README.md

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
2d_mb_pcasl	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, 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

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

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

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
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

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
xeeg_hed_score	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
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
eeg_ds003645s_hed_library	HED annotation using HED library vocabularies (schema).	eeg	channels, eeg, events	link	@VisLab
xeeg_hed_score	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 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