Merge branch 'bids-standard:master' into stim_structure

Author: neuromechanist

.codespellrc

@@ -0,0 +1,4 @@
+[codespell]
+skip = .git,env,venv,ds*,asl*,qmr*,genetics*,fnirs*,eeg*,meg*,pet*,ieeg*,motion*,synthetic*
+builtin = clear,rare
+ignore-words-list = nd,te

.github/workflows/validate_datasets.yml

@@ -21,7 +21,7 @@ jobs:
       fail-fast: false
       matrix:
         platform: [ubuntu-latest, macos-latest, windows-latest]
-        bids-validator: [master, stable]
+        bids-validator: [master, stable, master-deno]
 
     runs-on: ${{ matrix.platform }}
 
@@ -33,6 +33,7 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Set up Node.js
+      if: "matrix.bids-validator == 'stable' || matrix.bids-validator == 'master'"
       uses: actions/setup-node@v4
       with:
         node-version: 18
@@ -60,13 +61,27 @@ jobs:
         bash -c "npm install -g bids-validator-*.tgz"
         popd
 
+    - uses: denoland/setup-deno@v2
+      if: "matrix.bids-validator == 'master-deno'"
+      with:
+        deno-version: v1.x
+
+    - name: Install BIDS validator (master deno build)
+      if: "matrix.bids-validator == 'master-deno'"
+      run: |
+        # If unmerged validator PRs are needed for testing, you can use
+        # https://github.com/<FORK>/bids-validator/raw/<BRANCH>/bids-validator/src/bids-validator.ts
+        deno install -Agf https://github.com/bids-standard/bids-validator/raw/deno-build/bids-validator.js
+      shell: bash
+
     - name: Display versions and environment information
       run: |
         echo $TZ
         date
         echo "npm"; npm --version
         echo "node"; node --version
         echo "bids-validator"; bids-validator --version
+      shell: bash
 
     - name: Check that no large files are present
       if: "matrix.bids-validator == 'stable'"
@@ -83,8 +98,17 @@ jobs:
         fi
       shell: bash
 
+    - name: Skip MRS validation for legacy validator
+      run: for DS in mrs_* dwi_deriv; do touch $DS/.SKIP_VALIDATION; done
+      if: "matrix.bids-validator != 'master-deno'"
+      shell: bash
+
     - name: Validate all BIDS datasets using bids-validator
       run: |
         cat ./run_tests.sh
-        bash ./run_tests.sh
+        ./run_tests.sh
       shell: bash
+      env:
+        # When proposing new features, schema changes may be necessary.
+        # Update this URL to the schema.json from PRs to the spec, when needed.
+        BIDS_SCHEMA: https://bids-specification--1864.org.readthedocs.build/en/1864/schema.json

.github/workflows/validation.yml

@@ -0,0 +1,20 @@
+---
+name: Validation
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  # Check for common misspellings
+  codespell:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: codespell-project/actions-codespell@master

.gitignore

@@ -12,4 +12,6 @@ env/
 
 *.asv
 
-site/
+site/
+
+.vscode

README.md

@@ -2,7 +2,7 @@ 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_demo	Shows usage of Hierarchical Event Descriptor (HED) in .tsv files	[link](https://openneuro.org/datasets/ds003645)	[@VisLab](https://github.com/VisLab)	eeg, beh	channels, eeg, events, participants, scans
+eeg_ds003645s_hed_demo	Shows usage of Hierarchical Event Descriptor (HED) in .tsv files	[link](https://openneuro.org/datasets/ds003645)	[@VisLab](https://github.com/VisLab)	anat, beh, eeg, micr, motion	KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, motion, photo, samples, scans
 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
@@ -38,40 +38,45 @@ ds004332	Anat dataset with task entity	[link](https://openneuro.org/datasets/ds0
 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
+asl004	T1w, asl (Siemens, PCASL, multiPLD with pepolar), m0scan separate scans with pepolar approach	[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_mp2rage	MP2RAGE for T1 mapping	[link](https://osf.io/k4bs5/)	[@Gilles86](https://github.com/Gilles86)	anat	MP2RAGE, T1map, UNIT1, 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_qsm	Chimap using fast QSM	`not publicly available`	[@agahkarakuzu](https://github.com/agahkarakuzu)	anat	T1w
+qmri_sa2rage	Fast B1+ mapping using SA2RAGE	`not publicly available`	[@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
+qmri_irt1	Inversion Recovery T1 mapping	`not publicly available`	[@agahkarakuzu](https://github.com/agahkarakuzu)	anat	IRT1
+qmri_mese	Multi-Echo Spin-Echo for T2 or Myelin Water Fraction (MWF) mapping.	`not publicly available`	[@agahkarakuzu](https://github.com/agahkarakuzu)	anat	MESE
+qmri_megre	Multi-Echo Gradient-Echo for T2star mapping.	`not publicly available`	[@agahkarakuzu](https://github.com/agahkarakuzu)	anat	MEGRE
+qmri_tb1tfl	B1+ mapping with TurboFLASH readout.	`not publicly available`	[@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_SEMzarr	Example SEM dataset in PNG and OME-ZARR format with 1 sample imaged over 2 sessions		[@TheChymera](https://github.com/TheChymera)	micr	SEM, SPIM, 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
+micr_XPCTzarr	Example XPCT dataset in OME-ZARR format with 1 sample imaged	[link](https://human-organ-atlas.esrf.eu/datasets/572252538)	[@chourroutm](https://github.com/chourroutm)	micr	XPCT, photo, samples, sessions
+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
+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	FLASH, T1w, 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	T1w, channels, coordsystem, headshape, meg, photo, 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	T1w, channels, coordsystem, headshape, meg, 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
+genetics_ukbb	multiple tasks, T1w, DTI, BOLD, genetic info		[@cpernet](https://github.com/cpernet)	anat, dwi, func	FLAIR, T1w, bold, dwi, events, info
 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
+mrs_2dmrsi	2D sLASER MRSI data from 8 subjects	[link](https://zenodo.org/records/7701228)	[@markmikkelsen](https://github.com/markmikkelsen)	anat, mrs	T1w, mrsi
+mrs_biggaba	MEGA-PRESS and PRESS MRS data from 12 subjects from one site from the Big GABA project	[link](https://www.nitrc.org/projects/biggaba)	[@markmikkelsen](https://github.com/markmikkelsen)	anat, mrs	T1w, mrsref, svs
+mrs_fmrs	Functional MRS data involving a pain stimulus task from 15 subjects	[link](https://www.nitrc.org/projects/fmrs_2020)	[@markmikkelsen](https://github.com/markmikkelsen)	anat, mrs	T1w, events, mrsref, svs
+xeeg_hed_score	EEG and iEEG data with annotations of artifacts, seizures and modulators using HED-SCORE 		[@dorahermes](https://github.com/dorahermes)	eeg, anat, ieeg	channels, coordsystem, electrodes, events, ieeg, eeg, T1w

