/bids-examples

A set of BIDS compatible datasets with empty raw data files that can be used for writing lightweight software tests.

Primary LanguageMATLAB

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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:

  • synthetic
  • Most EEG or iEEG data in BrainVision format (e.g., eeg_matchingpennies)

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.

name errors ignored
genetics_ukbb SliceTiming 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.

name why skipped
ds000001-fmriprep lack of coverage for "derivatives" in bids-validator

Contributing

We are happy to receive contributions in the form of:

  • updates to existing examples, or the dataset index
  • new examples
    • only if they cover aspects that are currently not covered by existing examples
    • only if a maintainer can be found for this dataset
  • suggestions on how to improve the bids-examples repository

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

Dataset index

ASL

name description datatypes suffixes link to full data maintained by
asl001 T1w, asl (GE, PCASL, 3D_SPIRAL), m0scan within timeseries anat, perf T1w, asl, aslcontext, asllabeling link @patsycle
asl002 T1w, asl (Philips, PCASL, 2D_EPI), m0scan as separate scan anat, perf T1w, asl, aslcontext, asllabeling, m0scan link @patsycle
asl003 T1w, asl (Siemens, PASL, multiTI), M0scan as separate scan anat, perf T1w, asl, aslcontext, asllabeling, m0scan link @patsycle
asl004 T1w, asl (Siemens, PCASL, multiPLD with pepolar), m0scan separate scans with pepolar approach anat, fmap, perf T1w, asl, aslcontext, asllabeling, m0scan link @patsycle
asl005 T1w, asl (Siemens, PCASL, singleTI, 3D_GRASE), m0scan as separate scan anat, perf T1w, asl, aslcontext, asllabeling, m0scan link @patsycle

EEG

name description datatypes suffixes link to full data maintained by
eeg_cbm Rest EEG. European Data Format (.edf) eeg channels, eeg, events, scans n/a @cpernet
eeg_ds003645s_hed_library HED annotation using HED library vocabularies (schema). eeg channels, eeg, events link @VisLab
eeg_face13 Deconstructing the early visual electrocortical response to face and house stimuli. EDF format eeg channels, coordsystem, eeg, electrodes, events n/a @andesha
eeg_matchingpennies Offline data of BCI experiment decoding left vs. right hand movement. BrainVision data format (.eeg, .vhdr, .vmrk) eeg channels, eeg, events link @sappelhoff
eeg_rishikesh Mind wandering experiment. EEG data in Biosemi (.bdf) format eeg channels, eeg, events link @arnodelorme

iEEG

name description datatypes suffixes link to full data maintained by
ieeg_epilepsyNWB multiple sessions, tutorial — derivative dataset of ieeg_epilepsy showcasing the NWB file format alternative anat, ieeg T1w, channels, coordsystem, electrodes, events, ieeg, scans link @TheChymera
ieeg_epilepsy multiple sessions, tutorial anat, ieeg T1w, channels, coordsystem, electrodes, events, ieeg, scans link @ftadel
ieeg_epilepsy_ecog multiple sessions, tutorial anat, ieeg T1w, channels, coordsystem, electrodes, events, ieeg, photo, scans link @ftadel
ieeg_filtered_speech recordings of three seizures ieeg channels, coordsystem, electrodes, events, ieeg, photo n/a @choldgraf
ieeg_motorMiller2007 Cue-based hand & tongue movement data ieeg channels, coordsystem, electrodes, events, ieeg n/a @dorahermes
ieeg_visual Stimulus dependence of gamma oscillations in human visual cortex anat, ieeg T1w, channels, coordsystem, electrodes, events, ieeg n/a @dorahermes
ieeg_visual_multimodal n/a anat, fmap, func, ieeg T1w, bold, channels, coordsystem, electrodes, epi, events, ieeg, sbref n/a @irisgroen

MEG

name description datatypes suffixes link to full data maintained by
ds000117 A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual task anat, beh, dwi, fmap, func, meg FLASH, T1w, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans link @RikHenson
ds000246 Auditory dataset used for Brainstorm’s general online tutorial anat, meg T1w, channels, coordsystem, headshape, meg, photo, scans link @guiomar
ds000247 Five minutes, eyes-open, resting-state MEG data from 5 subjects. This is a sample from The Open MEG Archive (OMEGA). anat, meg T1w, channels, coordsystem, headshape, meg, scans link @guiomar
ds000248 MNE sample data: Data with visual and auditory stimuli anat, meg FLASH, T1w, channels, coordsystem, events, meg, scans link @agramfort

