Merge branch 'master' into dwi_scanner_derivatives

.github/workflows/validate_datasets.yml

@@ -69,14 +69,9 @@ jobs:
     - name: Install BIDS validator (master deno build)
       if: "matrix.bids-validator == 'master-deno'"
       run: |
-        LOCAL_BIN=$HOME/.local/bin
-        VALIDATOR=$LOCAL_BIN/bids-validator
-        mkdir -p $LOCAL_BIN
-        export PATH="$LOCAL_BIN:$PATH"
-        echo PATH="$PATH" >> $GITHUB_ENV
-        echo -e '#!/usr/bin/env'" -S deno run --allow-read --allow-write --allow-env --allow-net --allow-run\nimport 'https://github.com/bids-standard/bids-validator/raw/master/bids-validator/src/bids-validator.ts'" > $VALIDATOR
-        chmod +x $VALIDATOR
-        bids-validator --version
+        # 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
@@ -108,3 +103,7 @@ jobs:
         cat ./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.readthedocs.io/en/latest/schema.json

dataset_listing.tsv

@@ -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, headshape, 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
@@ -40,7 +40,7 @@ asl002	T1w, asl (Philips, PCASL, 2D_EPI), m0scan as separate scan	[link](https:/
 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 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
@@ -57,12 +57,12 @@ pet003	T1w, PET, blood		[@mnoergaard](https://github.com/mnoergaard)	anat, pet	T
 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
+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
+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, 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
@@ -72,6 +72,6 @@ ieeg_epilepsy	multiple sessions, tutorial	[link](https://neuroimage.usc.edu/bst/
 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

ieeg_epilepsy_ecog/dataset_description.json

@@ -10,11 +10,5 @@
     "License": "Property of the Epilepsy Centre, University Hospital Freiburg, Germany",
     "ReferencesAndLinks": [
         "https://neuroimage.usc.edu/brainstorm/Tutorials/ECoG"
-    ],
-    "Acknowledgements": "n/a",
-    "HowToAcknowledge": "n/a",
-    "Funding": [],
-	"EthicsApprovals": [],
-    "DatasetDOI": "n/a",
-	"HEDVersion": "n/a"
+    ]
 }

qmri_irt1/IRT1.json

@@ -1,9 +1,9 @@
 {
-  "MagneticFieldStrength": "3",
+  "MagneticFieldStrength": 3,
   "Manufacturer": "Siemens",
   "ManufacturerModelName": "Skyra",
   "PulseSequenceType": "IR",
-  "RepetitionTime": "2.550",
-  "FlipAngle": "3",
-  "EchoTime": "0.014"
+  "RepetitionTime": 2.550,
+  "FlipAngle": 3,
+  "EchoTime": 0.014
 }

qmri_irt1/derivatives/qMRLab/sub-01/anat/sub-01_M0map.json

@@ -5,7 +5,7 @@
     "sub-01/anat/sub-01_inv-03_IRT1.nii.gz",
     "sub-01/anat/sub-01_inv-04_IRT1.nii.gz"
   ],
-  "MagneticFieldStrength": "3",
+  "MagneticFieldStrength": 3,
   "Manufacturer": "Siemens",
   "ManufacturerModelName": "Skyra",
   "PulseSequenceType": "IR",

qmri_irt1/derivatives/qMRLab/sub-01/anat/sub-01_T1map.json

@@ -5,7 +5,7 @@
     "sub-01/anat/sub-01_inv-03_IRT1.nii.gz",
     "sub-01/anat/sub-01_inv-04_IRT1.nii.gz"
   ],
-  "MagneticFieldStrength": "3",
+  "MagneticFieldStrength": 3,
   "Manufacturer": "Siemens",
   "ManufacturerModelName": "Skyra",
   "PulseSequenceType": "IR",

qmri_irt1/sub-01/anat/sub-01_inv-01_IRT1.json

@@ -1,3 +1,3 @@
 {
-  "InversionTime": "0.050"
+  "InversionTime": 0.050
 }

qmri_irt1/sub-01/anat/sub-01_inv-02_IRT1.json

@@ -1,3 +1,3 @@
 {
-  "InversionTime": "0.4"
+  "InversionTime": 0.4
 }

qmri_irt1/sub-01/anat/sub-01_inv-03_IRT1.json

@@ -1,3 +1,3 @@
 {
-  "InversionTime": "1.1"
+  "InversionTime": 1.1
 }

qmri_irt1/sub-01/anat/sub-01_inv-04_IRT1.json

@@ -1,3 +1,3 @@
 {
-  "InversionTime": "2.5"
+  "InversionTime": 2.5
 }

qmri_megre/MEGRE.json

@@ -1,6 +1,6 @@
 {
 
-	"MagneticFieldStrength": "3",
+	"MagneticFieldStrength": 3,
 	"Manufacturer": "Siemens",
 	"ManufacturerModelName": "TrioTim",
 	"PulseSequenceType": "GR"