dataset_listing.tsv

@@ -28,5 +28,5 @@
  "HeadCoilCoordinateSystemDescription": "5 HPI coils used",
  "AnatomicalLandmarkCoordinateSystemDescription": "For images of anatomical landmarks, see http://imaging.mrc-cbu.cam.ac.uk/meg/SubjectPreparation",
  "FiducialsDescription": "For images of anatomical landmarks, see http://imaging.mrc-cbu.cam.ac.uk/meg/SubjectPreparation",
- "IntendedFor": "sub-01/ses-mri/anat/sub-01_ses-mri_acq-mprage_T1w.nii.gz"
+ "IntendedFor": "ses-mri/anat/sub-01_ses-mri_acq-mprage_T1w.nii.gz"
 }

ds000117/sub-01/ses-meg/meg/sub-01_ses-meg_coordsystem.json

@@ -9,7 +9,7 @@
  "DigitizedHeadPointsCoordinateSystem": "ElektaNeuromag",
  "DigitizedHeadPointsCoordinateUnits": "mm",
  "DigitizedHeadPointsCoordinateSystemDescription": "Headpoints include arcs of points along front of head and around nose, as well as centre of 70 EEG electrodes spread across scalp, which also help define headshape. Beware that nose points can bias coregistration with MRI if MRI image does not include all of the nose.",
- "IntendedFor": "sub-02/ses-mri/anat/sub-02_ses-mri_acq-mprage_T1w.nii.gz",
+ "IntendedFor": "ses-mri/anat/sub-02_ses-mri_acq-mprage_T1w.nii.gz",
  "AnatomicalLandmarkCoordinates": {
   "LPA": [-69.66,0,0],
   "RPA": [71.69,0,0],

ds000117/sub-02/ses-meg/meg/sub-02_ses-meg_coordsystem.json

@@ -9,7 +9,7 @@
  "DigitizedHeadPointsCoordinateSystem": "ElektaNeuromag",
  "DigitizedHeadPointsCoordinateUnits": "mm",
  "DigitizedHeadPointsCoordinateSystemDescription": "Headpoints include arcs of points along front of head and around nose, as well as centre of 70 EEG electrodes spread across scalp, which also help define headshape. Beware that nose points can bias coregistration with MRI if MRI image does not include all of the nose.",
- "IntendedFor": "sub-03/ses-mri/anat/sub-03_ses-mri_acq-mprage_T1w.nii.gz",
+ "IntendedFor": "ses-mri/anat/sub-03_ses-mri_acq-mprage_T1w.nii.gz",
  "AnatomicalLandmarkCoordinates": {
   "LPA": [-72.22,0,0],
   "RPA": [73.09,0,0],

ds000117/sub-03/ses-meg/meg/sub-03_ses-meg_coordsystem.json

@@ -9,7 +9,7 @@
  "DigitizedHeadPointsCoordinateSystem": "ElektaNeuromag",
  "DigitizedHeadPointsCoordinateUnits": "mm",
  "DigitizedHeadPointsCoordinateSystemDescription": "Headpoints include arcs of points along front of head and around nose, as well as centre of 70 EEG electrodes spread across scalp, which also help define headshape. Beware that nose points can bias coregistration with MRI if MRI image does not include all of the nose.",
- "IntendedFor": "sub-04/ses-mri/anat/sub-04_ses-mri_acq-mprage_T1w.nii.gz",
+ "IntendedFor": "ses-mri/anat/sub-04_ses-mri_acq-mprage_T1w.nii.gz",
  "AnatomicalLandmarkCoordinates": {
   "LPA": [-70.16,0,0],
   "RPA": [75.06999999999999,0,0],