Microscopy

name description datatypes suffixes link to full data maintained by
eeg_ds003645s_hed_demo Shows usage of Hierarchical Event Descriptor (HED) in .tsv files anat, beh, eeg, micr, motion KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, motion, photo, samples, scans link @VisLab
micr_SEM Example SEM dataset in PNG format with 1 sample imaged over 2 sessions micr SEM, photo, samples, sessions link @jcohenadad
micr_SEMzarr Example SEM dataset in PNG and OME-ZARR format with 1 sample imaged over 2 sessions micr SEM, SPIM, samples, sessions n/a @TheChymera
micr_SPIM Example SPIM dataset in OME-TIFF format with 2 samples from the same subject with 4 chunks each micr SPIM, photo, samples link @jcohenadad
micr_XPCTzarr Example XPCT dataset in OME-ZARR format with 1 sample imaged micr XPCT, photo, samples, sessions link @chourroutm

Motion

name description datatypes suffixes link to full data maintained by
eeg_ds003645s_hed_demo Shows usage of Hierarchical Event Descriptor (HED) in .tsv files anat, beh, eeg, micr, motion KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, motion, photo, samples, scans link @VisLab
motion_dualtask older and younger participants walking while performing discrimination task eeg, motion channels, eeg, events, motion, scans n/a @sjeung
motion_spotrotation participants rotated heading using full-body motion or joystick eeg, motion channels, coordsystem, eeg, electrodes, events, motion, scans link @sjeung
motion_systemvalidation Example dataset of two different motion captured system recorded almost simultaneously, but no brain data motion channels, motion, scans link @JuliusWelzel

MRI

name description datatypes suffixes link to full data maintained by
7t_trt n/a anat, fmap, func T1map, T1w, bold, magnitude1, magnitude2, phasediff, physio, scans, sessions link n/a
ds000117 A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual task anat, beh, dwi, fmap, func, meg FLASH, T1w, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans link @RikHenson
ds001 single task, multiple runs anat, func T1w, bold, events, inplaneT2 link n/a
ds002 multiple tasks, multiple runs anat, func T1w, bold, events, inplaneT2 link n/a
ds003 single task, single run anat, func T1w, bold, events, inplaneT2 link n/a
ds005 single task, multiple runs anat, func T1w, bold, events, inplaneT2 link n/a
ds006 single task, multiple sessions, multiple runs anat, func T1w, bold, events, inplaneT2 link n/a
ds007 single task, multiple runs anat, func T1w, bold, events, inplaneT2 link n/a
ds008 multiple tasks, multiple runs anat, func T1w, bold, events, inplaneT2 link n/a
ds009 multiple tasks, multiple runs anat, func T1w, bold, events, inplaneT2, scans link n/a
ds011 multiple tasks, multiple runs anat, func T1w, bold, events, inplaneT2 link n/a
ds051 multiple tasks, multiple runs anat, func T1w, bold, events, inplaneT2 link n/a
ds052 multiple tasks, multiple runs anat, func T1w, bold, events, inplaneT2 link n/a
ds101 single task, multiple runs anat, func T1w, bold, events link n/a
ds102 single task, multiple runs anat, func T1w, bold, events link n/a
ds105 single task, multiple runs anat, func T1w, bold, events link n/a
ds107 single task, multiple runs anat, func T1w, bold, events link n/a
ds108 single task, multiple runs anat, func T1w, bold, events link n/a
ds109 multiple tasks, multiple runs anat, func T1w, bold, events link n/a
ds110 single task, multiple runs anat, func T1w, bold, events, inplaneT2 link n/a
ds113b forrest gump watching, multiple sessions, multiple runs func bold, events link n/a
ds114 multiple tasks, multiple runs anat, dwi, func T1w, bold, dwi, events link n/a
ds116 multiple tasks, multiple runs anat, func T1w, bold, events, inplaneT2 link n/a
ds210 multiple tasks, multiple runs func bold, physio link n/a
eeg_rest_fmri Resting state with simultaneous fMRI. BrainVision data format (.eeg, .vhdr, .vmrk) anat, dwi, eeg, func T1w, bold, dwi, eeg n/a @cpernet
genetics_ukbb multiple tasks, T1w, DTI, BOLD, genetic info anat, dwi, func FLAIR, T1w, bold, dwi, events, info n/a @cpernet
ieeg_visual_multimodal n/a anat, fmap, func, ieeg T1w, bold, channels, coordsystem, electrodes, epi, events, ieeg, sbref n/a @irisgroen
synthetic A synthetic dataset anat, beh, func T1w, beh, bold, events, physio, scans, sessions, stim n/a @effigies

