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[MAINT] update listing and add validation
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@Remi-Gau
Remi-Gau committed Mar 3, 2025
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15 changes: 14 additions & 1 deletion .github/workflows/validation.yml
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Expand Up @@ -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
16 changes: 9 additions & 7 deletions dataset_listing.tsv
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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

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