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 | |:--------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------|:-----------------|:------------------------------------------|:------------------------------|:-----------------------------------------| | 2dmbpcasl | Siemens 2D MultiBand Multi-delay PCASL (m0 and noRF included within timeseries) | anat, fmap, perf | T1w, asl, aslcontext, epi | link | @aptinis | | asl001 | T1w, asl (GE, PCASL, 3DSPIRAL), m0scan within timeseries | anat, perf | T1w, asl, aslcontext, asllabeling | link | @patsycle | | asl002 | T1w, asl (Philips, PCASL, 2DEPI), 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 |

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 | | eegds003645shed_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 |

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 | | eegds003645shed_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 |

DWI

| 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 | | ds114 | multiple tasks, multiple runs | anat, dwi, func | T1w, bold, dwi, events | link | n/a | | dwi_deriv | exemplifies the storage of diffusion MRI derivates that may be generated on the Siemens XA platform. | dwi | dwi | n/a | n/a | | eegrestfmri | 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

| 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 | | ieegepilepsyecog | multiple sessions, tutorial | anat, ieeg | T1w, channels, coordsystem, electrodes, events, ieeg, photo, scans | link | @ftadel | | ieegfilteredspeech | 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 | | ieegvisualmultimodal | n/a | anat, fmap, func, ieeg | T1w, bold, channels, coordsystem, electrodes, epi, events, ieeg, sbref | n/a | @irisgroen | | xeeghedscore | EEG and iEEG data with annotations of artifacts, seizures and modulators using HED-SCORE | anat, eeg, ieeg | T1w, channels, coordsystem, eeg, electrodes, events, ieeg | n/a | @dorahermes |

HED

| name | description | datatypes | suffixes | link to full data | maintained by | |:------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------|:-----------------------------|:---------------------------------------------------------------------------------------------------------------|:------------------------------------------------|:---------------------------------------------| | eegds003645shed_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 | | eegds003645shed_library | HED annotation using HED library vocabularies (schema). | eeg | channels, eeg, events | link | @VisLab | | xeeghedscore | EEG and iEEG data with annotations of artifacts, seizures and modulators using HED-SCORE | anat, eeg, ieeg | T1w, channels, coordsystem, eeg, electrodes, events, ieeg | n/a | @dorahermes |

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 Brainstorms 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 | |:------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------|:-----------------------------|:---------------------------------------------------------------------------------------------------------------|:-------------------------------------------------------------|:---------------------------------------------| | eegds003645shed_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 | |:--------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------|:-----------------------------|:---------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------|:-------------------------------------------------| | eegds003645shed_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 | | eegrestfmri | 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 | | ieegvisualmultimodal | 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 | | volume_timing | Sparse BOLD acquisitions | func | bold | 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 | | pet006 | PET | pet | pet | n/a | @bendhouseart |

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 |

Phenotype

| name | description | datatypes | suffixes | link to full data | maintained by | |:--------------------------------------------------------------------------------|:-----------------------------------------------------------------|:----------------|:-----------|:--------------------|:-----------------------------------------| | pheno004 | Minimal dataset with subjects with imaging and/or phenotype data | phenotype, anat | T1w | n/a | @ericearl |

Provenance

| name | description | datatypes | suffixes | link to full data | maintained by | |--------|---------------|-------------|------------|---------------------|-----------------|