Merge branch 'bids-standard:master' into bep029_motion

.github/dependabot.yml

@@ -0,0 +1,8 @@
+# Documentation
+# https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/deploy.yml

@@ -0,0 +1,33 @@
+name: Build and Deploy
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+on:
+    push:
+        branches:
+        - master
+
+permissions:
+    contents: write
+
+jobs:
+    build-and-deploy:
+        runs-on: ubuntu-latest
+        steps:
+            -   name: Checkout 🛎️
+                uses: actions/checkout@v3
+            -   uses: actions/setup-python@v4
+                with:
+                    python-version: "3.11"
+            -   name: Install and Build 🔧
+                run: |
+                    python -m pip install --upgrade pip
+                    python -m pip install -r requirements.txt
+                    mkdocs build
+
+            -   name: Deploy 🚀
+                uses: JamesIves/github-pages-deploy-action@v4
+                with:
+                    folder: site

.github/workflows/validate_datasets.yml

@@ -30,10 +30,10 @@ jobs:
       FORCE_COLOR: 1
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
     - name: Set up Node.js
-      uses: actions/setup-node@v2
+      uses: actions/setup-node@v3
       with:
         node-version: 14
 

.gitignore

@@ -1,7 +1,15 @@
 .DS_Store
+*.DS_Store
+
+.idea/
+
 .ipynb_checkpoints
+
 desktop.ini
-*.asv
-.idea/
+
 venv/
-*.DS_Store
+env/
+
+*.asv
+
+site/

CONTRIBUTING.md

@@ -27,7 +27,7 @@ functionality. Because the tests cannot go beyond very basic checks of
 filenames and directory structures.
 
 To provide a remedy for that, we provide some datasets with intact data headers,
-see the [Dataset Index Table](https://github.com/bids-standard/bids-examples/blob/master/README.md#dataset-index).
+see the [Dataset Index Table](./README.md#dataset-index).
 