MRS

name description datatypes suffixes link to full data maintained by
mrs_2dmrsi 2D sLASER MRSI data from 8 subjects anat, mrs T1w, mrsi link @markmikkelsen
mrs_biggaba MEGA-PRESS and PRESS MRS data from 12 subjects from one site from the Big GABA project anat, mrs T1w, mrsref, svs link @markmikkelsen
mrs_fmrs Functional MRS data involving a pain stimulus task from 15 subjects anat, mrs T1w, events, mrsref, svs link @markmikkelsen

NIRS

name description datatypes suffixes link to full data maintained by
fnirs_automaticity 24 subjects performing (non-)automatic finger tapping and foot stepping nirs channels, coordsystem, events, nirs, optodes, practicelogbook, scans link @robertoostenveld
fnirs_tapping Example fNIRS measurement with three conditions from five subjects nirs channels, coordsystem, events, nirs, optodes, scans link @rob-luke

PET

name description datatypes suffixes link to full data maintained by
pet001 T1w, PET, blood anat, pet T1w, blood, pet n/a @mnoergaard
pet002 T1w, PET anat, pet T1w, pet link @mnoergaard
pet003 T1w, PET, blood anat, pet T1w, blood, pet n/a @mnoergaard
pet004 PET, blood pet blood, pet n/a @mnoergaard
pet005 T1w, PET anat, pet T1w, events, pet n/a @mnoergaard

qMRI

name description datatypes suffixes link to full data maintained by
qmri_irt1 Inversion Recovery T1 mapping anat IRT1 not publicly available @agahkarakuzu
qmri_megre Multi-Echo Gradient-Echo for T2star mapping. anat MEGRE not publicly available @agahkarakuzu
qmri_mese Multi-Echo Spin-Echo for T2 or Myelin Water Fraction (MWF) mapping. anat MESE not publicly available @agahkarakuzu
qmri_mp2rage MP2RAGE for T1 mapping anat MP2RAGE, T1map, UNIT1, defacemask link @Gilles86
qmri_mp2rageme Multi-echo MP2RAGE anat, fmap MP2RAGE, TB1map link @Gilles86
qmri_mpm Multi-parametric mapping for R1, R2star, MTsat and PD mapping anat, fmap MPM, RB1COR, TB1EPI, magnitude1, magnitude2, phasediff link @ChristophePhillips
qmri_mtsat Example dataset for T1 and MTsat mapping. Includes a double-angle B1+ mapping example. anat, fmap MTS, TB1DAM link @agahkarakuzu
qmri_qsm Chimap using fast QSM anat T1w not publicly available @agahkarakuzu
qmri_sa2rage Fast B1+ mapping using SA2RAGE fmap TB1SRGE not publicly available @agahkarakuzu
qmri_tb1tfl B1+ mapping with TurboFLASH readout. fmap TB1TFL not publicly available @agahkarakuzu
qmri_vfa Variable Flip Angle T1 mapping. Includes an Actual Flip Angle (AFI) B1+ mapping example. anat, fmap TB1AFI, VFA link @agahkarakuzu

Behavioral

name description datatypes suffixes link to full data maintained by
ds000117 A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual task anat, beh, dwi, fmap, func, meg FLASH, T1w, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans link @RikHenson
eeg_ds003645s_hed_demo Shows usage of Hierarchical Event Descriptor (HED) in .tsv files anat, beh, eeg, micr, motion KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, motion, photo, samples, scans link @VisLab
synthetic A synthetic dataset anat, beh, func T1w, beh, bold, events, physio, scans, sessions, stim n/a @effigies