qmri_megre/sub-01/anat/sub-01_echo-01_MEGRE.json

@@ -1,3 +1,3 @@
 {
-	"EchoTime": "0.02"
+	"EchoTime": 0.02
 }

qmri_megre/sub-01/anat/sub-01_echo-02_MEGRE.json

@@ -1,3 +1,3 @@
 {
-	"EchoTime": "0.04"
+	"EchoTime": 0.04
 }

qmri_megre/sub-01/anat/sub-01_echo-03_MEGRE.json

@@ -1,3 +1,3 @@
 {
-	"EchoTime": "0.06"
+	"EchoTime": 0.06
 }

qmri_megre/sub-01/anat/sub-01_echo-04_MEGRE.json

@@ -1,3 +1,3 @@
 {
-	"EchoTime": "0.08"
+	"EchoTime": 0.08
 }

qmri_megre/sub-01/anat/sub-01_echo-05_MEGRE.json

@@ -1,3 +1,3 @@
 {
-	"EchoTime": "0.1"
+	"EchoTime": 0.1
 }

qmri_megre/sub-01/anat/sub-01_echo-06_MEGRE.json

@@ -1,3 +1,3 @@
 {
-	"EchoTime": "0.12"
+	"EchoTime": 0.12
 }

qmri_megre/sub-01/anat/sub-01_echo-07_MEGRE.json

@@ -1,3 +1,3 @@
 {
-	"EchoTime": "0.14"
+	"EchoTime": 0.14
 }

qmri_megre/sub-01/anat/sub-01_echo-08_MEGRE.json

@@ -1,3 +1,3 @@
 {
-	"EchoTime": "0.16"
+	"EchoTime": 0.16
 }

qmri_mese/derivatives/qMRLab/sub-01/anat/sub-01_M0map.json

@@ -33,7 +33,7 @@
     "sub-01/anat/sub-31_MESE.nii.gz",
     "sub-01/anat/sub-32_MESE.nii.gz"
   ],
-	"MagneticFieldStrength": "3",
+	"MagneticFieldStrength": 3,
 	"Manufacturer": "Siemens",
   "ManufacturerModelName": "TrioTim",
   "PulseSequenceType": "SE",

qmri_mese/derivatives/qMRLab/sub-01/anat/sub-01_MWFmap.json

@@ -33,7 +33,7 @@
     "sub-01/anat/sub-31_MESE.nii.gz",
     "sub-01/anat/sub-32_MESE.nii.gz"
   ],
-  "MagneticFieldStrength": "3",
+  "MagneticFieldStrength": 3,
   "Manufacturer": "Siemens",
   "ManufacturerModelName": "TrioTim",
   "PulseSequenceType": "SE",

qmri_mese/derivatives/qMRLab/sub-01/anat/sub-01_T2map.json

@@ -33,7 +33,7 @@
     "sub-01/anat/sub-31_MESE.nii.gz",
     "sub-01/anat/sub-32_MESE.nii.gz"
   ],
-	"MagneticFieldStrength": "3",
+	"MagneticFieldStrength": 3,
 	"Manufacturer": "Siemens",
   "ManufacturerModelName": "TrioTim",
   "PulseSequenceType": "SE",

qmri_mese/sub-01/anat/sub-01_echo-01_MESE.json

@@ -1,7 +1,7 @@
 {
-	"MagneticFieldStrength": "3",
+	"MagneticFieldStrength": 3,
 	"Manufacturer": "Siemens",
 	"ManufacturerModelName": "TrioTim",
 	"PulseSequenceType": "SE",
-	"EchoTime": "0.01"
+	"EchoTime": 0.01
 }

qmri_mese/sub-01/anat/sub-01_echo-02_MESE.json

@@ -1,8 +1,8 @@
 {
 
-	"MagneticFieldStrength": "3",
+	"MagneticFieldStrength": 3,
 	"Manufacturer": "Siemens",
 	"ManufacturerModelName": "TrioTim",
 	"PulseSequenceType": "SE",
-	"EchoTime": "0.02"
+	"EchoTime": 0.02
 }

qmri_mese/sub-01/anat/sub-01_echo-03_MESE.json

@@ -1,7 +1,7 @@
 {
-	"MagneticFieldStrength": "3",
+	"MagneticFieldStrength": 3,
 	"Manufacturer": "Siemens",
 	"ManufacturerModelName": "TrioTim",
 	"PulseSequenceType": "SE",
-	"EchoTime": "0.03"
+	"EchoTime": 0.03
 }

qmri_mese/sub-01/anat/sub-01_echo-04_MESE.json

@@ -1,8 +1,8 @@
 {
 
-	"MagneticFieldStrength": "3",
+	"MagneticFieldStrength": 3,
 	"Manufacturer": "Siemens",
 	"ManufacturerModelName": "TrioTim",
 	"PulseSequenceType": "SE",
-	"EchoTime": "0.04"
+	"EchoTime": 0.04
 }

qmri_mese/sub-01/anat/sub-01_echo-05_MESE.json

@@ -1,8 +1,8 @@
 {
 
-	"MagneticFieldStrength": "3",
+	"MagneticFieldStrength": 3,
 	"Manufacturer": "Siemens",
 	"ManufacturerModelName": "TrioTim",
 	"PulseSequenceType": "SE",
-	"EchoTime": "0.05"
+	"EchoTime": 0.05
 }

qmri_mese/sub-01/anat/sub-01_echo-06_MESE.json

@@ -1,8 +1,8 @@
 {
 
-	"MagneticFieldStrength": "3",
+	"MagneticFieldStrength": 3,
 	"Manufacturer": "Siemens",
 	"ManufacturerModelName": "TrioTim",
 	"PulseSequenceType": "SE",
-	"EchoTime": "0.06"
+	"EchoTime": 0.06
 }

qmri_mese/sub-01/anat/sub-01_echo-07_MESE.json

@@ -1,8 +1,8 @@
 {
 
-	"MagneticFieldStrength": "3",
+	"MagneticFieldStrength": 3,
 	"Manufacturer": "Siemens",
 	"ManufacturerModelName": "TrioTim",
 	"PulseSequenceType": "SE",
-	"EchoTime": "0.07"
+	"EchoTime": 0.07
 }

qmri_mese/sub-01/anat/sub-01_echo-08_MESE.json

@@ -1,8 +1,8 @@
 {
 
-	"MagneticFieldStrength": "3",
+	"MagneticFieldStrength": 3,
 	"Manufacturer": "Siemens",
 	"ManufacturerModelName": "TrioTim",
 	"PulseSequenceType": "SE",
-	"EchoTime": "0.08"
+	"EchoTime": 0.08
 }

qmri_mese/sub-01/anat/sub-01_echo-09_MESE.json

@@ -1,8 +1,8 @@
 {
 
-	"MagneticFieldStrength": "3",
+	"MagneticFieldStrength": 3,
 	"Manufacturer": "Siemens",
 	"ManufacturerModelName": "TrioTim",
 	"PulseSequenceType": "SE",
-	"EchoTime": "0.09"
+	"EchoTime": 0.09
 }

qmri_mese/sub-01/anat/sub-01_echo-10_MESE.json

@@ -1,8 +1,8 @@
 {
 
-	"MagneticFieldStrength": "3",
+	"MagneticFieldStrength": 3,
 	"Manufacturer": "Siemens",
 	"ManufacturerModelName": "TrioTim",
 	"PulseSequenceType": "SE",
-	"EchoTime": "0.1"
+	"EchoTime": 0.1
 }

qmri_mese/sub-01/anat/sub-01_echo-11_MESE.json

@@ -1,8 +1,8 @@
 {
 
-	"MagneticFieldStrength": "3",
+	"MagneticFieldStrength": 3,
 	"Manufacturer": "Siemens",
 	"ManufacturerModelName": "TrioTim",
 	"PulseSequenceType": "SE",
-	"EchoTime": "0.11"
+	"EchoTime": 0.11
 }

qmri_mese/sub-01/anat/sub-01_echo-12_MESE.json

@@ -1,7 +1,7 @@
 {
-	"MagneticFieldStrength": "3",
+	"MagneticFieldStrength": 3,
 	"Manufacturer": "Siemens",
 	"ManufacturerModelName": "TrioTim",
 	"PulseSequenceType": "SE",
-	"EchoTime": "0.12"
+	"EchoTime": 0.12
 }

qmri_mese/sub-01/anat/sub-01_echo-13_MESE.json

@@ -1,8 +1,8 @@
 {
 
-	"MagneticFieldStrength": "3",
+	"MagneticFieldStrength": 3,
 	"Manufacturer": "Siemens",
 	"ManufacturerModelName": "TrioTim",
 	"PulseSequenceType": "SE",
-	"EchoTime": "0.13"
+	"EchoTime": 0.13
 }

qmri_mese/sub-01/anat/sub-01_echo-14_MESE.json

@@ -1,8 +1,8 @@
 {
 
-	"MagneticFieldStrength": "3",
+	"MagneticFieldStrength": 3,
 	"Manufacturer": "Siemens",
 	"ManufacturerModelName": "TrioTim",
 	"PulseSequenceType": "SE",
-	"EchoTime": "0.14"
+	"EchoTime": 0.14
 }

qmri_mese/sub-01/anat/sub-01_echo-15_MESE.json

@@ -1,8 +1,8 @@
 {
 
-	"MagneticFieldStrength": "3",
+	"MagneticFieldStrength": 3,
 	"Manufacturer": "Siemens",
 	"ManufacturerModelName": "TrioTim",
 	"PulseSequenceType": "SE",
-	"EchoTime": "0.15"
+	"EchoTime": 0.15
 }

qmri_mese/sub-01/anat/sub-01_echo-16_MESE.json

@@ -1,8 +1,8 @@
 {
 
-	"MagneticFieldStrength": "3",
+	"MagneticFieldStrength": 3,
 	"Manufacturer": "Siemens",
 	"ManufacturerModelName": "TrioTim",
 	"PulseSequenceType": "SE",
-	"EchoTime": "0.16"
+	"EchoTime": 0.16
 }