 ## How to truncate data files to 0kb
 
@@ -40,15 +40,25 @@ find <path_to_ds> -type f -name '*.fif' -exec truncate -s 0 {} +
 ```
 
 which means:
-- in this directory `<path_to_ds>`
-- ... find everything of type "file" (or specify `d` for directory, ...)
-- [optional] ... use `-name` with wildcard `*` to match to particular file types
-- ... for each file, execute something
-- ... namely, truncate the file
-- ... to size 0
-- `{}` is where a file name is put automatically (do not modify it)
-- `+` means, this is performed not file-wise but with a bunch of files at once.
-  Could also be `\;` to have it one after the other
+
+-   in this directory `<path_to_ds>`
+-   ... find everything of type "file" (or specify `d` for directory, ...)
+-   [optional] ... use `-name` with wildcard `*` to match to particular file types
+-   ... for each file, execute something
+-   ... namely, truncate the file
+-   ... to size 0
+-   `{}` is where a file name is put automatically (do not modify it)
+-   `+` means, this is performed not file-wise but with a bunch of files at once.
+    Could also be `\;` to have it one after the other
+
+## How to generate the tables in the readme 
+
+Note that these steps must be executed whenever a new dataset is added to the repository.
+
+1. Edit the `dataset_listing.tsv` file to add or update datasets from the table.
+1. Install all the necessary dependencies: `pip install -r tools/requirements.txt`
+1. Then run the script: `python tools/print_dataset_listing.py`
+1. Finally, `git commit` all changes and `git push` them to your remote (for example when you are working on a Pull Request)
 
 ## How to make a release
 

dataset_listing.tsv

@@ -0,0 +1,79 @@
+name	description	link to full data	maintained by	datatypes	suffixes
+eeg_matchingpennies	Offline data of BCI experiment decoding left vs. right hand movement. BrainVision data format (.eeg, .vhdr, .vmrk)	[link](https://doi.org/10.17605/OSF.IO/CJ2DR)	[@sappelhoff](https://github.com/sappelhoff)	eeg	channels, eeg, events
+eeg_rishikesh	Mind wandering experiment. EEG data in Biosemi (.bdf) format	[link](https://openneuro.org/datasets/ds001787)	[@arnodelorme](https://github.com/arnodelorme)	eeg	channels, eeg, events
+eeg_face13	Deconstructing the early visual electrocortical response to face and house stimuli. EDF format		[@andesha](https://github.com/andesha)	eeg	channels, coordsystem, eeg, electrodes, events
+eeg_ds003645s_hed	Shows usage of Hierarchical Event Descriptor (HED) in events files	[link](https://openneuro.org/datasets/ds003645)	[@VisLab](https://github.com/VisLab)	eeg	channels, eeg, events
+eeg_ds003645s_hed_inheritance	HED annotation with multiple inherited sidecars	[link](https://openneuro.org/datasets/ds003645)	[@VisLab](https://github.com/VisLab)	eeg	channels, eeg, events
+eeg_ds003645s_hed_longform	HED annotation using tags in long form.	[link](https://openneuro.org/datasets/ds003645)	[@VisLab](https://github.com/VisLab)	eeg	channels, eeg, events
+eeg_ds003645s_hed_library	HED annotation using HED library vocabularies (schema).	[link](https://openneuro.org/datasets/ds003645)	[@VisLab](https://github.com/VisLab)	eeg	channels, eeg, events
+eeg_cbm	Rest EEG. European Data Format (.edf)		[@cpernet](https://github.com/cpernet)	eeg	channels, eeg, events, scans
+ieeg_filtered_speech	recordings of three seizures		[@choldgraf](https://github.com/choldgraf)	ieeg	channels, coordsystem, electrodes, events, ieeg, photo
+ieeg_motorMiller2007	Cue-based hand & tongue movement data		[@dorahermes](https://github.com/dorahermes)	ieeg	channels, coordsystem, electrodes, events, ieeg
+ieeg_visual	Stimulus dependence of gamma oscillations in human visual cortex		[@dorahermes](https://github.com/dorahermes)	anat, ieeg	T1w, channels, coordsystem, electrodes, events, ieeg
+7t_trt		[link](https://bit.ly/2H0Z6Qt)		anat, fmap, func	T1map, T1w, bold, magnitude1, magnitude2, phasediff, physio, scans, sessions
+ds001	single task, multiple runs	[link](https://openneuro.org/datasets/ds000001/versions/00006)		anat, func	T1w, bold, events, inplaneT2
+ds002	multiple tasks, multiple runs	[link](https://openneuro.org/datasets/ds000002/versions/00002)		anat, func	T1w, bold, events, inplaneT2
+ds003	single task, single run	[link](https://openneuro.org/datasets/ds000003/versions/00001)		anat, func	T1w, bold, events, inplaneT2
+ds005	single task, multiple runs	[link](https://openneuro.org/datasets/ds000005/versions/00001)		anat, func	T1w, bold, events, inplaneT2
+ds006	single task, multiple sessions, multiple runs	[link](https://openneuro.org/datasets/ds000006/versions/00001)		anat, func	T1w, bold, events, inplaneT2
+ds007	single task, multiple runs	[link](https://openneuro.org/datasets/ds000007/versions/00001)		anat, func	T1w, bold, events, inplaneT2
+ds008	multiple tasks, multiple runs	[link](https://openneuro.org/datasets/ds000008/versions/00001)		anat, func	T1w, bold, events, inplaneT2
+ds009	multiple tasks, multiple runs	[link](https://openneuro.org/datasets/ds000009/versions/00002)		anat, func	T1w, bold, events, inplaneT2, scans
+ds011	multiple tasks, multiple runs	[link](https://openneuro.org/datasets/ds000011/versions/00001)		anat, func	T1w, bold, events, inplaneT2
+ds051	multiple tasks, multiple runs	[link](https://openneuro.org/datasets/ds000051/versions/00001)		anat, func	T1w, bold, events, inplaneT2
+ds052	multiple tasks, multiple runs	[link](https://openneuro.org/datasets/ds000052/versions/00001)		anat, func	T1w, bold, events, inplaneT2
+ds101	single task, multiple runs	[link](https://openneuro.org/datasets/ds000101/versions/00004)		anat, func	T1w, bold, events
+ds102	single task, multiple runs	[link](https://openneuro.org/datasets/ds000102/versions/00001)		anat, func	T1w, bold, events
+ds105	single task, multiple runs	[link](https://openneuro.org/datasets/ds000105/versions/00001)		anat, func	T1w, bold, events
+ds107	single task, multiple runs	[link](https://openneuro.org/datasets/ds000107/versions/00001)		anat, func	T1w, bold, events
+ds108	single task, multiple runs	[link](https://openneuro.org/datasets/ds000108/versions/00002)		anat, func	T1w, bold, events
+ds109	multiple tasks, multiple runs	[link](https://openneuro.org/datasets/ds000109/versions/00001)		anat, func	T1w, bold, events
+ds110	single task, multiple runs	[link](https://openneuro.org/datasets/ds000110/versions/00001)		anat, func	T1w, bold, events, inplaneT2
+ds113b	forrest gump watching, multiple sessions, multiple runs	[link](https://openneuro.org/datasets/ds000113/versions/1.3.0)		func	bold, events
+ds114	multiple tasks, multiple runs	[link](https://openneuro.org/datasets/ds000114/versions/1.0.1)		anat, dwi, func	T1w, bold, dwi, events
+ds116	multiple tasks, multiple runs	[link](https://openneuro.org/datasets/ds000116/versions/00003)		anat, func	T1w, bold, events, inplaneT2
+ds210	multiple tasks, multiple runs	[link](https://openneuro.org/datasets/ds000210/versions/00002)		func	bold, physio
+hcp_example_bids		[link](https://bit.ly/2H0Z6Qt)	[@robertoostenveld](https://github.com/robertoostenveld)	anat, fmap	T1w, T2w, magnitude1, magnitude2, phasediff
+synthetic	A synthetic dataset		[@effigies](https://github.com/effigies)	anat, beh, func	T1w, beh, bold, events, physio, scans, sessions, stim
+ds000001-fmriprep	Common derivatives example	[link](https://openneuro.org/datasets/ds000001/versions/1.0.0)	[@effigies](https://github.com/effigies)	n/a	n/a
+ds004332	Anat dataset with task entity	[link](https://openneuro.org/datasets/ds004332/versions/1.0.2)	[@Remi-Gau](https://github.com/Remi-Gau)	anat	FLAIR, T1w, T2starw, T2w
+asl001	T1w, asl (GE, PCASL, 3D_SPIRAL), m0scan within timeseries	[link](https://osf.io/yru2q/)	[@patsycle](https://github.com/patsycle)	anat, perf	T1w, asl, aslcontext, asllabeling
+asl002	T1w, asl (Philips, PCASL, 2D_EPI), m0scan as separate scan	[link](https://osf.io/yru2q/)	[@patsycle](https://github.com/patsycle)	anat, perf	T1w, asl, aslcontext, asllabeling, m0scan
+asl003	T1w, asl (Siemens, PASL, multiTI), M0scan as separate scan	[link](https://osf.io/yru2q/)	[@patsycle](https://github.com/patsycle)	anat, perf	T1w, asl, aslcontext, asllabeling, m0scan
