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 bash 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 idiosyncracies 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

Below you find several tables with information about the datasets available in bids-examples (in alphabetical order).

• EEG datasets
• iEEG datasets
• MRI datasets
• ASL datasets
• qMRI datasets
• PET datasets
• Microscopy datasets
• NIRS datasets
• Multimodal datasets

EEG datasets

name	maintained by	description	link to full data
eeg_matchingpennies	@sappelhoff	Offline data of BCI experiment decoding left vs. right hand movement. BrainVision data format (.eeg, .vhdr, .vmrk)	https://doi.org/10.17605/OSF.IO/CJ2DR
eeg_rishikesh	@arnodelorme	Mind wandering experiment. EEG data in Biosemi (.bdf) format	https://openneuro.org/datasets/ds001787
eeg_face13	@andesha	Deconstructing the early visual electrocortical response to face and house stimuli. EDF format
eeg_ds003654s_hed	@VisLab	Shows usage of Hierarchical Event Descriptor (HED) in events files	https://openneuro.org/datasets/ds003645
eeg_ds003654s_hed_inheritance	@VisLab	HED annotation with multiple inherited sidecars	https://openneuro.org/datasets/ds003645
eeg_ds003654s_hed_longform	@VisLab	HED annotation using tags in long form.	https://openneuro.org/datasets/ds003645
eeg_ds003654s_hed_library	@VisLab	HED annotation using HED library vocabularies (schema).	https://openneuro.org/datasets/ds003645
eeg_cbm	@cpernet	Rest EEG. European Data Format (.edf)

iEEG datasets

name	maintained by	description
ieeg_filtered_speech	@choldgraf	recordings of three seizures
ieeg_motorMiller2007	@dorahermes	Cue-based hand & tongue movement data
ieeg_visual	@dorahermes	Stimulus dependence of gamma oscillations in human visual cortex

MRI datasets

name	maintained by	description	func	anat	other	link to link to full data
7t_trt			bold, physio	T1w, quantitative T1 maps	fmap	https://bit.ly/2H0Z6Qt
ds001		single task, multiple runs	bold, events	T1w, in-plane T2		https://openneuro.org/datasets/ds000001/versions/00006
ds002		multiple tasks, multiple runs	bold, events	T1w, in-plane T2		https://openneuro.org/datasets/ds000002/versions/00002
ds003		single task, single run	bold, events	T1w, in-plane T2		https://openneuro.org/datasets/ds000003/versions/00001
ds005		single task, multiple runs	bold, events	T1w, in-plane T2		https://openneuro.org/datasets/ds000005/versions/00001
ds006		single task, multiple sessions, multiple runs	bold, events	T1w, in-plane T2		https://openneuro.org/datasets/ds000006/versions/00001
ds007		single task, multiple runs	bold, events	T1w, in-plane T2		https://openneuro.org/datasets/ds000007/versions/00001
ds008		multiple tasks, multiple runs	bold, events	T1w, in-plane T2		https://openneuro.org/datasets/ds000008/versions/00001
ds009		multiple tasks, multiple runs	bold, events	T1w, in-plane T2		https://openneuro.org/datasets/ds000009/versions/00002
ds011		multiple tasks, multiple runs	bold	T1w		https://openneuro.org/datasets/ds000011/versions/00001
ds051		multiple tasks, multiple runs	bold	T1w, in-plane T2		https://openneuro.org/datasets/ds000051/versions/00001
ds052		multiple tasks, multiple runs	bold	T1w, in-plane T2		https://openneuro.org/datasets/ds000052/versions/00001
ds101		single task, multiple runs	bold	T1w		https://openneuro.org/datasets/ds000101/versions/00004
ds102		single task, multiple runs	bold	T1w		https://openneuro.org/datasets/ds000102/versions/00001
ds105		single task, multiple runs	bold	T1w		https://openneuro.org/datasets/ds000105/versions/00001
ds107		single task, multiple runs	bold	T1w		https://openneuro.org/datasets/ds000107/versions/00001
ds108		single task, multiple runs	bold	T1w		https://openneuro.org/datasets/ds000108/versions/00002
ds109		multiple tasks, multiple runs	bold	T1w		https://openneuro.org/datasets/ds000109/versions/00001
ds110		single task, multiple runs	bold	T1w, in-plane T2		https://openneuro.org/datasets/ds000110/versions/00001
ds113b		forrest gump watching, multiple sessions, multiple runs	bold	T1w, T2w	angiography, dwi, fmap	https://openneuro.org/datasets/ds000113/versions/1.3.0
ds114		multiple tasks, multiple runs	bold	T1w	DWI	https://openneuro.org/datasets/ds000114/versions/1.0.1
ds116		multiple tasks, multiple runs	bold	T1w, in-plane T2		https://openneuro.org/datasets/ds000116/versions/00003
ds210		multiple tasks, multiple runs	bold	T1w		https://openneuro.org/datasets/ds000210/versions/00002
hcp_example_bids	@robertoostenveld		bold	T1w		https://bit.ly/2H0Z6Qt
synthetic	@effigies	A synthetic dataset	bold	T1w		n/a
ds000001-fmriprep	@effigies	Common derivatives example	bold	T1w		https://openneuro.org/datasets/ds000001/versions/1.0.0

ASL datasets

name	maintained by	description	link to link to full data
asl001	@patsycle	T1w, asl (GE, PCASL, 3D_SPIRAL), m0scan within timeseries	https://osf.io/yru2q/
asl002	@patsycle	T1w, asl (Philips, PCASL, 2D_EPI), m0scan as separate scan	https://osf.io/yru2q/
asl003	@patsycle	T1w, asl (Siemens, PASL, multiTI), M0scan as separate scan	https://osf.io/yru2q/
asl004	@patsycle	T1w, asl (Siemens, PCASL, multiPLD with pepolar), m0scan separate scans with pepolar appraoch	https://osf.io/yru2q/
asl005	@patsycle	T1w, asl (Siemens, PCASL, singleTI, 3D_GRASE), m0scan as separate scan	https://osf.io/yru2q/

qMRI datasets

name	maintained by	description	link to link to full data
qmri_mp2rage	@Gilles86	MP2RAGE for T1 mapping	https://osf.io/k4bs5/
qmri_mp2rageme	@Gilles86	Multi-echo MP2RAGE	https://osf.io/k4bs5/
qmri_mpm	@ChristophePhillips	Multi-parametric mapping for R1, R2star, MTsat and PD mapping	https://osf.io/k4bs5/
qmri_mtsat	@agahkarakuzu	Example dataset for T1 and MTsat mapping. Includes a double-angle B1+ mapping example.	https://osf.io/k4bs5/
qmri_qsm	@agahkarakuzu	Chimap using fast QSM	not publicly availabe
qmri_sa2rage	@agahkarakuzu	Fast B1+ mapping using SA2RAGE	not publicly availabe
qmri_vfa	@agahkarakuzu	Variable Flip Angle T1 mapping. Includes an Actual Flip Angle (AFI) B1+ mapping example.	https://osf.io/k4bs5/
qmri_irt1	@agahkarakuzu	Inversion Recovery T1 mapping	not publicly availabe
qmri_mese	@agahkarakuzu	Multi-Echo Spin-Echo for T2 or Myelin Water Fraction (MWF) mapping.	not publicly availabe
qmri_megre	@agahkarakuzu	Multi-Echo Gradient-Echo for T2star mapping.	not publicly availabe
qmri_tb1tfl	@agahkarakuzu	B1+ mapping with TurboFLASH readout.	not publicly availabe

PET datasets

name	maintained by	description	link to full data
pet001	@mnoergaard	T1w, PET, blood
pet002	@mnoergaard	T1w, PET	https://openneuro.org/datasets/ds001420/
pet003	@mnoergaard	T1w, PET, blood
pet004	@mnoergaard	PET, blood
pet005	@mnoergaard	T1w, PET

Microscopy datasets

name	maintained by	description
micr_SEM	@jcohenadad	Example SEM dataset in PNG format with 1 sample imaged over 2 sessions
micr_SEMzarr	@TheChymera	Example SEM dataset in PNG and OME-ZARR format with 1 sample imaged over 2 sessions
micr_SPIM	@jcohenadad	Example SPIM dataset in OME-TIFF format with 2 samples from the same subject with 4 chunks each

NIRS datasets

name	maintained by	description	link to full data
fnirs_tapping	@rob_luke	Example fNIRS measurement with three conditions from five subjects	https://doi.org/10.5281/zenodo.5529797
fnirs_automaticiy	@robertoostenveld	24 subjects performing (non-)automatic finger tapping and foot stepping	https://doi.org/10.34973/vesb-mh30

Multimodal datasets

name	maintained by	description	mri	meg	eeg	ieeg	genetics	link to full data
ds000117	@RikHenson	A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual task	anat, dwi, func, fmap	meg	eeg			https://openneuro.org/datasets/ds000117/
ds000246	@guiomar	Auditory dataset used for Brainstorm’s general online tutorial	anat	meg				https://openneuro.org/datasets/ds000246/versions/00001
ds000247	@guiomar	Five minutes, eyes-open, resting-state MEG data from 5 subjects. This is a sample from The Open MEG Archive (OMEGA).	anat	meg				https://openneuro.org/datasets/ds000247/versions/00001
ds000248	@agramfort	MNE sample data: Data with visual and auditory stimuli	anat	meg				https://openneuro.org/datasets/ds000248/versions/00001
eeg_ds000117	@robertoostenveld	Multimodal (fMRI, MEG, EEG) stripped down to EEG with MRI anatomical scan and electrode coordinates. EEGLAB data format (.set, .fdt)	anat		eeg			https://openneuro.org/datasets/ds000117/
eeg_rest_fmri	@cpernet	Resting state with simultaneous fMRI. BrainVision data format (.eeg, .vhdr, .vmrk)	anat, dwi, func		eeg
ieeg_epilepsy	@ftadel	multiple sessions, tutorial	anat			ieeg		https://neuroimage.usc.edu/bst/getupdate.php?s=tutorial_epimap_bids
ieeg_epilepsy_ecog	@ftadel	multiple sessions, tutorial	anat			ieeg		https://neuroimage.usc.edu/bst/getupdate.php?s=sample_ecog
ieeg_visual_multimodal	@irisgroen		anat, fmap, func			ieeg
genetics_ukbb	@cpernet	multiple tasks, T1w, DTI, BOLD, genetic info	anat, dwi, func, fmap				genetics