Home

Awesome

GitHub Actions GitHub repo size

The content of this repository can also be viewed here:

https://bids-standard.github.io/bids-examples/

bids-examples

This repository contains a set of BIDS-compatible datasets with empty raw data files. These datasets can be useful to:

  1. write lightweight software tests
  2. serve as an example on how a BIDS dataset can be structured

ALL RAW DATA FILES IN THIS REPOSITORY ARE EMPTY!

However for some of the data, the headers containing the metadata are still intact. (For example the NIfTI headers for .nii files, the BrainVision data headers for .vhdr files, or the OME-XML headers for .ome.tif files.)

Headers are intact for the following datasets:

Validating BIDS examples

The next three sections mention a few details on how the bids-examples can be validated using bids-validator.

For general information on the bids-validator, including installation and usage, see the bids-validator README file.

Validating individual examples

Since all raw data files in this repository are empty, the bids-validator must to be configured to not report empty data files as errors. (See more on bids-validator configuration in the bids-validator README.)

Just run the validator as follows (using the eeg_matchingpennies dataset as an example, and assuming you are in a command line at the root of the bids-examples repository):

bids-validator eeg_matchingpennies --config.ignore=99

The --config.ignore=99 "flag" tells the bids-validator to ignore empty data files rather than to report the "empty file" error .

For datasets that contain NIfTI .nii files, you also need to add the ignoreNiftiHeaders flag to the bids-validator call, to suppress the issue that NIfTI headers are not found.

For example:

bids-validator ds003 --config.ignore=99 --ignoreNiftiHeaders

Validating all examples

If you want to validate all examples in one go, you can use the run_tests.sh script that is provided in this repository. This script makes use of the bidsconfig.json configuration file for the bids-validator, and appropriately handles some special case examples (see Validator Exceptions).

Simply run ./run_tests.sh in a command line from the root of the bids-examples repository.

Validator exceptions

Some datasets may include a custom .bids-validator-config.json to ignore errors generated from idiosyncrasies of the datasets as they existed on creation.

nameerrors ignored
genetics_ukbbSliceTiming values for tasks is larger than given TR, EchoTime1 and EchoTime2 are not provided for any of the phasediff files.

Other datasets may include a .SKIP_VALIDATION file, to skip the validation with the continuous integration service. This is useful for datasets that cannot pass at the moment due to lack of coverage in the bids-validator.

Note however, that the .SKIP_VALIDATION file only impacts the continuous integration service, or validation when run with the run_tests.sh script (see Validating all examples). This file does not have any effect when running bids-validator from custom scripts, the web-based validator, docker, or from the command line.

namewhy skipped
ds000001-fmripreplack of coverage for "derivatives" in bids-validator

Contributing

We are happy to receive contributions in the form of:

For more information, please see our CONTRIBUTING.md file or open a new GitHub Issue and ask us directly.

Dataset index

<!-- ADD EXAMPLE LISTING HERE --> <!-- TABLE BELOW IS GENERATED AUTOMATICALLY. DO NOT EDIT DIRECTLY. -->

ASL

<!-- TABLE BELOW IS GENERATED AUTOMATICALLY. DO NOT EDIT DIRECTLY. -->
namedescriptiondatatypessuffixeslink to full datamaintained by
asl001T1w, asl (GE, PCASL, 3D_SPIRAL), m0scan within timeseriesanat, perfT1w, asl, aslcontext, asllabelinglink@patsycle
asl002T1w, asl (Philips, PCASL, 2D_EPI), m0scan as separate scananat, perfT1w, asl, aslcontext, asllabeling, m0scanlink@patsycle
asl003T1w, asl (Siemens, PASL, multiTI), M0scan as separate scananat, perfT1w, asl, aslcontext, asllabeling, m0scanlink@patsycle
asl004T1w, asl (Siemens, PCASL, multiPLD with pepolar), m0scan separate scans with pepolar approachanat, fmap, perfT1w, asl, aslcontext, asllabeling, m0scanlink@patsycle
asl005T1w, asl (Siemens, PCASL, singleTI, 3D_GRASE), m0scan as separate scananat, perfT1w, asl, aslcontext, asllabeling, m0scanlink@patsycle