+asl004	T1w, asl (Siemens, PCASL, multiPLD with pepolar), m0scan separate scans with pepolar appraoch	[link](https://osf.io/yru2q/)	[@patsycle](https://github.com/patsycle)	anat, fmap, perf	T1w, asl, aslcontext, asllabeling, m0scan
+asl005	T1w, asl (Siemens, PCASL, singleTI, 3D_GRASE), m0scan as separate scan	[link](https://osf.io/yru2q/)	[@patsycle](https://github.com/patsycle)	anat, perf	T1w, asl, aslcontext, asllabeling, m0scan
+qmri_mp2rage	MP2RAGE for T1 mapping	[link](https://osf.io/k4bs5/)	[@Gilles86](https://github.com/Gilles86)	anat	MP2RAGE, defacemask
+qmri_mp2rageme	Multi-echo MP2RAGE	[link](https://osf.io/k4bs5/)	[@Gilles86](https://github.com/Gilles86)	anat, fmap	MP2RAGE, TB1map
+qmri_mpm	Multi-parametric mapping for R1, R2star, MTsat and PD mapping	[link](https://osf.io/k4bs5/)	[@ChristophePhillips](https://github.com/ChristophePhillips)	anat, fmap	MPM, RB1COR, TB1EPI, magnitude1, magnitude2, phasediff
+qmri_mtsat	Example dataset for T1 and MTsat mapping. Includes a double-angle B1+ mapping example.	[link](https://osf.io/k4bs5/)	[@agahkarakuzu](https://github.com/agahkarakuzu)	anat, fmap	MTS, TB1DAM
+qmri_qsm	Chimap using fast QSM	`not publicly availabe`	[@agahkarakuzu](https://github.com/agahkarakuzu)	anat	T1w
+qmri_sa2rage	Fast B1+ mapping using SA2RAGE	`not publicly availabe`	[@agahkarakuzu](https://github.com/agahkarakuzu)	fmap	TB1SRGE
+qmri_vfa	Variable Flip Angle T1 mapping. Includes an Actual Flip Angle (AFI) B1+ mapping example.	[link](https://osf.io/k4bs5/)	[@agahkarakuzu](https://github.com/agahkarakuzu)	anat, fmap	TB1AFI, VFA
+qmri_irt1	Inversion Recovery T1 mapping	`not publicly availabe`	[@agahkarakuzu](https://github.com/agahkarakuzu)	anat	IRT1
+qmri_mese	Multi-Echo Spin-Echo for T2 or Myelin Water Fraction (MWF) mapping.	`not publicly availabe`	[@agahkarakuzu](https://github.com/agahkarakuzu)	anat	MESE
+qmri_megre	Multi-Echo Gradient-Echo for T2star mapping.	`not publicly availabe`	[@agahkarakuzu](https://github.com/agahkarakuzu)	anat	MEGRE
+qmri_tb1tfl	B1+ mapping with TurboFLASH readout.	`not publicly availabe`	[@agahkarakuzu](https://github.com/agahkarakuzu)	fmap	TB1TFL
+pet001	T1w, PET, blood		[@mnoergaard](https://github.com/mnoergaard)	anat, pet	T1w, blood, pet
+pet002	T1w, PET	[link](https://openneuro.org/datasets/ds001420/)	[@mnoergaard](https://github.com/mnoergaard)	anat, pet	T1w, pet
+pet003	T1w, PET, blood		[@mnoergaard](https://github.com/mnoergaard)	anat, pet	T1w, blood, pet
+pet004	PET, blood		[@mnoergaard](https://github.com/mnoergaard)	pet	blood, pet
+pet005	T1w, PET		[@mnoergaard](https://github.com/mnoergaard)	anat, pet	T1w, events, pet
+micr_SEM	Example SEM dataset in PNG format with 1 sample imaged over 2 sessions	[link](https://doi.org/10.5281/zenodo.5498378)	[@jcohenadad](https://github.com/jcohenadad)	micr	SEM, photo, samples, sessions
+micr_SEMzarr	Example SEM dataset in PNG and OME-ZARR format with 1 sample imaged over 2 sessions		[@TheChymera](https://github.com/TheChymera)	micr	SEM, samples, sessions
+micr_SPIM	Example SPIM dataset in OME-TIFF format with 2 samples from the same subject with 4 chunks each	[link](https://doi.org/10.5281/zenodo.5517223)	[@jcohenadad](https://github.com/jcohenadad)	micr	SPIM, photo, samples
+fnirs_tapping	Example fNIRS measurement with three conditions from five subjects	[link](https://doi.org/10.5281/zenodo.5529797)	[@rob_luke](https://github.com/rob_luke)	nirs	channels, coordsystem, events, nirs, optodes, scans
+fnirs_automaticity	24 subjects performing (non-)automatic finger tapping and foot stepping	[link](https://doi.org/10.34973/vesb-mh30)	[@robertoostenveld](https://github.com/robertoostenveld)	nirs	channels, coordsystem, events, nirs, optodes, practicelogbook, scans
+motion_systemvalidation	Example dataset of two different motion captured system recorded almost simultaneously, but no brain data	[link](https://doi.org/10.6084/m9.figshare.20238006.v2)	[@JuliusWelzel](https://github.com/JuliusWelzel)	motion	channels, motion, scans
+ds000117	A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual task	[link](https://openneuro.org/datasets/ds000117/)	[@RikHenson](https://github.com/RikHenson)	anat, beh, dwi, fmap, func, meg	T1w, beh, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans
+ds000246	Auditory dataset used for Brainstorm’s general online tutorial	[link](https://openneuro.org/datasets/ds000246/versions/00001)	[@guiomar](https://github.com/guiomar)	anat, meg	ChannelGroupSet, ClassFile, MarkerFile, T1w, channels, coordsystem, default, headshape, meg, params, photo, processing, scans
+ds000247	Five minutes, eyes-open, resting-state MEG data from 5 subjects. This is a sample from The Open MEG Archive (OMEGA).	[link](https://openneuro.org/datasets/ds000247/versions/00001)	[@guiomar](https://github.com/guiomar)	anat, meg	ClassFile, T1w, bad, channels, coordsystem, default, headshape, meg, params, processing, scans
+ds000248	MNE sample data: Data with visual and auditory stimuli	[link](https://openneuro.org/datasets/ds000248/versions/00001)	[@agramfort](https://github.com/agramfort)	anat, meg	FLASH, T1w, channels, coordsystem, events, meg, scans
+eeg_ds000117	Multimodal (fMRI, MEG, EEG) stripped down to EEG with MRI anatomical scan and electrode coordinates. EEGLAB data format (.set, .fdt)	[link](https://openneuro.org/datasets/ds000117/)	[@robertoostenveld](https://github.com/robertoostenveld)	anat, eeg	T1w, channels, coordsystem, eeg, electrodes, events
+eeg_rest_fmri	Resting state with simultaneous fMRI. BrainVision data format (.eeg, .vhdr, .vmrk)		[@cpernet](https://github.com/cpernet)	anat, dwi, eeg, func	T1w, bold, dwi, eeg
+ieeg_epilepsy	multiple sessions, tutorial	[link](https://neuroimage.usc.edu/bst/getupdate.php?s=tutorial_epimap_bids)	[@ftadel](https://github.com/ftadel)	anat, ieeg	T1w, channels, coordsystem, electrodes, events, ieeg, scans
+ieeg_epilepsyNWB	multiple sessions, tutorial — derivative dataset of `ieeg_epilepsy` showcasing the NWB file format alternative	[link](https://neuroimage.usc.edu/bst/getupdate.php?s=tutorial_epimap_bids)	[@TheChymera](https://github.com/TheChymera)	anat, ieeg	T1w, channels, coordsystem, electrodes, events, ieeg, scans
+ieeg_epilepsy_ecog	multiple sessions, tutorial	[link](https://neuroimage.usc.edu/bst/getupdate.php?s=sample_ecog)	[@ftadel](https://github.com/ftadel)	anat, ieeg	T1w, channels, coordsystem, electrodes, events, ieeg, photo, scans
+ieeg_visual_multimodal			[@irisgroen](https://github.com/irisgroen)	anat, fmap, func, ieeg	T1w, bold, channels, coordsystem, electrodes, epi, events, ieeg, sbref
+genetics_ukbb	multiple tasks, T1w, DTI, BOLD, genetic info		[@cpernet](https://github.com/cpernet)	anat, dwi, fmap, func	FLAIR, T1w, bold, dwi, events, info, magnitude1, phasediff
+motion_dualtask	older and younger participants walking while performing discrimination task		[@sjeung](https://github.com/sjeung)	eeg, motion	channels, eeg, events, motion, scans
+motion_spotrotation	participants rotated heading using full-body motion or joystick	[link](https://openneuro.org/datasets/ds004460)	[@sjeung](https://github.com/sjeung)	eeg, motion	channels, coordsystem, eeg, electrodes, events, motion, scans

docs/CONTRIBUTING.md

@@ -0,0 +1 @@
+../CONTRIBUTING.md

docs/README.md

@@ -0,0 +1 @@
+../README.md

mkdocs.yml

@@ -0,0 +1,36 @@
+site_name: bids-examples
+
+nav:
+    - The BIDS examples:
+      - Introduction: README.md
+      - Contributing: CONTRIBUTING.md
+
+theme:
+    name: material
+    favicon: images/favicon.png
+    logo: images/logo.png
+
+
+copyright: Copyright &copy; 2018-2023, BIDS Contributors - <a href="https://creativecommons.org/licenses/by/4.0/">CC BY 4.0</a>
+
+extra:
+    generator: false
+    social:
+      - icon: fontawesome/brands/twitter
+        link: https://twitter.com/BIDSstandard/
+      - icon: fontawesome/brands/github
+        link: https://github.com/bids-standard/bids-specification/
+      - icon: fontawesome/brands/google
+        link: https://groups.google.com/g/bids-discussion
+
+markdown_extensions:
+    - toc:
+        anchorlink: true
+    - pymdownx.superfences
+
+plugins:
+    - search
+
+docs_dir: 'docs'
+
+use_directory_urls: false

requirements.txt

@@ -0,0 +1,3 @@
+mkdocs
+mkdocs-material
+pymdown-extensions