[MAINT] update listing and add validation

Remi-Gau · Remi-Gau · commit e1c247ff17eb · 2025-03-03T10:43:50.000+01:00
diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
@@ -17,4 +17,17 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: codespell-project/actions-codespell@master
+      - uses: codespell-project/actions-codespell@master
+
+  check_listing:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: install python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.13
+      - name: install dependencies
+        run: pip install -r tools/requirements.txt
+      - name: check that all datasets are listed in dataset_listing.tsv
+        run: python tools/print_dataset_listing.py
diff --git a/dataset_listing.tsv b/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)	anat, beh, eeg, micr, motion	KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, motion, photo, samples, 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
@@ -59,13 +59,13 @@ pet005	T1w, PET		[@mnoergaard](https://github.com/mnoergaard)	anat, pet	T1w, eve
 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, 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
-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
+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	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	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
+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
@@ -76,9 +76,11 @@ ieeg_visual_multimodal			[@irisgroen](https://github.com/irisgroen)	anat, fmap,
 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
+mrs_2dmrsi	2D sLASER MRSI data from 8 subjects	[link](https://zenodo.org/records/7701228)	[@markmikkelsen](https://github.com/markmikkelsen)	anat	T1w
+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	T1w
+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	T1w, events
 2d_mb_pcasl	Siemens 2D MultiBand Multi-delay PCASL (m0 and noRF included within timeseries)	[link](https://osf.io/xrkc4/)	[@aptinis](https://github.com/aptinis)	anat, fmap, perf	T1w, asl, aslcontext, epi
 xeeg_hed_score	EEG and iEEG data with annotations of artifacts, seizures and modulators using HED-SCORE 		[@dorahermes](https://github.com/dorahermes)	anat, eeg, ieeg	T1w, channels, coordsystem, eeg, electrodes, events, ieeg
 dwi_deriv	exemplifies the storage of diffusion MRI derivates that may be generated on the Siemens XA platform.			dwi	dwi
+pheno004	dataset containing a mismatch of subjects with MRI data and tabular phenotypic data to be considered a whole dataset of participants for the sake of the participants.tsv file		"[@ericearl](https://github.com/ericearl)
+"	anat	T1w, ace, demographics