EEG

<!-- TABLE BELOW IS GENERATED AUTOMATICALLY. DO NOT EDIT DIRECTLY. -->
namedescriptiondatatypessuffixeslink to full datamaintained by
eeg_cbmRest EEG. European Data Format (.edf)eegchannels, eeg, events, scansn/a@cpernet
eeg_ds003645s_hed_libraryHED annotation using HED library vocabularies (schema).eegchannels, eeg, eventslink@VisLab
eeg_face13Deconstructing the early visual electrocortical response to face and house stimuli. EDF formateegchannels, coordsystem, eeg, electrodes, eventsn/a@andesha
eeg_matchingpenniesOffline data of BCI experiment decoding left vs. right hand movement. BrainVision data format (.eeg, .vhdr, .vmrk)eegchannels, eeg, eventslink@sappelhoff
eeg_rishikeshMind wandering experiment. EEG data in Biosemi (.bdf) formateegchannels, eeg, eventslink@arnodelorme

iEEG

<!-- TABLE BELOW IS GENERATED AUTOMATICALLY. DO NOT EDIT DIRECTLY. -->
namedescriptiondatatypessuffixeslink to full datamaintained by
ieeg_epilepsyNWBmultiple sessions, tutorial — derivative dataset of ieeg_epilepsy showcasing the NWB file format alternativeanat, ieegT1w, channels, coordsystem, electrodes, events, ieeg, scanslink@TheChymera
ieeg_epilepsymultiple sessions, tutorialanat, ieegT1w, channels, coordsystem, electrodes, events, ieeg, scanslink@ftadel
ieeg_epilepsy_ecogmultiple sessions, tutorialanat, ieegT1w, channels, coordsystem, electrodes, events, ieeg, photo, scanslink@ftadel
ieeg_filtered_speechrecordings of three seizuresieegchannels, coordsystem, electrodes, events, ieeg, photon/a@choldgraf
ieeg_motorMiller2007Cue-based hand & tongue movement dataieegchannels, coordsystem, electrodes, events, ieegn/a@dorahermes
ieeg_visualStimulus dependence of gamma oscillations in human visual cortexanat, ieegT1w, channels, coordsystem, electrodes, events, ieegn/a@dorahermes
ieeg_visual_multimodaln/aanat, fmap, func, ieegT1w, bold, channels, coordsystem, electrodes, epi, events, ieeg, sbrefn/a@irisgroen

MEG

<!-- TABLE BELOW IS GENERATED AUTOMATICALLY. DO NOT EDIT DIRECTLY. -->
namedescriptiondatatypessuffixeslink to full datamaintained by
ds000117A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual taskanat, beh, dwi, fmap, func, megFLASH, T1w, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scanslink@RikHenson
ds000246Auditory dataset used for Brainstorm’s general online tutorialanat, megT1w, channels, coordsystem, headshape, meg, photo, scanslink@guiomar
ds000247Five minutes, eyes-open, resting-state MEG data from 5 subjects. This is a sample from The Open MEG Archive (OMEGA).anat, megT1w, channels, coordsystem, headshape, meg, scanslink@guiomar
ds000248MNE sample data: Data with visual and auditory stimulianat, megFLASH, T1w, channels, coordsystem, events, meg, scanslink@agramfort

Microscopy

<!-- TABLE BELOW IS GENERATED AUTOMATICALLY. DO NOT EDIT DIRECTLY. -->
namedescriptiondatatypessuffixeslink to full datamaintained by
eeg_ds003645s_hed_demoShows usage of Hierarchical Event Descriptor (HED) in .tsv filesanat, beh, eeg, micr, motionKSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, motion, photo, samples, scanslink@VisLab
micr_SEMExample SEM dataset in PNG format with 1 sample imaged over 2 sessionsmicrSEM, photo, samples, sessionslink@jcohenadad
micr_SEMzarrExample SEM dataset in PNG and OME-ZARR format with 1 sample imaged over 2 sessionsmicrSEM, SPIM, samples, sessionsn/a@TheChymera
micr_SPIMExample SPIM dataset in OME-TIFF format with 2 samples from the same subject with 4 chunks eachmicrSPIM, photo, sampleslink@jcohenadad
micr_XPCTzarrExample XPCT dataset in OME-ZARR format with 1 sample imagedmicrXPCT, photo, samples, sessionslink@chourroutm

