This repository contains a set of BIDS-compatible datasets with empty raw data files. These datasets can be useful to:
- write lightweight software tests
- 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)
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.
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
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.
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 |
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.
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
| 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) |
| 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 |
| 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 |
| 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/ |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |