogPOID = 'http://www.cogpo.org/ontologies/CogPOver1.owl#FIXME';
%% Institution information metadata fields
json.InstitutionName = '';
json.InstitutionAddress = '';
json.InstitutionalDepartmentName = '';
%% Write JSON
% Make sure the directory exists
bids.util.mkdir(fileparts(json_name));
bids.util.jsonencode(json_name, json);
================================================
FILE: matlabCode/func/createBIDS_bold_json_short.m
================================================
%% Template Matlab script to create an BIDS compatible _bold.json file
% This example only lists the required fields.
% When adding additional metadata please use CamelCase
% Use version of DICOM ontology terms whenever possible.
%
% DHermes, 2017
% Writing json files relies on the JSONio library
% https://github.com/bids-standard/bids-matlab
%
% Make sure it is in the matab/octave path
try
bids.bids_matlab_version;
catch
warning('%s\n%s\n%s\n%s', ...
'Writing the JSON file seems to have failed.', ...
'Make sure that the following library is in the matlab/octave path:', ...
'https://github.com/bids-standard/bids-matlab');
end
%%
clear;
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project = 'templates';
sub_label = '01';
ses_label = '01';
task_label = 'ShortExample';
run_label = '01';
name_spec.modality = 'func';
name_spec.suffix = 'bold';
name_spec.ext = '.json';
name_spec.entities = struct('sub', sub_label, ...
'ses', ses_label, ...
'task', task_label, ...
'run', run_label);
% using the 'use_schema', true
% ensures that the entities will be in the correct order
bids_file = bids.File(name_spec, 'use_schema', true);
% Contrust the fullpath version of the filename
json_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.filename);
%% Adding metadata
% to get the definition of each metadata,
% you can use the bids.Schema class from bids matlab
% For example
schema = bids.Schema;
def = schema.get_definition('TaskName');
fprintf(def.description);
%% Required fields
json.TaskName = 'ShortExample';
json.RepetitionTime = [];
json.SliceTiming = [];
%% Required fields if using a fieldmap
json.PhaseEncodingDirection = '';
json.EffectiveEchoSpacing = [];
json.EchoTime = [];
%% Write JSON
% Make sure the directory exists
bids.util.mkdir(fileparts(json_name));
bids.util.jsonencode(json_name, json);
================================================
FILE: matlabCode/general/README.md
================================================
# Code to generate "modality agnostic" BIDS files
## bids_spreadsheet2participants
This function requires Matlab 2018a or above to run.
Run the following in Matlab:
```matlab
cd matlabCode/general
input_file = fullfile(pwd, 'input', 'input_to_create_participants_file.xlsx')
files_out = bids_spreadsheet2participants(input_file, 'ignore', 'comment')
```
================================================
FILE: matlabCode/general/bids_spreadsheet2participants.m
================================================
function files_out = bids_spreadsheet2participants(varargin)
%
% routine to takes an spreadsheet file (for example: excel) as input and export as participants.tsv
% and participants.json
%
% FORMAT files_out = bids_spreadsheet2participants(file_in,'ignore','field1','field2',...)
%
% INPUTS if empty user is prompted:
%
% - 'file_in' is the excel file, with at least the 3 BIDS mandatory fields in the 1st sheet:
% - participant_id,
% - age,
% - gender
%
% A second sheet can be used to specify variables for the json file column format:
% - variable name (same as sheet 1),
% - description,
% - values (optional)
%
% - 'ignore' is the key to ignore specific fields (columns) in the excel file
% for example: 'ignore', 'variableX', 'variableY'
%
% - 'export_dir' is the directory to save output files
%
% OUTPUT:
%
% - 'files_out' is a cell array with:
% - files_out{1} the full name of the particpiants.tsv
% - files_out{2} the full name of the particpiants.json
%
% EXAMPLE:
%
% files_out = bids_spreadsheet2participants('D:\icpsr_subset.xlsx','ignore','EEGtesttime')
%
% the spreadsheet must have:
% worksheet 1 with data, each column has a variable name and values
% -- note missing values MUST be n/a or nill
% worksheet 2 is optional with columns variables, Description, Levels, Units to describe worksheet 1
% variables similar to
% https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#participants-file
% -- note the order of 'Levels' names should match the order of apparition in the data
% to have an exact match
%
% Requires matlab 2018a or above
%
% Cyril Pernet - March 2021
% ---------------------------------
if verLessThan('matlab', '9.4')
error('This function requires matlab 2018a or above.');
end
files_out = cell(2, 1);
% check library
if ~exist('jsonwrite.m', 'file')
if exist(fullfile(fileparts(which('bids_spreadsheet2participants.m')), 'JSONio'), 'dir')
addpath(fullfile(fileparts(which('bids_spreadsheet2participants.m')), 'JSONio'));
else
error(['JSONio library needed, available with EEGLAB bids-matlab-tools or', ...
'at https://github.com/gllmflndn/JSONio']);
end
end
%% deal with input file
if nargin == 0
[filename, pathname] = uigetfile({'*.xlsx;*.ods;*.xls'}, 'Pick an spreadsheet file');
if isequal(filename, 0) || isequal(pathname, 0)
disp('Selection cancelled');
return
else
filein = fullfile(pathname, filename);
disp(['file selected: ', filein]);
end
else
filein = varargin{1};
if ~exist(filein, 'file')
error('%s not found', filein);
end
end
% detect what's inside the selected file
sheet1_opts = detectImportOptions(filein, 'Sheet', 1);
try
sheet2_opts = detectImportOptions(filein, 'PreserveVariableNames', true, 'Sheet', 2);
catch one_sheet
fprintf('import only variables: %s\n', one_sheet.message);
sheet2_opts = [];
end
%% quickly check other arguments are valid
if nargin > 1
if ~any(contains(varargin, {'ignore', 'export'}, 'IgnoreCase', true))
error('key input arguments in are missing ''ignore'' and/or ''export_dir''');
else
if any(contains(varargin, 'export', 'IgnoreCase', true))
export_dir = varargin{find(contains(varargin, 'export', 'IgnoreCase', true)) + 1};
end
if any(contains(varargin, 'ignore', 'IgnoreCase', true))
if any(contains(varargin, 'export', 'IgnoreCase', true))
if find(contains(varargin, 'ignore', 'IgnoreCase', true)) < ...
find(contains(varargin, 'export', 'IgnoreCase', true))
ignore_var = find(contains(varargin, 'ignore', 'IgnoreCase', true)) + ...
1:find(contains(varargin, 'export', 'IgnoreCase', true)) - 1;
else
ignore_var = find(contains(varargin, 'ignore', 'IgnoreCase', true)) + 1:nargin;
end
else
ignore_var = find(contains(varargin, 'ignore', 'IgnoreCase', true)) + 1:nargin;
end
end
end
end
%% create particpiants.tsv
Data = readtable(filein, sheet1_opts);
% 1st check mandatory/recommended fields are presents
participant_idvar = any(strcmpi(Data.Properties.VariableNames, 'participant_id'));
idvar = any(strcmpi(Data.Properties.VariableNames, 'id'));
if idvar == 0 && participant_idvar == 0
error('no participant ID variable detected, invalid file');
elseif idvar == 1 && participant_idvar == 0
disp('ID variable detected, the BIDS value exported will be participant_id ');
Data.Properties.VariableNames(strcmpi(Data.Properties.VariableNames, 'id')) = {'participant_id'};
end
if length(unique(Data.participant_id)) ~= length(Data.participant_id)
[~, idx] = unique(Data.participant_id);
non_unique = setdiff(1:length(Data.participant_id), idx);
non_unique = cell2mat(Data.participant_id(non_unique));
for id = 1:size(non_unique, 1)
warning('some IDs are duplicate: %s', non_unique(id, :));
end
error('non unique IDS are not permitted');
end
if any(strcmp(Data.Properties.VariableNames, 'Sex'))
Data.Properties.VariableNames(strcmpi(Data.Properties.VariableNames, 'Sex')) = {'sex'};
end
sexvar = any(strcmpi(Data.Properties.VariableNames, 'sex'));
gendervar = any(strcmpi(Data.Properties.VariableNames, 'gender'));
if gendervar == 1 && sexvar == 0
disp('gender variable detected - the recommended optional field is ''sex'' but ok using gender');
end
if any(strcmp(Data.Properties.VariableNames, 'Age'))
Data.Properties.VariableNames(strcmpi(Data.Properties.VariableNames, 'Age')) = {'age'};
end
if ~any(strcmpi(Data.Properties.VariableNames, 'age'))
disp('age variable is missing - this is only an optional field still exporting');
else
if ~isnumeric(Data.age)
for v = 1:length(Data.age)
Data.age{v} = str2double(Data.age{v});
end
Data.age = cell2mat(Data.age); % ensure age treated as number
end
end
% 2nd check if any of those variable should be removed - and feedback if
% some input variable names were not found
if nargin > 1
if any(contains(varargin, 'ignore', 'IgnoreCase', true))
for var = ignore_var
if any(contains(Data.Properties.VariableNames, varargin{var}, 'IgnoreCase', true))
Data = removevars(Data, varargin{var});
else
fprintf('''%s'' input variable to ignore not recognized - skipping it\n', varargin{var});
end
end
else
warning('ignore argument not recognized - skipping any options');
end
end
% last check variable values (also useful for metadata)
if any(~contains(Data.participant_id, 'sub-'))
disp('participant_id should include ''sub-'', adding it to current IDs');
for sub = 1:length(Data.participant_id)
if ~contains(Data.participant_id{sub}, 'sub-')
Data.participant_id{sub} = ['sub-' Data.participant_id{sub}];
end
end
end
value_types = varfun(@class, Data, 'OutputFormat', 'cell');
for v = length(value_types):-1:1
values{v} = unique(Data.(Data.Properties.VariableNames{v}));
end
export_data = convert_NAN_to_na(Data);
if ~exist('export_dir', 'var')
export_dir = uigetdir(fileparts(filein), 'Select directory to save exported files');
if export_dir == 0
export_dir = fileparts(filein);
end
end
try
writetable(export_data, [export_dir filesep 'participants.tsv'], 'FileType', 'text', 'Delimiter', '\t');
files_out{1} = fullfile(export_dir, 'participants.tsv');
fprintf('participants.tsv file saved in %s\n', export_dir);
clear export_data;
catch tsv_error
files_out{2} = 'particpants.tsv file not created';
error('participants.tsv not saved %s\n', tsv_error.mewsage);
end
%% create participants.json
if ~isempty(sheet2_opts)
GivenMetaData = readtable(filein, sheet2_opts);
if any(contains(GivenMetaData.Properties.VariableNames, 'Variable'))
GivenMetaData.Properties.VariableNames(strcmpi(GivenMetaData.Properties.VariableNames, 'Variable')) = ...
{'variables'};
elseif any(contains(GivenMetaData.Properties.VariableNames, 'variable'))
GivenMetaData.Properties.VariableNames(strcmpi(GivenMetaData.Properties.VariableNames, 'variable')) = ...
{'variables'};
end
if ~any(strcmpi('variables', GivenMetaData.Properties.VariableNames))
warning('metadata sheet provided but ''variables name'' not found - using worksheet 1');
else
% given variables present check description
if ~any(contains(GivenMetaData.Properties.VariableNames, 'description', 'IgnoreCase', true))
warning('metadata sheet provided but ''description of variables'' not found - using worksheet 1');
else
matched_var = cellfun(@(x) find(strcmpi(x, Data.Properties.VariableNames)), GivenMetaData.variables, ...
'UniformOutput', false);
matched_var(cellfun(@(x) isempty(x), matched_var')) = {0}; % mark empty as 0
try
matched_var = cell2mat(matched_var); % works if unique, ie one value per cell
if any(contains(GivenMetaData.Properties.VariableNames, 'description'))
GivenMetaData.Properties.VariableNames(strcmpi(GivenMetaData.Properties.VariableNames, ...
'description')) = ...
{'Description'};
end
catch matched_var_err
warning(['variable names between worksheets likely not unique,', ...
' skipping provided metadata \n%s\n'], ...
matched_var_err.message); %#ok<MEXCEP>
end
end
% given variables present check levels
if ~any(contains(GivenMetaData.Properties.VariableNames, 'level', 'IgnoreCase', true))
warning('metadata sheet provided but ''levels'' not found - using worksheet 1');
else
if any(contains(GivenMetaData.Properties.VariableNames, 'level'))
GivenMetaData.Properties.VariableNames(strcmpi(GivenMetaData.Properties.VariableNames, ...
'level')) = ...
{'Levels'};
elseif any(contains(GivenMetaData.Properties.VariableNames, 'levels'))
GivenMetaData.Properties.VariableNames(strcmpi(GivenMetaData.Properties.VariableNames, ...
'levels')) = ...
{'Levels'};
end
end
% given variables present check unit
if ~any(contains(GivenMetaData.Properties.VariableNames, 'unit', 'IgnoreCase', true))
warning('metadata sheet provided but ''Units'' of variables not found');
else
if any(contains(GivenMetaData.Properties.VariableNames, 'unit'))
GivenMetaData.Properties.VariableNames(strcmpi(GivenMetaData.Properties.VariableNames, ...
'unit')) = ...
{'Units'};
elseif any(contains(GivenMetaData.Properties.VariableNames, 'units'))
GivenMetaData.Properties.VariableNames(strcmpi(GivenMetaData.Properties.VariableNames, ...
'units')) = ...
{'Units'};
end
end
end
else
matched_var = zeros(length(Data.Properties.VariableNames), 1);
end
% prepare json variables from worksheet 1
% 'values' are the unique values read on the data
% 'value_types' gives an indication if we want to use Level or Unit
% we can complement with GivenMetaData.Description, GivenMetaData.Levels and GivenMetaData.Units
% using 'matched_var' for instance: variables names match between worksheet
json = struct;
for var = 1:length(Data.Properties.VariableNames)
if ~strcmpi(Data.Properties.VariableNames{var}, 'participant_id')
% add description
if ismember(var, matched_var)
if any(contains(GivenMetaData.Properties.VariableNames, 'Description'))
if ~isempty(GivenMetaData.Description{matched_var == var})
json.(Data.Properties.VariableNames{var}).Description = ...
GivenMetaData.Description{matched_var == var};
else
json.(Data.Properties.VariableNames{var}).Description = [];
end
end
else
json.(Data.Properties.VariableNames{var}).Description = [];
end
% add Levels and Units
if strcmpi(value_types{var}, 'cell') % likely Levels
if ismember(var, matched_var) && any(contains(GivenMetaData.Properties.VariableNames, 'Levels'))
if ~isempty(GivenMetaData.Levels{matched_var == var})
tmp = lower(GivenMetaData.Levels{matched_var == var});
tmp = regexprep(tmp, '\t', ';'); % in case tab is used
tmp(isspace(tmp)) = []; % deblank as well
separators = sort([strfind(tmp, ';') strfind(tmp, ',') length(tmp)]);
index1 = 1;
index2 = separators(1) - 1;
for l = 1:length(separators)
Levels{l} = tmp(index1:index2);
if l < length(separators)
index1 = separators(l) + 1;
index2 = separators(l + 1);
end
end
tmp = values{var};
tmp(strcmpi(tmp, 'n/a')) = [];
tmp(strcmpi(tmp, 'nill')) = [];
if length(tmp) ~= length(Levels)
warning('Levels of ''%s'' between data and metadata don''t match', ...
Data.Properties.VariableNames{var});
% only write fields
for v = 1:length(tmp)
json.(Data.Properties.VariableNames{var}).Levels.(tmp{v}) = [];
end
else
% store levels
for v = 1:length(tmp)
json.(Data.Properties.VariableNames{var}).Levels.(tmp{v}) = Levels{v};
end
end
else
json.(Data.Properties.VariableNames{var}).Levels = [];
end
else % no metadata
json.(Data.Properties.VariableNames{var}).Levels = values{var};
end
else % likely units
if ismember(var, matched_var) && any(contains(GivenMetaData.Properties.VariableNames, 'Units'))
if ~isempty(GivenMetaData.Levels{var})
json.(Data.Properties.VariableNames{var}).Units = ...
lower(GivenMetaData.Units{matched_var == var});
else
json.(Data.Properties.VariableNames{var}).Units = [];
end
else % no metadata
json.(Data.Properties.VariableNames{var}).Units = [];
end
end
end
end
try
jsonwrite([export_dir filesep 'participants.json'], json, struct('indent', ' '));
files_out{2} = fullfile(export_dir, 'participants.json');
fprintf('participants.json file saved in %s\n', export_dir);
warndlg(sprintf('json file created, do check it ! \n it is almost certain it needs editing'), ...
'BIDS spec', 'modal');
catch json_err
files_out{2} = 'particpants.json file not created';
error('participants.json not saved %s\n', json_err.mewsage);
end
end
function export_data = convert_NAN_to_na(data)
% make sure to export NaN as n/a
export_data = data;
for v = 1:length(export_data.Properties.VariableNames)
if strcmp(class(export_data.(cell2mat(export_data.Properties.VariableNames(v)))), 'double')
export_data.(cell2mat(export_data.Properties.VariableNames(v))) = ...
num2cell(export_data.(cell2mat(export_data.Properties.VariableNames(v))));
for n = 1:size(export_data.(cell2mat(export_data.Properties.VariableNames(v))), 1)
if isnan(export_data.(cell2mat(export_data.Properties.VariableNames(v))){n})
export_data.(cell2mat(export_data.Properties.VariableNames(v))){n} = 'n/a';
end
end
end
end
end
================================================
FILE: matlabCode/general/createBIDS_dataset_description_json.m
================================================
%% Template Matlab script to create an BIDS compatible dataset_description.json file
% This example lists all required and optional fields.
% When adding additional metadata please use CamelCase
%
% DHermes, 2017
% Writing json files relies on the JSONio library
% https://github.com/bids-standard/bids-matlab
%
% Make sure it is in the matab/octave path
try
bids.bids_matlab_version;
catch
warning('%s\n%s\n%s\n%s', ...
'Writing the JSON file seems to have failed.', ...
'Make sure that the following library is in the matlab/octave path:', ...
'https://github.com/bids-standard/bids-matlab');
end
%%
clear;
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project_label = 'templates';
json_label = 'dataset_description';
json_name = fullfile(root_dir, project_label, 'dataset_description.json');
%% General fields, shared with MRI BIDS and MEG BIDS:
%% Required fields:
% name of the dataset
json.Name = '';
% The version of the BIDS standard that was used
json.BIDSVersion = '1.7.0';
% The interpretation of the dataset. MUST be one of "raw" or "derivative".
% For backwards compatibility, the default value is "raw".
json.DatasetType = 'raw';
%% Recommended fields:
% what license is this dataset distributed under? The
% use of license name abbreviations is suggested for specifying a license.
% A list of common licenses with suggested abbreviations can be found in appendix III.
json.License = '';
% List of individuals who contributed to the
% creation/curation of the dataset
json.Authors = {'', '', ''};
json.Acknowledgements = ''; % who should be acknowledge in helping to collect the data
% Instructions how researchers using this
% dataset should acknowledge the original authors. This field can also be used
% to define a publication that should be cited in publications that use the
% dataset.
json.HowToAcknowledge = '';
% sources of funding (grant numbers)
json.Funding = {'', '', ''};
% List of ethics committee approvals of the research protocols and/or protocol identifiers.
json.EthicsApprovals = {''};
% a list of references to
% publication that contain information on the dataset, or links.
json.ReferencesAndLinks = {'', '', ''};
% the Document Object Identifier of the dataset
% (not the corresponding paper).
json.DatasetDOI = 'doi:';
%% Write JSON
% Make sure the directory exists
bids.util.mkdir(fileparts(json_name));
bids.util.jsonencode(json_name, json);
================================================
FILE: matlabCode/general/createBIDS_events_tsv_json_full.m
================================================
%% Template Matlab script to create an BIDS compatible sub-01_ses-01_task-FullExample-01_events.tsv file
% This example lists all required and optional fields.
% When adding additional metadata please use CamelCase
%
% anushkab, 2018
% Writing json files relies on the JSONio library
% https://github.com/bids-standard/bids-matlab
%
% Make sure it is in the matab/octave path
try
bids.bids_matlab_version;
catch
warning('%s\n%s\n%s\n%s', ...
'Writing the JSON file seems to have failed.', ...
'Make sure that the following library is in the matlab/octave path:', ...
'https://github.com/bids-standard/bids-matlab');
end
%%
clear;
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project = 'templates';
sub_label = '01';
ses_label = '01';
task_label = 'FullExample';
run_label = '01';
name_spec.modality = 'func';
name_spec.suffix = 'events';
name_spec.ext = '.tsv';
name_spec.entities = struct('sub', sub_label, ...
'ses', ses_label, ...
'task', task_label, ...
'run', run_label);
% using the 'use_schema', true
% ensures that the entities will be in the correct order
bids_file = bids.File(name_spec, 'use_schema', true);
% Contrust the fullpath version of the filename
events_tsv_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.filename);
events_json_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.json_filename);
%% make an event table and save
%% CONTAINS a set of REQUIRED and OPTIONAL columns
% REQUIRED Onset (in seconds) of the event measured from the beginning of
% the acquisition of the first volume in the corresponding task imaging data file.
% If any acquired scans have been discarded before forming the imaging data file,
% ensure that a time of 0 corresponds to the first image stored. In other words
% negative numbers in onset are allowed.
tsv.onset = 0;
% REQUIRED. Duration of the event (measured from onset) in seconds.
% Must always be either zero or positive. A "duration" value of zero implies
% that the delta function or event is so short as to be effectively modeled as an impulse.
tsv.duration = 0;
% OPTIONAL Primary categorisation of each trial to identify them as instances
% of the experimental conditions
tsv.trial_type = {'afraid'};
% OPTIONAL. Response time measured in seconds. A negative response time can be
% used to represent preemptive responses and n/a denotes a missed response.
tsv.response_time = 0;
% OPTIONAL Represents the location of the stimulus file (image, video, sound etc.)
% presented at the given onset time
tsv.stim_file = {' '};
% OPTIONAL Hierarchical Event Descriptor (HED) Tag.
tsv.HED = {' '};
%% Save table
bids.util.tsvwrite(events_tsv_name, tsv);
%% associated data dictionary
template = struct('LongName', '', ...
'Description', '', ...
'Levels', [], ...
'Units', '', ...
'TermURL', '');
json.trial_type = template;
json.trial_type.Description = 'Emotion image type';
json.trial_type.Levels = struct('afraid', 'A face showing fear is displayed', ...
'angry', 'A face showing anger is displayed');
json.identifier.LongName = 'Unique identifier from Karolinska (KDEF) database';
json.identifier.Description = 'ID from KDEF database used to identify the displayed image';
json.StimulusPresentation.OperatingSystem = 'Linux Ubuntu 18.04.5';
json.StimulusPresentation.SoftwareName = 'Psychtoolbox';
json.StimulusPresentation.SoftwareRRID = 'SCR_002881';
json.StimulusPresentation.SoftwareVersion = '3.0.14';
json.StimulusPresentation.Code = 'doi:10.5281/zenodo.3361717';
%% Write JSON
% Make sure the directory exists
bids.util.mkdir(fileparts(events_json_name));
bids.util.jsonencode(events_json_name, json);
================================================
FILE: matlabCode/general/createBIDS_participants_tsv.m
================================================
%% Template Matlab script to create an BIDS compatible participants.tsv file
% This example lists all required and optional fields.
% When adding additional metadata please use CamelCase
%
% DHermes, 2017
% Writing json files relies on the JSONio library
% https://github.com/bids-standard/bids-matlab
%
% Make sure it is in the matab/octave path
try
bids.bids_matlab_version;
catch
warning('%s\n%s\n%s\n%s', ...
'Writing the JSON file seems to have failed.', ...
'Make sure that the following library is in the matlab/octave path:', ...
'https://github.com/bids-standard/bids-matlab');
end
%%
clear;
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project_label = 'templates';
participants_tsv_name = fullfile(root_dir, project_label, 'participants.tsv');
%% make a participants table and save
tsv.participant_id = {'sub-01'; 'sub-epilepsy01'};
tsv.age = [0; 10];
tsv.sex = {'m'; 'f'};
tsv.handedness = {'l'; 'r'};
bids.util.tsvwrite(participants_tsv_name, tsv);
%% associated data dictionary
template = struct( ...
'LongName', '', ...
'Description', '', ...
'Levels', struct(), ...
'Units', '', ...
'TermURL', 'http://www.todo.com/fixme');
json.age = template;
json.age.Description = 'age of the participant';
json.age.Units = 'years';
json.sex = template;
json.sex.Description = 'sex of the participant as reported by the participant';
json.sex.Levels = struct( ...
'm', 'male', ...
'f', 'female');
json.handedness = template;
json.handedness.Description = 'handedness of the participant as reported by the participant';
json.handedness.Levels = struct( ...
'l', 'left', ...
'r', 'right');
json_name = fullfile(root_dir, project_label, 'participants.json');
% Write JSON
% Make sure the directory exists
bids.util.mkdir(fileparts(json_name));
bids.util.jsonencode(json_name, json);
================================================
FILE: matlabCode/general/createBIDS_samples_tsv.m
================================================
%% Template Matlab script to create an BIDS compatible samples.tsv file
% Writing json files relies on the JSONio library
% https://github.com/bids-standard/bids-matlab
%
% Make sure it is in the matab/octave path
try
bids.bids_matlab_version;
catch
warning('%s\n%s\n%s\n%s', ...
'Writing the JSON file seems to have failed.', ...
'Make sure that the following library is in the matlab/octave path:', ...
'https://github.com/bids-standard/bids-matlab');
end
%%
clear;
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project_label = 'templates';
samples_tsv_name = fullfile(root_dir, project_label, 'samples.tsv');
%% make a participants table and save
tsv.sample_id = {'sample-01'; 'sample-02'};
tsv.participant_id = {'sub-01'; 'sub-epilepsy01'};
tsv.sample_type = {'tissue'; 'tissue'};
bids.util.tsvwrite(samples_tsv_name, tsv);
%% associated data dictionary
% use the BIDS schema to get the official definitions
schema = bids.Schema;
columns = fieldnames(tsv);
for i = 1:numel(columns)
def = schema.get_definition(columns{i});
json.(columns{i}).LongName = def.display_name;
json.(columns{i}).Description = def.description;
end
json_name = fullfile(root_dir, project_label, 'samples.json');
% Write JSON
% Make sure the directory exists
bids.util.mkdir(fileparts(json_name));
bids.util.jsonencode(json_name, json);
================================================
FILE: matlabCode/general/tests/data/participants.json
================================================
{
"collectionIssues": {
"Description": [],
"Levels": [
"broken trigger cable, no EEG codes",
"nill",
"no EEG",
"no MRI",
"none"
]
},
"CognitiveTest1": {
"Description": [],
"Units": []
},
"CognitiveTest2": {
"Description": [],
"Units": []
},
"testdate": {
"Description": "data collection start time",
"Units": []
},
"age": {
"Description": "Age in years",
"Units": []
},
"sex": {
"Description": "Sex",
"Levels": {
"Female": "male",
"Male": "female"
}
}
}
================================================
FILE: matlabCode/general/tests/data/participants.tsv
================================================
participant_id collectionIssues CognitiveTest1 CognitiveTest2 testdate age sex
sub-control1 none 8 1 01-Nov-2019 n/a nill
sub-control2 none 11 2 01-Nov-2019 n/a nill
sub-control3 no MRI n/a 1 NaT n/a Male
sub-control4 none 8 1 07-Nov-2019 5.52328767123288 Female
sub-control5 none 8 2 07-Nov-2019 5.06575342465753 Female
sub-control6 none 11 1 04-Feb-2020 5.4986301369863 Male
sub-patient1 nill n/a 5 NaT n/a Female
sub-patient2 no EEG 7 4 NaT n/a nill
sub-patient3 none 11 3 12-Dec-2019 5.68219178082192 Male
sub-patient4 none 8 1 20-Feb-2020 n/a nill
sub-patient5 none 11 4 05-Dec-2019 5.12054794520548 Female
sub-control7 none 9 1 12-Dec-2019 5.35342465753425 Male
sub-control8 none 9 2 05-Dec-2019 5.71506849315069 Female
sub-control9 none 9 1 04-Feb-2020 5.2 Female
sub-control10 broken trigger cable, no EEG codes 9 2 NaT n/a Female
sub-patient6 none 11 5 11-Feb-2020 5.63013698630137 Female
================================================
FILE: matlabCode/general/tests/test_bids_spreadsheet2participants.m
================================================
% requires:
% - moxunit: https://github.com/MOxUnit/MOxUnit
% - bids-matlab
addpath(fullfile(pwd, '..'));
input_file = fullfile(pwd, '..', 'input', 'spreadsheet_to_convert.xlsx');
files_out = bids_spreadsheet2participants(input_file, 'ignore', 'comment', 'export', pwd);
json_expected = jsonread(fullfile(pwd, 'data', 'participants.json'));
json_actual = jsonread(fullfile(pwd, 'participants.json'));
% uses moxunit assertEqual
assertEqual(json_actual, json_expected);
tsv_expected = bids.util.tsvread(fullfile(pwd, 'data', 'participants.tsv'));
tsv_actual = bids.util.tsvread(fullfile(pwd, 'participants.tsv'));
assertEqual(tsv_actual, tsv_expected);
================================================
FILE: matlabCode/ieeg/createBIDS_channels_tsv.m
================================================
%% Template Matlab script to create an BIDS compatible electrodes.tsv file
% This example lists all required and optional fields.
% When adding additional metadata please use CamelCase
%
% DHermes, 2017
% modified Jaap van der Aar 30.11.18
% Writing json files relies on the JSONio library
% https://github.com/bids-standard/bids-matlab
%
% Make sure it is in the matab/octave path
try
bids.bids_matlab_version;
catch
warning('%s\n%s\n%s\n%s', ...
'Writing the JSON file seems to have failed.', ...
'Make sure that the following library is in the matlab/octave path:', ...
'https://github.com/bids-standard/bids-matlab');
end
%%
clear;
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project = 'templates';
sub_label = '01';
ses_label = '01';
task_label = 'LongExample';
run_label = '01';
name_spec.modality = 'ieeg';
name_spec.suffix = 'channels';
name_spec.ext = '.tsv';
name_spec.entities = struct('sub', sub_label, ...
'ses', ses_label, ...
'task', task_label, ...
'run', run_label);
% using the 'use_schema', true
% ensures that the entities will be in the correct order
bids_file = bids.File(name_spec, 'use_schema', true);
% Contrust the fullpath version of the filename
channels_tsv_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.filename);
%% make a participants table and save
%% required columns
name = {'n/a'}; % Label of the channel, only contains letters and numbers. The label must
% correspond to _electrodes.tsv name and all ieeg type channels are required to have \
% a position. The reference channel name MUST be provided in the reference column
type = {'n/a'}; % Type of channel, see below for adequate keywords in this field
units = {'n/a'}; % Physical unit of the value represented in this channel, for example: V for Volt,
% specified according to the SI unit symbol and possibly prefix symbol (for example: mV, ?V),
% see the BIDS spec (section 15 Appendix V: Units) for guidelines for Units and Prefixes.
low_cutoff = [0]; % Frequencies used for the low pass filter applied to the
% channel in Hz. If no low pass filter was applied, use n/a. Note that
% anti-alias is a low pass filter, specify its frequencies here if applicable.
high_cutoff = [0]; % Frequencies used for the high pass filter applied to
% the channel in Hz. If no high pass filter applied, use n/a.
%% recommended columns:
reference = {'n/a'}; % Specification of the reference (for example: "mastoid", "ElectrodeName01",
% "intracranial", "CAR", "other", "n/a"). If the channel is not an electrode channel
% (for example: a microphone channel) use `n/a`.
group = {'n/a'}; % Which group of channels (grid/strip/probe) this channel belongs to.
% One group has one wire and noise can be shared. This can be a name or number.
% Note that any groups specified in `_electrodes.tsv` must match those present here.
%% optional columns
sampling_frequency = [0]; % Sampling rate of the channel in Hz.
description = {'n/a'}; % Brief free-text description of the channel, or other information of
% interest (for example: position (for example: 'left lateral temporal surface', 'unipolar/bipolar', etc.)).
notch = [0]; % Frequencies used for the notch filter applied to the channel,
% in Hz. If no notch filter applied, use n/a.
status = {'bad'}; % Data quality observed on the channel (good/bad). A channel is considered bad
% if its data quality is compromised by excessive noise. Description of noise type SHOULD be
% provided in [status_description].
status_description = {'n/a'}; % Freeform text description of noise or artifact affecting data
% quality on the channel. It is meant to explain why the channel was declared bad in [status].
%% write
t = table(name, type, units, low_cutoff, high_cutoff, reference, ...
group, sampling_frequency, description, notch, status, status_description);
writetable(t, channels_tsv_name, 'FileType', 'text', 'Delimiter', '\t');
================================================
FILE: matlabCode/ieeg/createBIDS_coordsystem_json.m
================================================
%% Template Matlab script to create an BIDS compatible _electrodes.json file
% For BIDS-iEEG
% This example lists all required and optional fields.
% When adding additional metadata please use CamelCase
%
% DHermes, 2017
% modified Jaap van der Aar 30.11.18
% Writing json files relies on the JSONio library
% https://github.com/bids-standard/bids-matlab
%
% Make sure it is in the matab/octave path
try
bids.bids_matlab_version;
catch
warning('%s\n%s\n%s\n%s', ...
'Writing the JSON file seems to have failed.', ...
'Make sure that the following library is in the matlab/octave path:', ...
'https://github.com/bids-standard/bids-matlab');
end
%%
clear;
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project = 'templates';
sub_label = '01';
ses_label = '01';
name_spec.modality = 'ieeg';
name_spec.suffix = 'coordsystem';
name_spec.ext = '.json';
name_spec.entities = struct('sub', sub_label, ...
'ses', ses_label);
% using the 'use_schema', true
% ensures that the entities will be in the correct order
bids_file = bids.File(name_spec, 'use_schema', true);
% Contrust the fullpath version of the filename
json_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.filename);
%% Adding metadata
% Assign the fields in the Matlab structure that can be saved as a json.
% The following fields must be defined:
% to get the definition of each metadata,
% you can use the bids.Schema class from bids matlab
% For example
schema = bids.Schema;
def = schema.get_definition('iEEGCoordinateSystem');
fprintf(def.description);
%% Required fields
json.iEEGCoordinateSystem = '';
json.iEEGCoordinateUnits = '';
%% Recommended fields
json.iEEGCoordinateProcessingDescripton = '';
json.IndendedFor = '';
json.iEEGCoordinateProcessingDescription = '';
json.iEEGCoordinateProcessingReference = '';
%% Write JSON
% Make sure the directory exists
bids.util.mkdir(fileparts(json_name));
bids.util.jsonencode(json_name, json);
================================================
FILE: matlabCode/ieeg/createBIDS_data_WriteBrainVisionWithFieldtrip.m
================================================
% %%%%% save data as BrainVision BIDS %%%%%
%
% Sample script that calls Fieldtrip functions to write a Brainvision dataset
% Added fields are examples, read these from the raw data
%
% Fieldtrip has to be in the path!
%
% D. Hermes 2018
% provide necessary labels and path to save the data:
dataRootPath = '';
sub_label = '01';
ses_label = '01';
task_label = 'visual';
run_label = '01';
% name to save data:
ieeg_name_save = fullfile(dataRootPath, ['sub-' sub_label], ['ses-' ses_label], 'ieeg', ...
['sub-' sub_label...
'_ses-' ses_label...
'_task-' task_label...
'_run-' run_label ...
'_ieeg']);
%%%% assign header fields:
% sampling frequency
dataStruct.hdr.Fs = 1000;
dataStruct.hdr.nChans = 128;
% number of channels
dataStruct.hdr.label = cell(dataStruct.hdr.nChans, 1);
for kk = 1:dataStruct.hdr.nChans
dataStruct.hdr.label{kk} = ['iEEG' int2str(kk)];
end
% number of samples
dataStruct.hdr.nSamples = 10000;
% ?
dataStruct.hdr.nSamplesPre = 0;
% 1 trial for continuous data
dataStruct.hdr.nTrials = 1;
% channels type, see BIDS list of types
dataStruct.hdr.chantype = cell(dataStruct.hdr.nChans, 1);
for kk = 1:dataStruct.hdr.nChans
dataStruct.hdr.chantype{kk} = ['ECOG'];
end
% I still don't how to indicate the mu in BIDS, now using letter u
dataStruct.hdr.chanunit = repmat({'uV'}, size(d.data, 2), 1);
% labels again, same as before
dataStruct.label = dataStruct.hdr.label;
% time vector
dataStruct.time{1} = [1:dataStruct.hdr.nSamples] / dataStruct.hdr.Fs;
% put the data matrix here: electrodes x samples
dataStruct.trial{1} = data;
% sampling freq again, same as before
dataStruct.fsample = dataStruct.hdr.Fs;
% ?
dataStruct.sampleinfo = [1 dataStruct.hdr.nSamples];
% now fetch a header
hdr_data = ft_fetch_header(dataStruct);
% save the data
ft_write_data(ieeg_name_save, dataStruct.trial{1}, 'header', hdr_data, 'dataformat', 'brainvision_eeg');
================================================
FILE: matlabCode/ieeg/createBIDS_electrodes_tsv.m
================================================
%% Template Matlab script to create an BIDS compatible electrodes.tsv file
% This example lists all required and optional fields.
% When adding additional metadata please use CamelCase
%
% DHermes, 2017
% modified Giulio Castegnaro 201811
% Writing json files relies on the JSONio library
% https://github.com/bids-standard/bids-matlab
%
% Make sure it is in the matab/octave path
try
bids.bids_matlab_version;
catch
warning('%s\n%s\n%s\n%s', ...
'Writing the JSON file seems to have failed.', ...
'Make sure that the following library is in the matlab/octave path:', ...
'https://github.com/bids-standard/bids-matlab');
end
%%
clear;
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project = 'templates';
sub_label = '01';
ses_label = '01';
name_spec.modality = 'ieeg';
name_spec.suffix = 'electrodes';
name_spec.ext = '.tsv';
name_spec.entities = struct('sub', sub_label, ...
'ses', ses_label);
% using the 'use_schema', true
% ensures that the entities will be in the correct order
bids_file = bids.File(name_spec, 'use_schema', true);
% Contrust the fullpath version of the filename
electrodes_tsv_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.filename);
%% make a participants table and save
% to get the definition of each column,
% you can use the bids.Schema class from bids matlab
% For example
schema = bids.Schema;
def = schema.get_definition('size');
fprintf(def.description);
%% required columns
tsv.name = {'n/a'};
tsv.x = 0;
tsv.y = 0;
tsv.z = 0;
tsv.size = 0;
%% recommended columns
tsv.material = {'n/a'};
tsv.manufacturer = {'n/a'};
tsv.group = {'n/a'};
tsv.hemisphere = {'n/a'};
%% optional columns
tsv.type = {'n/a'};
tsv.impedance = nan;
%% write
bids.util.tsvwrite(electrodes_tsv_name, tsv);
================================================
FILE: matlabCode/ieeg/createBIDS_ieeg_json.m
================================================
%% Template Matlab script to create an BIDS compatible _ieeg.json file
% This example lists all required and optional fields.
% When adding additional metadata please use CamelCase
%
% DHermes, 2017
% modified Jaap van der Aar & Giulio Castegnaro 30.11.18
% Writing json files relies on the JSONio library
% https://github.com/bids-standard/bids-matlab
%
% Make sure it is in the matab/octave path
try
bids.bids_matlab_version;
catch
warning('%s\n%s\n%s\n%s', ...
'Writing the JSON file seems to have failed.', ...
'Make sure that the following library is in the matlab/octave path:', ...
'https://github.com/bids-standard/bids-matlab');
end
%%
clear;
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project = 'templates';
sub_label = '01';
ses_label = '01';
task_label = 'LongExample';
run_label = '01';
name_spec.modality = 'ieeg';
name_spec.suffix = 'ieeg';
name_spec.ext = '.json';
name_spec.entities = struct('sub', sub_label, ...
'ses', ses_label, ...
'task', task_label, ...
'run', run_label);
% using the 'use_schema', true
% ensures that the entities will be in the correct order
bids_file = bids.File(name_spec, 'use_schema', true);
% Contrust the fullpath version of the filename
json_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.filename);
%% General fields, shared with MRI BIDS and MEG BIDS
% to get the definition of each column,
% you can use the bids.Schema class from bids matlab
% For example
schema = bids.Schema;
def = schema.get_definition('TaskName');
fprintf(def.description);
%% Required fields:
json.TaskName = task_label;
json.SamplingFrequency = [];
json.PowerLineFrequency = [];
json.SoftwareFilters = '';
%% Recommended fields:
HardwareFilters.HighpassFilter.CutoffFrequency = [];
HardwareFilters.LowpassFilter.CutoffFrequency = [];
json.HardwareFilters = HardwareFilters; %
json.Manufacturer = '';
json.ManufacturersModelName = '';
json.TaskDescription = '';
json.Instructions = '';
json.CogAtlasID = 'https://www.cognitiveatlas.org/FIXME';
json.CogPOID = 'http://www.cogpo.org/ontologies/CogPOver1.owl#FIXME';
json.InstitutionName = '';
json.InstitutionAddress = '';
json.DeviceSerialNumber = '';
json.ECOGChannelCount = [];
json.SEEGChannelCount = [];
json.EEGChannelCount = [];
json.EOGChannelCount = [];
json.ECGChannelCount = [];
json.EMGChannelCount = [];
json.MiscChannelCount = [];
json.TriggerChannelCount = [];
json.RecordingDuration = [];
json.RecordingType = '';
json.EpochLength = [];
json.SubjectArtefactDescription = '';
json.SoftwareVersions = '';
%% Specific iEEG fields:
% If mixed types of references, manufacturers or electrodes are used, please
% specify in the corresponding table in the _electrodes.tsv file
%% Required fields:
json.iEEGReference = '';
%% Recommended fields:
json.ElectrodeManufacturer = '';
json.ElectrodeManufacturersModelName = '';
json.iEEGGround = '';
json.iEEGPlacementScheme = '';
json.iEEGElectrodeGroups = '';
%% Optional fields:
json.ElectricalStimulation = '';
json.ElectricalStimulationParameters = '';
%% Write JSON
% Make sure the directory exists
bids.util.mkdir(fileparts(json_name));
bids.util.jsonencode(json_name, json);
================================================
FILE: matlabCode/micr/createBIDS_micr_json_full.m
================================================
%% Template Matlab script to create an BIDS compatible _bold.json file
% This example lists all required and optional fields.
% When adding additional metadata please use CamelCase
% Use version of DICOM ontology terms whenever possible.
%
% DHermes, 2017
% Writing json files relies on the JSONio library
% https://github.com/bids-standard/bids-matlab
%
% Make sure it is in the matab/octave path
try
bids.bids_matlab_version;
catch
warning('%s\n%s\n%s\n%s', ...
'Writing the JSON file seems to have failed.', ...
'Make sure that the following library is in the matlab/octave path:', ...
'https://github.com/bids-standard/bids-matlab');
end
%%
clear;
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project = 'templates';
sub_label = '01';
ses_label = '01';
sample_label = '01';
chunk_label = '01';
stain_label = '03';
acq_label = 'Short';
name_spec.modality = 'micr';
name_spec.suffix = 'SEM';
name_spec.ext = '.json';
name_spec.entities = struct('sub', sub_label, ...
'sample', sample_label, ...
'stain', stain_label, ...
'acq', acq_label, ...
'ses', ses_label, ...
'chunk', chunk_label);
% using the 'use_schema'; true
% ensures that the entities will be in the correct order
bids_file = bids.File(name_spec, 'use_schema', true);
% Contrust the fullpath version of the filename
json_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.filename);
%% Adding metadata
% to get the definition of each metadata,
% you can use the bids.Schema class from bids matlab
% For example
schema = bids.Schema;
def = schema.get_definition('Manufacturer');
fprintf(def.description);
% Image Acquisition
json.PixelSize = 'REQUIRED';
json.PixelSizeUnits = 'REQUIRED';
%% Write JSON
% Make sure the directory exists
bids.util.mkdir(fileparts(json_name));
bids.util.jsonencode(json_name, json);
================================================
FILE: matlabCode/micr/createBIDS_micr_json_short.m
================================================
%% Template Matlab script to create an BIDS compatible _bold.json file
% This example lists all required and optional fields.
% When adding additional metadata please use CamelCase
% Use version of DICOM ontology terms whenever possible.
%
% DHermes, 2017
% Writing json files relies on the JSONio library
% https://github.com/bids-standard/bids-matlab
%
% Make sure it is in the matab/octave path
try
bids.bids_matlab_version;
catch
warning('%s\n%s\n%s\n%s', ...
'Writing the JSON file seems to have failed.', ...
'Make sure that the following library is in the matlab/octave path:', ...
'https://github.com/bids-standard/bids-matlab');
end
%%
clear;
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project = 'templates';
sub_label = '01';
ses_label = '01';
sample_label = '01';
chunk_label = '01';
stain_label = '03';
acq_label = 'Full';
name_spec.modality = 'micr';
name_spec.suffix = 'SEM';
name_spec.ext = '.json';
name_spec.entities = struct('sub', sub_label, ...
'sample', sample_label, ...
'stain', stain_label, ...
'acq', acq_label, ...
'ses', ses_label, ...
'chunk', chunk_label);
% using the 'use_schema'; true
% ensures that the entities will be in the correct order
bids_file = bids.File(name_spec, 'use_schema', true);
% Contrust the fullpath version of the filename
json_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.filename);
%% Adding metadata
% to get the definition of each metadata,
% you can use the bids.Schema class from bids matlab
% For example
schema = bids.Schema;
def = schema.get_definition('Manufacturer');
fprintf(def.description);
% Device Hardware
json.Manufacturer = 'RECOMMENDED';
json.ManufacturersModelName = 'RECOMMENDED';
json.DeviceSerialNumber = 'RECOMMENDED';
json.StationName = 'RECOMMENDED';
json.SoftwareVersions = 'RECOMMENDED';
json.InstitutionName = 'RECOMMENDED';
json.InstitutionAddress = 'RECOMMENDED';
json.InstitutionalDepartmentName = 'RECOMMENDED';
% Image Acquisition
json.PixelSize = 'REQUIRED';
json.PixelSizeUnits = 'REQUIRED';
json.Immersion = 'OPTIONAL';
json.NumericalAperture = 'OPTIONAL';
json.Magnification = 'OPTIONAL';
json.ImageAcquisitionProtocol = 'OPTIONAL';
json.OtherAcquisitionParameters = 'OPTIONAL';
% Sample
json.BodyPart = 'RECOMMENDED';
json.BodyPartDetails = 'RECOMMENDED';
json.SampleEnvironment = 'RECOMMENDED';
json.SampleStaining = 'RECOMMENDED';
json.SamplePrimaryAntibody = 'RECOMMENDED';
json.SampleSecondaryAntibody = 'RECOMMENDED';
json.BodyPartDetailsOntology = 'OPTIONAL';
json.SampleEmbedding = 'OPTIONAL';
json.SampleFixation = 'OPTIONAL';
json.SliceThickness = 'OPTIONAL';
json.TissueDeformationScaling = 'OPTIONAL';
json.SampleExtractionProtocol = 'OPTIONAL';
json.SampleExtractionInstitution = 'OPTIONAL';
% Chunk
json.ChunkTransformationMatrix = 'RECOMMENDED if <chunk-index> is used in filenames';
json.ChunkTransformationMatrixAxis = 'REQUIRED if ChunkTransformationMatrix is present';
%% Write JSON
% Make sure the directory exists
bids.util.mkdir(fileparts(json_name));
bids.util.jsonencode(json_name, json);
================================================
FILE: matlabCode/miss_hit.cfg
================================================
# styly guide (https://florianschanda.github.io/miss_hit/style_checker.html)
line_length: 120
regex_function_name: "[a-zA-Z0-9]+(_[a-zA-Z0-9]+)*"
regex_parameter_name: "[a-z]+(_[a-z]+)*"
regex_script_name: "[a-zA-Z0-9]+(_[a-zA-Z0-9]+)*"
tab_width: 4
suppress_rule: "copyright_notice"
# metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
metric "cnest": limit 7
metric "file_length": limit 400
metric "cyc": limit 70
metric "parameters": limit 6
================================================
FILE: matlabCode/pet/createBIDS_blood_auto_tsv_and_json_short.m
================================================
% Template Matlab script to create a BIDS compatible:
%
% sub-01_ses-01_recording-AutosamplerShortExample_blood.tsv
% sub-01_ses-01_recording-AutosamplerShortExample_blood.json
%
% This example lists all REQUIRED, RECOMMENDED and OPTIONAL fields.
% Writing json files relies on the JSONio library
% https://github.com/bids-standard/bids-matlab
%
% Make sure it is in the matab/octave path
try
bids.bids_matlab_version;
catch
warning('%s\n%s\n%s\n%s', ...
'Writing the JSON file seems to have failed.', ...
'Make sure that the following library is in the matlab/octave path:', ...
'https://github.com/bids-standard/bids-matlab');
end
clear;
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project = 'templates';
sub_label = '01';
ses_label = '01';
recording_label = 'AutosamplerShortExample';
name_spec.modality = 'pet';
name_spec.suffix = 'blood';
name_spec.ext = '.tsv';
name_spec.entities = struct('sub', sub_label, ...
'ses', ses_label, ...
'recording', recording_label);
% using the 'use_schema', true
% ensures that the entities will be in the correct order
bids_file = bids.File(name_spec, 'use_schema', true);
% Contrust the fullpath version of the filename
tsv_file_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.filename);
json_file_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.json_filename);
%% Write TSV
tsv.time = 0;
tsv.whole_blood_radioactivity = 0;
bids.util.tsvwrite(tsv_file_name, tsv);
%% Write JSON
% this makes the json look prettier when opened in a txt editor
json.PlasmaAvail = false;
json.WholeBloodAvail = true;
json.MetaboliteMethod = false;
json.DispersionCorrected = false;
% get the definition of each column,
% use the bids.Schema class from bids matlab
schema = bids.Schema;
def = schema.get_definition('time');
json.time.Description = def.description;
json.time.Unit = def.unit;
def = schema.get_definition('whole_blood_radioactivity');
json.whole_blood_radioactivity.Description = def.description;
json.whole_blood_radioactivity.Unit = def.unit;
%% Write JSON
% Make sure the directory exists
bids.util.mkdir(fileparts(json_file_name));
bids.util.jsonencode(json_file_name, json);
================================================
FILE: matlabCode/pet/createBIDS_blood_manual_tsv_and_json_full.m
================================================
% Template Matlab script to create a BIDS compatible:
%
% sub-01_ses-01_recording-ManualFullExample_blood.tsv
% sub-01_ses-01_recording-ManualFullExample_blood.json
%
% This example lists all REQUIRED, RECOMMENDED and OPTIONAL fields.
% Writing json files relies on the JSONio library
% https://github.com/bids-standard/bids-matlab
%
% Make sure it is in the matab/octave path
try
bids.bids_matlab_version;
catch
warning('%s\n%s\n%s\n%s', ...
'Writing the JSON file seems to have failed.', ...
'Make sure that the following library is in the matlab/octave path:', ...
'https://github.com/bids-standard/bids-matlab');
end
clear;
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project = 'templates';
sub_label = '01';
ses_label = '01';
recording_label = 'ManualFullExample';
name_spec.modality = 'pet';
name_spec.suffix = 'blood';
name_spec.ext = '.tsv';
name_spec.entities = struct('sub', sub_label, ...
'ses', ses_label, ...
'recording', recording_label);
% using the 'use_schema', true
% ensures that the entities will be in the correct order
bids_file = bids.File(name_spec, 'use_schema', true);
% Contrust the fullpath version of the filename
tsv_file_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.filename);
json_file_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.json_filename);
%% Write TSV
tsv.time = 0;
tsv.plasma_radioactivity = 0;
tsv.metabolite_parent_fraction = 0;
tsv.metabolite_polar_fraction = 0;
tsv.hplc_recovery_fractions = 0;
tsv.whole_blood_radioactivity = 0;
bids.util.tsvwrite(tsv_file_name, tsv);
%% Write JSON
json.PlasmaAvail = '';
json.MetaboliteAvail = '';
json.WholeBloodAvail = '';
json.DispersionCorrected = '';
json.WithdrawalRate = '';
json.TubingType = '';
json.TubingLength = '';
json.DispersionConstant = '';
json.Haematocrit = '';
json.BloodDensity = '';
json.PlasmaFreeFraction = '';
json.PlasmaFreeFractionMethod = '';
json.MetaboliteMethod = '';
json.MetaboliteRecoveryCorrectionApplied = '';
% get the definition of several columns,
% use the bids.Schema class from bids matlab
schema = bids.Schema;
columns = {'time'
'plasma_radioactivity'
'metabolite_parent_fraction'
'metabolite_polar_fraction'
'hplc_recovery_fractions'
'whole_blood_radioactivity'};
for i = 1:numel(columns)
def = schema.get_definition(columns{i});
json.(columns{i}).Description = def.description;
if isfield(def, 'unit')
json.(columns{i}).Unit = def.unit;
end
end
json.plasma_radioactivity.unit = 'kBq/ml';
json.whole_blood_radioactivity.unit = 'kBq/ml';
json.metabolite_parent_fraction.unit = 'unitless';
json.metabolite_polar_fraction.unit = 'unitless';
%% Write JSON
% Make sure the directory exists
bids.util.mkdir(fileparts(json_file_name));
bids.util.jsonencode(json_file_name, json);
================================================
FILE: matlabCode/pet/createBIDS_blood_manual_tsv_and_json_short.m
================================================
% Template Matlab script to create a BIDS compatible:
%
% sub-01_ses-01_recording-ManualFullExample_blood.tsv
% sub-01_ses-01_recording-ManualFullExample_blood.json
%
% This example lists all REQUIRED, RECOMMENDED and OPTIONAL fields.
% Writing json files relies on the JSONio library
% https://github.com/bids-standard/bids-matlab
%
% Make sure it is in the matab/octave path
try
bids.bids_matlab_version;
catch
warning('%s\n%s\n%s\n%s', ...
'Writing the JSON file seems to have failed.', ...
'Make sure that the following library is in the matlab/octave path:', ...
'https://github.com/bids-standard/bids-matlab');
end
clear;
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project = 'templates';
sub_label = '01';
ses_label = '01';
recording_label = 'ManualShortExample';
name_spec.modality = 'pet';
name_spec.suffix = 'blood';
name_spec.ext = '.tsv';
name_spec.entities = struct('sub', sub_label, ...
'ses', ses_label, ...
'recording', recording_label);
% using the 'use_schema', true
% ensures that the entities will be in the correct order
bids_file = bids.File(name_spec, 'use_schema', true);
% Contrust the fullpath version of the filename
tsv_file_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.filename);
json_file_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.json_filename);
%% Write TSV
tsv.time = 0;
tsv.metabolite_parent_fraction = 0;
bids.util.tsvwrite(tsv_file_name, tsv);
%% Write JSON
% get the definition of each column,
% use the bids.Schema class from bids matlab
% example:
%
% schema = bids.Schema;
% def = schema.get_definition('metabolite_parent_fraction');
json.PlasmaAvail = '';
json.MetaboliteAvail = '';
json.WholeBloodAvail = '';
json.DispersionCorrected = '';
json.MetaboliteMethod = '';
json.MetaboliteRecoveryCorrectionApplied = '';
json.time = struct('Description', ...
'Time in relation to time zero defined by the _pet.json', ...
'Units', 's');
json.metabolite_parent_fraction = struct('Description', ...
'Parent fraction of the radiotracer.', ...
'Units', 'unitless');
%% Write JSON
% Make sure the directory exists
bids.util.mkdir(fileparts(json_file_name));
bids.util.jsonencode(json_file_name, json);
================================================
FILE: matlabCode/pet/createBIDS_pet_json_full.m
================================================
% Template Matlab script to create a BIDS compatible:
%
% sub-01_ses-01_task-FullExample_pet.json
%
% This example lists all REQUIRED, RECOMMENDED and OPTIONAL fields.
% Writing json files relies on the JSONio library
% https://github.com/bids-standard/bids-matlab
%
% Make sure it is in the matab/octave path
try
bids.bids_matlab_version;
catch
warning('%s\n%s\n%s\n%s', ...
'Writing the JSON file seems to have failed.', ...
'Make sure that the following library is in the matlab/octave path:', ...
'https://github.com/bids-standard/bids-matlab');
end
clear;
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project = 'templates';
sub_label = '01';
ses_label = '01';
task_label = 'FullExample';
name_spec.modality = 'pet';
name_spec.suffix = 'pet';
name_spec.ext = '.json';
name_spec.entities = struct('sub', sub_label, ...
'ses', ses_label, ...
'task', task_label);
% using the 'use_schema', true
% ensures that the entities will be in the correct order
bids_file = bids.File(name_spec, 'use_schema', true);
% Contrust the fullpath version of the filename
json_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.filename);
% get the definition of each column,
% use the bids.Schema class from bids matlab
% example:
%
% schema = bids.Schema;
% def = schema.get_definition('TaskName');
json.TaskName = task_label;
json.Manufacturer = '';
json.ManufacturersModelName = '';
json.Units = '';
json.InstitutionName = '';
json.InstitutionAddress = '';
json.InstitutionalDepartmentName = '';
json.BodyPart = '';
json.TracerName = '';
json.TracerRadionuclide = '';
json.InjectedRadioactivity = '';
json.InjectedRadioactivityUnits = '';
json.InjectedMass = '';
json.InjectedMassUnits = '';
json.SpecificRadioactivity = '';
json.SpecificRadioactivityUnits = '';
json.ModeOfAdministration = '';
json.TracerRadLex = '';
json.TracerSNOMED = '';
json.TracerMolecularWeight = '';
json.TracerMolecularUnits = '';
json.InjectedMassPerWeight = '';
json.InjectedMassPerWeightUnits = '';
json.SpecificRadioactivityMeasTime = '';
json.MolarActivity = '';
json.MolarActivityUnits = '';
json.MolarActivityMeasTime = '';
json.InfusionRadioActivity = '';
json.InfusionStart = '';
json.InfusionSpeed = '';
json.InfusionSpeedUnits = '';
json.InjectedVolume = '';
json.Purity = '';
json.PharamceuticalName = '';
json.PharmaceuticalDoseAmount = [];
json.PharmaceuticalDoseUnits = '';
json.PharmaceuticalDoseRegimen = '';
json.PharmaceuticalDoseTime = [];
json.Anaesthesia = '';
json.TimeZero = '';
json.ScanStart = '';
json.InjectionStart = '';
json.FrameTimesStart = [];
json.FrameDuration = [];
json.ScanDate = '';
json.InjectionEnd = '';
json.AcquisitionMode = '';
json.ImageDecayCorrected = '';
json.ImageDecayCorrectionTime = '';
json.ReconMethodName = '';
json.ReconMethodParameterLabels = [];
json.ReconMethodParameterUnits = [];
json.ReconMethodParameterValues = [];
json.ReconFilterType = [];
json.ReconFilterSize = [];
json.AttenuationCorrection = '';
json.ReconMethodImplementationVersion = '';
json.AttenuationCorrectionMethodReference = '';
json.ScaleFactor = [];
json.ScatterFraction = [];
json.DecayCorrectionFactor = [];
json.PromptRate = [];
json.RandomRate = [];
json.SinglesRate = [];
%% Write JSON
% Make sure the directory exists
bids.util.mkdir(fileparts(json_name));
bids.util.jsonencode(json_name, json);
================================================
FILE: matlabCode/pet/createBIDS_pet_json_short.m
================================================
% Template Matlab script to create a BIDS compatible:
%
% sub-01_ses-01_task-ShortExample_pet.json
%
% This example lists all REQUIRED fields.
% Writing json files relies on the JSONio library
% https://github.com/bids-standard/bids-matlab
%
% Make sure it is in the matab/octave path
try
bids.bids_matlab_version;
catch
warning('%s\n%s\n%s\n%s', ...
'Writing the JSON file seems to have failed.', ...
'Make sure that the following library is in the matlab/octave path:', ...
'https://github.com/bids-standard/bids-matlab');
end
clear;
this_dir = fileparts(mfilename('fullpath'));
root_dir = fullfile(this_dir, '..', filesep, '..');
project = 'templates';
sub_label = '01';
ses_label = '01';
task_label = 'ShortExample';
name_spec.modality = 'pet';
name_spec.suffix = 'pet';
name_spec.ext = '.json';
name_spec.entities = struct('sub', sub_label, ...
'ses', ses_label, ...
'task', task_label);
% using the 'use_schema', true
% ensures that the entities will be in the correct order
bids_file = bids.File(name_spec, 'use_schema', true);
% Contrust the fullpath version of the filename
json_name = fullfile(root_dir, project, bids_file.bids_path, bids_file.filename);
% get the definition of each column,
% use the bids.Schema class from bids matlab
% example:
%
% schema = bids.Schema;
% def = schema.get_definition('TaskName');
json.TaskName = task_label;
json.Manufacturer = '';
json.ManufacturersModelName = '';
json.Units = '';
json.TracerName = '';
json.TracerRadionuclide = '';
json.InjectedRadioactivity = '';
json.InjectedRadioactivityUnits = '';
json.InjectedMass = '';
json.InjectedMassUnits = '';
json.SpecificRadioactivity = '';
json.SpecificRadioactivityUnits = '';
json.ModeOfAdministration = '';
json.TimeZero = '';
json.ScanStart = '';
json.InjectionStart = '';
json.FrameTimesStart = [];
json.FrameDuration = [];
json.AcquisitionMode = '';
json.ImageDecayCorrected = '';
json.ImageDecayCorrectionTime = '';
json.ReconMethodName = '';
json.ReconMethodParameterLabels = [];
json.ReconMethodParameterUnits = [];
json.ReconMethodParameterValues = [];
json.ReconFilterType = [];
json.ReconFilterSize = [];
json.AttenuationCorrection = '';
%% Write JSON
% Make sure the directory exists
bids.util.mkdir(fileparts(json_name));
bids.util.jsonencode(json_name, json);
================================================
FILE: pythonCode/createBIDS_MP2RAGE_json.py
================================================
"""
WARNING:
This script was created in October 2018 when the specification
for MP2RAGE files was not fully finalized. Please double check with
latest version of the specs to make sure this is accurate.
This script will create the JSON files required for an MP2RAGE file.
To function it requires a BIDS data set with properly named image files:
The script will go through all the folders of a BIDS data set and will create
the JSON files in every folder where it finds a file ending
with '_inv-1_part-mag_MPRAGE.nii.gz'.
Created by RG 2018-10-03
"""
import glob
import json
import os
from collections import OrderedDict
start_dir = "" # insert here path to your BIDS data set
# DEFINE CONTENT OF JSON FILES
# defining the content of the JSON file for the
# first inversion image (sub-*_inv-1_MPRAGE.json)
data_inv_1 = OrderedDict([("InversionTime", "900"), ("FlipAngle", "5")]) # ms
# defining the content of the JSON file for the
# second inversion image (sub-*_inv-2_MPRAGE.json)
data_inv_2 = OrderedDict([("InversionTime", "2750"), ("FlipAngle", "3")]) # ms
# defining the content of the JSON files for the
# T1w (sub-*_T1w.json) and the T1map (sub-*_T1map.json)
data_T1 = OrderedDict(
[
("EstimationMethod", "Marques et al., 2013"),
]
)
# defining the content of the main JSON file (sub-*_MPRAGE.json)
data_MP2RAGE = OrderedDict(
[
("MagneticFieldStrength", ""),
("ExcitationRepetitionTime", ""),
("InversionRepetitionTime", ""),
("NumberShots", ""),
("Manufacturer", ""),
("ManufacturersModelName", ""),
("DeviceSerialNumber", ""),
("SoftwareVersions", ""),
("StationName", ""),
("InstitutionName", ""),
("InstitutionAddress", ""),
("InstitutionalDepartmentName", ""),
("ReceiveCoilName", ""),
("ReceiveCoilActiveElements", ""),
("GradientSetType", ""),
("MRTransmitCoilSequence", ""),
("MatrixCoilMode", ""),
("CoilCombinationMethod", ""),
("NonlinearGradientCorrection", ""),
("WaterFatShift", ""),
("EchoTrainLength", ""),
("DwellTime", ""),
("MultibandAccelerationFactor", ""),
("AnatomicalLandmarkCoordinates", ""),
("MRAcquisitionType", ""),
("ScanningSequence", ""),
("SequenceVariant", ""),
("ScanOptions", ""),
("SequenceName", ""),
("PulseSequenceType", "MP2RAGE"),
("PulseSequenceDetails", ""),
("ParallelReductionFactorInPlane", ""),
("ParallelAcquisitionTechnique", ""),
("PartialFourier", ""),
("PartialFourierDirection", ""),
("EffectiveEchoSpacing", ""),
("TotalReadoutTime", ""),
("PhaseEncodingDirection", ""),
("EchoTime1", ""), # sec
("EchoTime2", ""), # sec
("SliceThickness", ""), # mm
]
)
# WRITE THEM
indent = 4
# list all subjects and create iterator with full path for subjects folder
file_ls = glob.glob(
os.path.join(start_dir, "sub*", "**", "*_inv-1_part-mag_MPRAGE.nii.gz"),
recursive=True,
)
for f in file_ls:
# creates the json files in the folder where the magnitude image
# of the first inversion is found
path, fname = os.path.split(f)
# define filename, excluding last three key-value pairs
sid = "_".join(fname.split("_")[:-3])
# adding content to JSON files for the T1w and T1map
# as its content is subject dependent
inv1_mag = os.path.join("anat", f"{sid}_inv1_part-mag_MPRAGE.nii.gz")
inv1_phs = os.path.join("anat", f"{sid}_inv1_part-phase_MPRAGE.nii.gz")
inv2_mag = os.path.join("anat", f"{sid}_inv2_part-mag_MPRAGE.nii.gz")
inv2_phs = os.path.join("anat", f"{sid}_inv2_part-phase_MPRAGE.nii.gz")
data_T1["BasedOn"] = f"{inv1_mag}, {inv1_phs}, {inv2_mag}, {inv2_phs}, "
# define json files for all image types
json_names = [
"{}_inv-1_MPRAGE.json",
"{}_inv-2_MPRAGE.json",
"{}_MPRAGE.json",
"{}_T1map.json",
"{}_T1w.json",
]
data_types = [data_inv_1, data_inv_2, data_MP2RAGE, data_T1, data_T1]
out_files = zip(json_names, data_types)
for out_file in out_files:
json_name, data_type = out_file[0], out_file[1]
with open(os.path.join(path, json_name.format(sid)), "w") as ff:
json.dump(data_type, ff, sort_keys=False, indent=indent)
================================================
FILE: pythonCode/createBIDS_dataset_description_json.py
================================================
import json
from collections import OrderedDict
data = OrderedDict()
# General fields, shared with MRI BIDS and MEG BIDS:
# Required fields:
# name of the dataset
data["Name"] = ""
# The version of the BIDS standard that was used
data["BIDSVersion"] = "1.0.2"
# Recommended fields:
# what license is this dataset distributed under?
# The use of license name abbreviations is suggested for specifying a license.
# A list of common licenses with suggested abbreviations can be found in appendix III.
data["License"] = ""
# List of individuals who con
gitextract_ajxyoq0h/
├── .all-contributorsrc
├── .github/
│ └── workflows/
│ └── deploy_book.yml
├── .gitignore
├── LICENSE
├── Makefile
├── README.md
├── interactiveTreeVisualization/
│ └── epilepsyClassification2017/
│ ├── tree.html
│ ├── treeData.js
│ ├── treeFunctions.js
│ └── treeStyle.css
├── matlabCode/
│ ├── anat/
│ │ ├── createBIDS_T1w_json_full.m
│ │ ├── createBIDS_T1w_json_full_schma_based.m
│ │ └── createBIDS_T1w_json_short.m
│ ├── eeg-meg/
│ │ ├── createBIDS_meg_json_full.m
│ │ ├── createBIDS_meg_json_short.m
│ │ └── rename_brainvision_files.m
│ ├── fmap/
│ │ └── createBIDS_fmap_json.m
│ ├── func/
│ │ ├── createBIDS_bold_json_full.m
│ │ └── createBIDS_bold_json_short.m
│ ├── general/
│ │ ├── README.md
│ │ ├── bids_spreadsheet2participants.m
│ │ ├── createBIDS_dataset_description_json.m
│ │ ├── createBIDS_events_tsv_json_full.m
│ │ ├── createBIDS_participants_tsv.m
│ │ ├── createBIDS_samples_tsv.m
│ │ ├── input/
│ │ │ └── spreadsheet_to_convert.xlsx
│ │ └── tests/
│ │ ├── data/
│ │ │ ├── participants.json
│ │ │ └── participants.tsv
│ │ └── test_bids_spreadsheet2participants.m
│ ├── ieeg/
│ │ ├── createBIDS_channels_tsv.m
│ │ ├── createBIDS_coordsystem_json.m
│ │ ├── createBIDS_data_WriteBrainVisionWithFieldtrip.m
│ │ ├── createBIDS_electrodes_tsv.m
│ │ └── createBIDS_ieeg_json.m
│ ├── micr/
│ │ ├── createBIDS_micr_json_full.m
│ │ └── createBIDS_micr_json_short.m
│ ├── miss_hit.cfg
│ └── pet/
│ ├── createBIDS_blood_auto_tsv_and_json_short.m
│ ├── createBIDS_blood_manual_tsv_and_json_full.m
│ ├── createBIDS_blood_manual_tsv_and_json_short.m
│ ├── createBIDS_pet_json_full.m
│ └── createBIDS_pet_json_short.m
├── pythonCode/
│ ├── createBIDS_MP2RAGE_json.py
│ └── createBIDS_dataset_description_json.py
├── reports/
│ └── Google-2018-report.md
├── src/
│ ├── CONTRIBUTING.md
│ ├── _config.yml
│ ├── _toc.yml
│ ├── epilepsy_phenotype.rst
│ ├── index.md
│ ├── references.bib
│ └── tree.html
└── templates/
├── participants.json
├── participants.tsv
├── phenotype/
│ ├── EpilepsyClassification.tsv
│ └── EpilepsyClassification2017.json
├── samples.json
├── samples.tsv
├── sub-01/
│ └── ses-01/
│ ├── anat/
│ │ ├── sub-01_ses-01_acq-FullExample_run-01_T1w.json
│ │ └── sub-01_ses-01_acq-ShortExample_run-01_T1w.json
│ ├── eeg/
│ │ ├── sub-01_ses-01_task-FilterExample_eeg.json
│ │ ├── sub-01_ses-01_task-FullExample_eeg.json
│ │ ├── sub-01_ses-01_task-MinimalExample_eeg.json
│ │ └── sub-01_ses-01_task-ReferenceExample_eeg.json
│ ├── fmap/
│ │ ├── sub-01_ses-01_acq-Case1_run-01_phasediff.json
│ │ ├── sub-01_ses-01_acq-Case2_run-01_phase1.json
│ │ ├── sub-01_ses-01_acq-Case2_run-01_phase2.json
│ │ ├── sub-01_ses-01_acq-Case3_run-01_fieldmap.json
│ │ └── sub-01_ses-01_acq-Case4_dir-LR_run-01_epi.json
│ ├── func/
│ │ ├── sub-01_ses-01_task-FullExample_run-01_bold.json
│ │ ├── sub-01_ses-01_task-FullExample_run-01_events.json
│ │ ├── sub-01_ses-01_task-FullExample_run-01_events.tsv
│ │ └── sub-01_ses-01_task-ShortExample_run-01_bold.json
│ ├── ieeg/
│ │ ├── sub-01_ses-01_coordsystem.json
│ │ ├── sub-01_ses-01_electrodes.tsv
│ │ ├── sub-01_ses-01_task-LongExample_run-01_channels.tsv
│ │ └── sub-01_ses-01_task-LongExample_run-01_ieeg.json
│ ├── meg/
│ │ ├── sub-01_ses-01_task-FullExample_acq-CTF_run-1_proc-sss_meg.json
│ │ └── sub-01_ses-01_task-ShortExample_acq-CTF_run-1_proc-sss_meg.json
│ ├── micr/
│ │ ├── sub-01_ses-01_sample-01_acq-Full_stain-03_chunk-01_SEM.json
│ │ └── sub-01_ses-01_sample-01_acq-Short_stain-03_chunk-01_SEM.json
│ └── pet/
│ ├── sub-01_ses-01_recording-AutosamplerShortExample_blood.json
│ ├── sub-01_ses-01_recording-AutosamplerShortExample_blood.tsv
│ ├── sub-01_ses-01_recording-ManualFullExample_blood.json
│ ├── sub-01_ses-01_recording-ManualFullExample_blood.tsv
│ ├── sub-01_ses-01_recording-ManualShortExample_blood.json
│ ├── sub-01_ses-01_recording-ManualShortExample_blood.tsv
│ ├── sub-01_ses-01_task-FullExample_pet.json
│ └── sub-01_ses-01_task-ShortExample_pet.json
└── sub-epilepsy01/
└── ses-01/
└── ieeg/
├── sub-epilepsy01_ses-01_electrodes.json
└── sub-epilepsy01_ses-01_electrodes.tsv
SYMBOL INDEX (9 symbols across 1 files)
FILE: interactiveTreeVisualization/epilepsyClassification2017/treeFunctions.js
function update (line 53) | function update(source) {
function click (line 192) | function click(d) {
function expand (line 203) | function expand(d) {
function collapse (line 213) | function collapse(d) {
function expandAll (line 221) | function expandAll() {
function collapseAll (line 226) | function collapseAll() {
function save (line 238) | function save(dataBlob, filesize) {
function getSVGString (line 246) | function getSVGString(svgNode) {
function svgString2Image (line 316) | function svgString2Image(svgString, width, height, format, callback) {
Condensed preview — 91 files, each showing path, character count, and a content snippet. Download the .json file or copy for the full structured content (278K chars).
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{
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},
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"path": "matlabCode/anat/createBIDS_T1w_json_full_schma_based.m",
"chars": 2162,
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},
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"path": "matlabCode/anat/createBIDS_T1w_json_short.m",
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"chars": 6644,
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},
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"path": "matlabCode/func/createBIDS_bold_json_full.m",
"chars": 3709,
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},
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"path": "matlabCode/func/createBIDS_bold_json_short.m",
"chars": 2024,
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"path": "matlabCode/general/README.md",
"chars": 358,
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"path": "matlabCode/general/createBIDS_events_tsv_json_full.m",
"chars": 3911,
"preview": "%% Template Matlab script to create an BIDS compatible sub-01_ses-01_task-FullExample-01_events.tsv file\n% This example "
},
{
"path": "matlabCode/general/createBIDS_participants_tsv.m",
"chars": 2097,
"preview": "%% Template Matlab script to create an BIDS compatible participants.tsv file\n% This example lists all required and optio"
},
{
"path": "matlabCode/general/createBIDS_samples_tsv.m",
"chars": 1435,
"preview": "%% Template Matlab script to create an BIDS compatible samples.tsv file\n\n% Writing json files relies on the JSONio libra"
},
{
"path": "matlabCode/general/tests/data/participants.json",
"chars": 549,
"preview": "{\r\n \"collectionIssues\": {\r\n \"Description\": [],\r\n \"Levels\": [\r\n \"broken trigger cable, no EEG codes\",\r\n \"nill\",\r\n "
},
{
"path": "matlabCode/general/tests/data/participants.tsv",
"chars": 915,
"preview": "participant_id\tcollectionIssues\tCognitiveTest1\tCognitiveTest2\ttestdate\tage\tsex\r\nsub-control1\tnone\t8\t1\t01-Nov-2019\tn/a\tni"
},
{
"path": "matlabCode/general/tests/test_bids_spreadsheet2participants.m",
"chars": 658,
"preview": "% requires:\n% - moxunit: https://github.com/MOxUnit/MOxUnit\n% - bids-matlab\n\naddpath(fullfile(pwd, '..'));\n\ninput_file ="
},
{
"path": "matlabCode/ieeg/createBIDS_channels_tsv.m",
"chars": 4083,
"preview": "%% Template Matlab script to create an BIDS compatible electrodes.tsv file\n% This example lists all required and optiona"
},
{
"path": "matlabCode/ieeg/createBIDS_coordsystem_json.m",
"chars": 2056,
"preview": "%% Template Matlab script to create an BIDS compatible _electrodes.json file\n% For BIDS-iEEG\n% This example lists all re"
},
{
"path": "matlabCode/ieeg/createBIDS_data_WriteBrainVisionWithFieldtrip.m",
"chars": 2024,
"preview": "% %%%%% save data as BrainVision BIDS %%%%%\n%\n% Sample script that calls Fieldtrip functions to write a Brainvision data"
},
{
"path": "matlabCode/ieeg/createBIDS_electrodes_tsv.m",
"chars": 1869,
"preview": "%% Template Matlab script to create an BIDS compatible electrodes.tsv file\n% This example lists all required and optiona"
},
{
"path": "matlabCode/ieeg/createBIDS_ieeg_json.m",
"chars": 3329,
"preview": "%% Template Matlab script to create an BIDS compatible _ieeg.json file\n% This example lists all required and optional fi"
},
{
"path": "matlabCode/micr/createBIDS_micr_json_full.m",
"chars": 2039,
"preview": "%% Template Matlab script to create an BIDS compatible _bold.json file\n% This example lists all required and optional fi"
},
{
"path": "matlabCode/micr/createBIDS_micr_json_short.m",
"chars": 3280,
"preview": "%% Template Matlab script to create an BIDS compatible _bold.json file\n% This example lists all required and optional fi"
},
{
"path": "matlabCode/miss_hit.cfg",
"chars": 490,
"preview": "# styly guide (https://florianschanda.github.io/miss_hit/style_checker.html)\nline_length: 120\n\nregex_function_name: \"[a-"
},
{
"path": "matlabCode/pet/createBIDS_blood_auto_tsv_and_json_short.m",
"chars": 2323,
"preview": "% Template Matlab script to create a BIDS compatible:\n%\n% sub-01_ses-01_recording-AutosamplerShortExample_blood.tsv\n% "
},
{
"path": "matlabCode/pet/createBIDS_blood_manual_tsv_and_json_full.m",
"chars": 2992,
"preview": "% Template Matlab script to create a BIDS compatible:\n%\n% sub-01_ses-01_recording-ManualFullExample_blood.tsv\n% sub-"
},
{
"path": "matlabCode/pet/createBIDS_blood_manual_tsv_and_json_short.m",
"chars": 2468,
"preview": "% Template Matlab script to create a BIDS compatible:\n%\n% sub-01_ses-01_recording-ManualFullExample_blood.tsv\n% sub-"
},
{
"path": "matlabCode/pet/createBIDS_pet_json_full.m",
"chars": 3478,
"preview": "% Template Matlab script to create a BIDS compatible:\n%\n% sub-01_ses-01_task-FullExample_pet.json\n%\n% This example lis"
},
{
"path": "matlabCode/pet/createBIDS_pet_json_short.m",
"chars": 2414,
"preview": "% Template Matlab script to create a BIDS compatible:\n%\n% sub-01_ses-01_task-ShortExample_pet.json\n%\n% This example li"
},
{
"path": "pythonCode/createBIDS_MP2RAGE_json.py",
"chars": 4405,
"preview": "\"\"\"\nWARNING:\nThis script was created in October 2018 when the specification\nfor MP2RAGE files was not fully finalized. P"
},
{
"path": "pythonCode/createBIDS_dataset_description_json.py",
"chars": 1517,
"preview": "import json\nfrom collections import OrderedDict\n\ndata = OrderedDict()\n# General fields, shared with MRI BIDS and MEG BID"
},
{
"path": "reports/Google-2018-report.md",
"chars": 8331,
"preview": "This is Patrick Park's Google Summer of Code final report for his work on the\n[BIDS Starter Kit](https://github.com/bids"
},
{
"path": "src/CONTRIBUTING.md",
"chars": 5086,
"preview": "# Contributing\n\n🐣 **We're so excited you're here and want to contribute.** 🐣\n\nThe point of this starter kit is to **welc"
},
{
"path": "src/_config.yml",
"chars": 6833,
"preview": "---\n#######################################################################################\n# A default configuration th"
},
{
"path": "src/_toc.yml",
"chars": 2238,
"preview": "---\nformat: jb-book\nroot: index.md\nparts:\n- caption: Folders and files\n chapters:\n - title: Folders\n url: https://b"
},
{
"path": "src/epilepsy_phenotype.rst",
"chars": 132,
"preview": ".. only:: html\n\n ===================\n Epilepsy phenotypes\n ===================\n\n .. raw:: html\n :file"
},
{
"path": "src/index.md",
"chars": 2494,
"preview": "---\njupyter:\n jupytext:\n text_representation:\n format_name: myst\n kernelspec:\n display_name: "
},
{
"path": "src/references.bib",
"chars": 0,
"preview": ""
},
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"path": "src/tree.html",
"chars": 2539,
"preview": "<div class=\"App\">\n\n <style>\n .node {\n cursor: pointer;\n }\n\n .node circle {\n "
},
{
"path": "templates/participants.json",
"chars": 773,
"preview": "{\n \"age\": {\n \"LongName\": \"\",\n \"Description\": \"age of the participant\",\n \"Levels\": {\n },\n \"Units\": \"years"
},
{
"path": "templates/participants.tsv",
"chars": 69,
"preview": "participant_id\tage\tsex\thandedness\nsub-01\t0\tm\tl\nsub-epilepsy01\t10\tf\tr\n"
},
{
"path": "templates/phenotype/EpilepsyClassification.tsv",
"chars": 408,
"preview": "participant_id\tseizure_type\tepilepsy_type\tepilepsy_syndrome\tetiology\nsub-01\t/Generalised/NonMotor/AtypicalAbsence, /Gene"
},
{
"path": "templates/phenotype/EpilepsyClassification2017.json",
"chars": 16254,
"preview": "{\n \"epilepsy_classification\": {\n \"LongName\": \"Epilepsy Classification\",\n \"Description\": \"ILAE classific"
},
{
"path": "templates/samples.json",
"chars": 549,
"preview": "{\n \"sample_id\": {\n \"LongName\": \"Sample ID\",\n \"Description\": \"A sample identifier of the form `sample-<label>`,\\nm"
},
{
"path": "templates/samples.tsv",
"chars": 93,
"preview": "sample_id\tparticipant_id\tsample_type\nsample-01\tsub-01\ttissue\nsample-02\tsub-epilepsy01\ttissue\n"
},
{
"path": "templates/sub-01/ses-01/anat/sub-01_ses-01_acq-FullExample_run-01_T1w.json",
"chars": 1080,
"preview": "{\n \"Manufacturer\": \" \",\n \"ManufacturersModelName\": \" \",\n \"MagneticFieldStrength\": \" \",\n \"DeviceSerialNumber\": \" \",\n "
},
{