Motion

<!-- TABLE BELOW IS GENERATED AUTOMATICALLY. DO NOT EDIT DIRECTLY. -->
namedescriptiondatatypessuffixeslink to full datamaintained by
eeg_ds003645s_hed_demoShows usage of Hierarchical Event Descriptor (HED) in .tsv filesanat, beh, eeg, micr, motionKSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, motion, photo, samples, scanslink@VisLab
motion_dualtaskolder and younger participants walking while performing discrimination taskeeg, motionchannels, eeg, events, motion, scansn/a@sjeung
motion_spotrotationparticipants rotated heading using full-body motion or joystickeeg, motionchannels, coordsystem, eeg, electrodes, events, motion, scanslink@sjeung
motion_systemvalidationExample dataset of two different motion captured system recorded almost simultaneously, but no brain datamotionchannels, motion, scanslink@JuliusWelzel

MRI

<!-- TABLE BELOW IS GENERATED AUTOMATICALLY. DO NOT EDIT DIRECTLY. -->
namedescriptiondatatypessuffixeslink to full datamaintained by
7t_trtn/aanat, fmap, funcT1map, T1w, bold, magnitude1, magnitude2, phasediff, physio, scans, sessionslinkn/a
ds000117A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual taskanat, beh, dwi, fmap, func, megFLASH, T1w, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scanslink@RikHenson
ds001single task, multiple runsanat, funcT1w, bold, events, inplaneT2linkn/a
ds002multiple tasks, multiple runsanat, funcT1w, bold, events, inplaneT2linkn/a
ds003single task, single runanat, funcT1w, bold, events, inplaneT2linkn/a
ds005single task, multiple runsanat, funcT1w, bold, events, inplaneT2linkn/a
ds006single task, multiple sessions, multiple runsanat, funcT1w, bold, events, inplaneT2linkn/a
ds007single task, multiple runsanat, funcT1w, bold, events, inplaneT2linkn/a
ds008multiple tasks, multiple runsanat, funcT1w, bold, events, inplaneT2linkn/a
ds009multiple tasks, multiple runsanat, funcT1w, bold, events, inplaneT2, scanslinkn/a
ds011multiple tasks, multiple runsanat, funcT1w, bold, events, inplaneT2linkn/a
ds051multiple tasks, multiple runsanat, funcT1w, bold, events, inplaneT2linkn/a
ds052multiple tasks, multiple runsanat, funcT1w, bold, events, inplaneT2linkn/a
ds101single task, multiple runsanat, funcT1w, bold, eventslinkn/a
ds102single task, multiple runsanat, funcT1w, bold, eventslinkn/a
ds105single task, multiple runsanat, funcT1w, bold, eventslinkn/a
ds107single task, multiple runsanat, funcT1w, bold, eventslinkn/a
ds108single task, multiple runsanat, funcT1w, bold, eventslinkn/a
ds109multiple tasks, multiple runsanat, funcT1w, bold, eventslinkn/a
ds110single task, multiple runsanat, funcT1w, bold, events, inplaneT2linkn/a
ds113bforrest gump watching, multiple sessions, multiple runsfuncbold, eventslinkn/a
ds114multiple tasks, multiple runsanat, dwi, funcT1w, bold, dwi, eventslinkn/a
ds116multiple tasks, multiple runsanat, funcT1w, bold, events, inplaneT2linkn/a
ds210multiple tasks, multiple runsfuncbold, physiolinkn/a
eeg_rest_fmriResting state with simultaneous fMRI. BrainVision data format (.eeg, .vhdr, .vmrk)anat, dwi, eeg, funcT1w, bold, dwi, eegn/a@cpernet
genetics_ukbbmultiple tasks, T1w, DTI, BOLD, genetic infoanat, dwi, funcFLAIR, T1w, bold, dwi, events, infon/a@cpernet
ieeg_visual_multimodaln/aanat, fmap, func, ieegT1w, bold, channels, coordsystem, electrodes, epi, events, ieeg, sbrefn/a@irisgroen
syntheticA synthetic datasetanat, beh, funcT1w, beh, bold, events, physio, scans, sessions, stimn/a@effigies

MRS

<!-- TABLE BELOW IS GENERATED AUTOMATICALLY. DO NOT EDIT DIRECTLY. -->
namedescriptiondatatypessuffixeslink to full datamaintained by
mrs_2dmrsi2D sLASER MRSI data from 8 subjectsanat, mrsT1w, mrsilink@markmikkelsen
mrs_biggabaMEGA-PRESS and PRESS MRS data from 12 subjects from one site from the Big GABA projectanat, mrsT1w, mrsref, svslink@markmikkelsen
mrs_fmrsFunctional MRS data involving a pain stimulus task from 15 subjectsanat, mrsT1w, events, mrsref, svslink@markmikkelsen

NIRS

<!-- TABLE BELOW IS GENERATED AUTOMATICALLY. DO NOT EDIT DIRECTLY. -->
namedescriptiondatatypessuffixeslink to full datamaintained by
fnirs_automaticity24 subjects performing (non-)automatic finger tapping and foot steppingnirschannels, coordsystem, events, nirs, optodes, practicelogbook, scanslink@robertoostenveld
fnirs_tappingExample fNIRS measurement with three conditions from five subjectsnirschannels, coordsystem, events, nirs, optodes, scanslink@rob-luke

PET

<!-- TABLE BELOW IS GENERATED AUTOMATICALLY. DO NOT EDIT DIRECTLY. -->
namedescriptiondatatypessuffixeslink to full datamaintained by
pet001T1w, PET, bloodanat, petT1w, blood, petn/a@mnoergaard
pet002T1w, PETanat, petT1w, petlink@mnoergaard
pet003T1w, PET, bloodanat, petT1w, blood, petn/a@mnoergaard
pet004PET, bloodpetblood, petn/a@mnoergaard
pet005T1w, PETanat, petT1w, events, petn/a@mnoergaard

qMRI

<!-- TABLE BELOW IS GENERATED AUTOMATICALLY. DO NOT EDIT DIRECTLY. -->
namedescriptiondatatypessuffixeslink to full datamaintained by
qmri_irt1Inversion Recovery T1 mappinganatIRT1not publicly available@agahkarakuzu
qmri_megreMulti-Echo Gradient-Echo for T2star mapping.anatMEGREnot publicly available@agahkarakuzu
qmri_meseMulti-Echo Spin-Echo for T2 or Myelin Water Fraction (MWF) mapping.anatMESEnot publicly available@agahkarakuzu
qmri_mp2rageMP2RAGE for T1 mappinganatMP2RAGE, T1map, UNIT1, defacemasklink@Gilles86
qmri_mp2ragemeMulti-echo MP2RAGEanat, fmapMP2RAGE, TB1maplink@Gilles86
qmri_mpmMulti-parametric mapping for R1, R2star, MTsat and PD mappinganat, fmapMPM, RB1COR, TB1EPI, magnitude1, magnitude2, phasedifflink@ChristophePhillips
qmri_mtsatExample dataset for T1 and MTsat mapping. Includes a double-angle B1+ mapping example.anat, fmapMTS, TB1DAMlink@agahkarakuzu
qmri_qsmChimap using fast QSManatT1wnot publicly available@agahkarakuzu
qmri_sa2rageFast B1+ mapping using SA2RAGEfmapTB1SRGEnot publicly available@agahkarakuzu
qmri_tb1tflB1+ mapping with TurboFLASH readout.fmapTB1TFLnot publicly available@agahkarakuzu
qmri_vfaVariable Flip Angle T1 mapping. Includes an Actual Flip Angle (AFI) B1+ mapping example.anat, fmapTB1AFI, VFAlink@agahkarakuzu

Behavioral

<!-- TABLE BELOW IS GENERATED AUTOMATICALLY. DO NOT EDIT DIRECTLY. -->
namedescriptiondatatypessuffixeslink to full datamaintained by
ds000117A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual taskanat, beh, dwi, fmap, func, megFLASH, T1w, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scanslink@RikHenson
eeg_ds003645s_hed_demoShows usage of Hierarchical Event Descriptor (HED) in .tsv filesanat, beh, eeg, micr, motionKSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, motion, photo, samples, scanslink@VisLab
syntheticA synthetic datasetanat, beh, funcT1w, beh, bold, events, physio, scans, sessions, stimn/a@effigies