"path": "templates/sub-01/ses-01/anat/sub-01_ses-01_acq-ShortExample_run-01_T1w.json",
"chars": 113,
"preview": "{\n \"PhaseEncodingDirection\": \" \",\n \"EffectiveEchoSpacing\": \" \",\n \"TotalReadoutTime\": \" \",\n \"EchoTime\": \" \"\n}\n"
},
{
"path": "templates/sub-01/ses-01/eeg/sub-01_ses-01_task-FilterExample_eeg.json",
"chars": 227,
"preview": "{\n \"HardwareFilters\": {\n \"Highpass RC filter\": {\n \"Half amplitude cutoff (Hz)\": 0.0159,\n "
},
{
"path": "templates/sub-01/ses-01/eeg/sub-01_ses-01_task-FullExample_eeg.json",
"chars": 936,
"preview": "{\n \"TaskName\": \"FullExample\",\n \"TaskDescription\": \"\",\n \"Instructions\": \"\",\n \"CogAtlasID\": \"https://www.cogni"
},
{
"path": "templates/sub-01/ses-01/eeg/sub-01_ses-01_task-MinimalExample_eeg.json",
"chars": 228,
"preview": "{\n \"TaskName\": \"MinimalExample\",\n \"SamplingFrequency\": [],\n \"EEGChannelCount\": [],\n \"EOGChannelCount\": [],\n "
},
{
"path": "templates/sub-01/ses-01/eeg/sub-01_ses-01_task-ReferenceExample_eeg.json",
"chars": 192,
"preview": "{\n \"Manufacturer\": \"Biosemi\",\n \"ManufacturersModelName\": \"ActiveTwo\",\n \"EEGReference\": \"CMS, placed on Cz\",\n "
},
{
"path": "templates/sub-01/ses-01/fmap/sub-01_ses-01_acq-Case1_run-01_phasediff.json",
"chars": 124,
"preview": "{\n \"EchoTime1\": \"\",\n \"EchoTime2\": \"\",\n \"IntendedFor\": [\n \"sub-01/ses-01/func/...\",\n \"sub-01/ses-01/func/...\"\n "
},
{
"path": "templates/sub-01/ses-01/fmap/sub-01_ses-01_acq-Case2_run-01_phase1.json",
"chars": 104,
"preview": "{\n \"EchoTime\": \"\",\n \"IntendedFor\": [\n \"sub-01/ses-01/func/...\",\n \"sub-01/ses-01/func/...\"\n ]\n}\n"
},
{
"path": "templates/sub-01/ses-01/fmap/sub-01_ses-01_acq-Case2_run-01_phase2.json",
"chars": 104,
"preview": "{\n \"EchoTime\": \"\",\n \"IntendedFor\": [\n \"sub-01/ses-01/func/...\",\n \"sub-01/ses-01/func/...\"\n ]\n}\n"
},
{
"path": "templates/sub-01/ses-01/fmap/sub-01_ses-01_acq-Case3_run-01_fieldmap.json",
"chars": 101,
"preview": "{\n \"Units\": \"\",\n \"IntendedFor\": [\n \"sub-01/ses-01/func/...\",\n \"sub-01/ses-01/func/...\"\n ]\n}\n"
},
{
"path": "templates/sub-01/ses-01/fmap/sub-01_ses-01_acq-Case4_dir-LR_run-01_epi.json",
"chars": 144,
"preview": "{\n \"PhaseEncodingDirection\": \"\",\n \"TotalReadoutTime\": \"\",\n \"IntendedFor\": [\n \"sub-01/ses-01/func/...\",\n \"sub-01"
},
{
"path": "templates/sub-01/ses-01/func/sub-01_ses-01_task-FullExample_run-01_bold.json",
"chars": 1429,
"preview": "{\n \"TaskName\": \"FullExample\",\n \"RepetitionTime\": [],\n \"PhaseEncodingDirection\": \"\",\n \"EffectiveEchoSpacing\": [],\n \""
},
{
"path": "templates/sub-01/ses-01/func/sub-01_ses-01_task-FullExample_run-01_events.json",
"chars": 644,
"preview": "{\n \"trial_type\": {\n \"LongName\": \"\",\n \"Description\": \"Emotion image type\",\n \"Levels\": {\n \"afraid\": \"A face"
},
{
"path": "templates/sub-01/ses-01/func/sub-01_ses-01_task-FullExample_run-01_events.tsv",
"chars": 67,
"preview": "onset\tduration\ttrial_type\tresponse_time\tstim_file\tHED\n0\t0\tafraid\t0\n"
},
{
"path": "templates/sub-01/ses-01/func/sub-01_ses-01_task-ShortExample_run-01_bold.json",
"chars": 228,
"preview": "{\n \"TaskName\": \"ShortExample\",\n \"RepetitionTime\": [],\n \"VolumeTiming\": [],\n \"DelayTime\": [],\n \"SliceTiming\": [],\n "
},
{
"path": "templates/sub-01/ses-01/ieeg/sub-01_ses-01_coordsystem.json",
"chars": 215,
"preview": "{\n \"iEEGCoordinateSystem\": \"\",\n \"iEEGCoordinateUnits\": \"\",\n \"iEEGCoordinateProcessingDescripton\": \"\",\n \"IndendedFor\""
},
{
"path": "templates/sub-01/ses-01/ieeg/sub-01_ses-01_electrodes.tsv",
"chars": 106,
"preview": "name\tx\ty\tz\tsize\tmaterial\tmanufacturer\tgroup\themisphere\ttype\timpedance\nn/a\t0\t0\t0\t0\tn/a\tn/a\tn/a\tn/a\tn/a\tn/a\n"
},
{
"path": "templates/sub-01/ses-01/ieeg/sub-01_ses-01_task-LongExample_run-01_channels.tsv",
"chars": 158,
"preview": "name\ttype\tunits\tlow_cutoff\thigh_cutoff\treference\tgroup\tsampling_frequency\tdescription\tnotch\tstatus\tstatus_description\nn/"
},
{
"path": "templates/sub-01/ses-01/ieeg/sub-01_ses-01_task-LongExample_run-01_ieeg.json",
"chars": 1147,
"preview": "{\n \"TaskName\": \"LongExample\",\n \"SamplingFrequency\": [],\n \"PowerLineFrequency\": [],\n \"SoftwareFilters\": \"\",\n \"Hardwa"
},
{
"path": "templates/sub-01/ses-01/meg/sub-01_ses-01_task-FullExample_acq-CTF_run-1_proc-sss_meg.json",
"chars": 1069,
"preview": "{\n \"TaskName\": \"FullExample\",\n \"InstitutionName\": \"\",\n \"InstitutionAddress\": \"\",\n \"Manufacturer\": \"\",\n \"Manufacture"
},
{
"path": "templates/sub-01/ses-01/meg/sub-01_ses-01_task-ShortExample_acq-CTF_run-1_proc-sss_meg.json",
"chars": 1070,
"preview": "{\n \"TaskName\": \"ShortExample\",\n \"InstitutionName\": \"\",\n \"InstitutionAddress\": \"\",\n \"Manufacturer\": \"\",\n \"Manufactur"
},
{
"path": "templates/sub-01/ses-01/micr/sub-01_ses-01_sample-01_acq-Full_stain-03_chunk-01_SEM.json",
"chars": 1210,
"preview": "{\n \"Manufacturer\": \"RECOMMENDED\",\n \"ManufacturersModelName\": \"RECOMMENDED\",\n \"DeviceSerialNumber\": \"RECOMMENDED\",\n \""
},
{
"path": "templates/sub-01/ses-01/micr/sub-01_ses-01_sample-01_acq-Short_stain-03_chunk-01_SEM.json",
"chars": 62,
"preview": "{\n \"PixelSize\": \"REQUIRED\",\n \"PixelSizeUnits\": \"REQUIRED\"\n}\n"
},
{
"path": "templates/sub-01/ses-01/pet/sub-01_ses-01_recording-AutosamplerShortExample_blood.json",
"chars": 382,
"preview": "{\n \"PlasmaAvail\": false,\n \"WholeBloodAvail\": true,\n \"MetaboliteMethod\": false,\n \"DispersionCorrected\": false,\n \"tim"
},
{
"path": "templates/sub-01/ses-01/pet/sub-01_ses-01_recording-AutosamplerShortExample_blood.tsv",
"chars": 35,
"preview": "time\twhole_blood_radioactivity\n0\t0\n"
},
{
"path": "templates/sub-01/ses-01/pet/sub-01_ses-01_recording-ManualFullExample_blood.json",
"chars": 1317,
"preview": "{\n \"PlasmaAvail\": \"\",\n \"MetaboliteAvail\": \"\",\n \"WholeBloodAvail\": \"\",\n \"DispersionCorrected\": \"\",\n \"WithdrawalRate\""
},
{
"path": "templates/sub-01/ses-01/pet/sub-01_ses-01_recording-ManualFullExample_blood.tsv",
"chars": 141,
"preview": "time\tplasma_radioactivity\tmetabolite_parent_fraction\tmetabolite_polar_fraction\thplc_recovery_fractions\twhole_blood_radio"
},
{
"path": "templates/sub-01/ses-01/pet/sub-01_ses-01_recording-ManualShortExample_blood.json",
"chars": 406,
"preview": "{\n \"PlasmaAvail\": \"\",\n \"MetaboliteAvail\": \"\",\n \"WholeBloodAvail\": \"\",\n \"DispersionCorrected\": \"\",\n \"MetaboliteMetho"
},
{
"path": "templates/sub-01/ses-01/pet/sub-01_ses-01_recording-ManualShortExample_blood.tsv",
"chars": 36,
"preview": "time\tmetabolite_parent_fraction\n0\t0\n"
},
{
"path": "templates/sub-01/ses-01/pet/sub-01_ses-01_task-FullExample_pet.json",
"chars": 1767,
"preview": "{\n \"TaskName\": \"FullExample\",\n \"Manufacturer\": \"\",\n \"ManufacturersModelName\": \"\",\n \"Units\": \"\",\n \"InstitutionName\":"
},
{
"path": "templates/sub-01/ses-01/pet/sub-01_ses-01_task-ShortExample_pet.json",
"chars": 773,
"preview": "{\n \"TaskName\": \"ShortExample\",\n \"Manufacturer\": \"\",\n \"ManufacturersModelName\": \"\",\n \"Units\": \"\",\n \"TracerName\": \"\","
},
{
"path": "templates/sub-epilepsy01/ses-01/ieeg/sub-epilepsy01_ses-01_electrodes.json",
"chars": 1430,
"preview": "{\n \"name\": {\n \"Description\": \"REQUIRED. Name of the electrode contact point.\"\n },\n \"x\": {\n \"Descr"
},
{
"path": "templates/sub-epilepsy01/ses-01/ieeg/sub-epilepsy01_ses-01_electrodes.tsv",
"chars": 74,
"preview": "name\tx\ty\tz\tsize\tseizure_zone\nTO1\t0\t0\t0\t5\tNonSOZ\nTO2\t0\t0\t0\t5\tSOZ, Resected\n"
}
]
// ... and 1 more files (download for full content)
About this extraction
This page contains the full source code of the bids-standard/bids-starter-kit GitHub repository, extracted and formatted as plain text for AI agents and large language models (LLMs). The extraction includes 91 files (251.4 KB), approximately 65.0k tokens, and a symbol index with 9 extracted functions, classes, methods, constants, and types. Use this with OpenClaw, Claude, ChatGPT, Cursor, Windsurf, or any other AI tool that accepts text input. You can copy the full output to your clipboard or download it as a .txt file.
Extracted by GitExtract — free GitHub repo to text converter for AI. Built by Nikandr Surkov.