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, or the BrainVision data
headers for .vhdr 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).
| 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 |
| name | maintained by | description | link to full data |
|---|---|---|---|
| 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 | link to link to full data |
|---|---|---|---|
| 7t_trt | field maps, physiological data, quantitative T1 maps, T1w, BOLD | https://bit.ly/2H0Z6Qt | |
| asl001 | @patsycle | T1w, asl (GE, PCASL, 3D_SPIRAL), m0scan within timeseries | |
| asl002 | @patsycle | T1w, asl (Philips, PCASL, 2D_EPI), m0scan as separate scan | |
| asl003 | @patsycle | T1w, asl (Siemens, PASL, multiTI), M0scan as separate scan | |
| asl004 | @patsycle | T1w, asl (Siemens, PCASL, multiPLD with pepolar), m0scan separate scans with pepolar appraoch | |
| asl005 | @patsycle | T1w, asl (Siemens, PCASL, singleTI, 3D_GRASE), m0scan as separate scan | |
| ds001 | single task, multiple runs, in-plane T2, events, T1w, BOLD | https://openneuro.org/datasets/ds000001/versions/00006 | |
| ds002 | multiple tasks, multiple runs, in-plane T2, events, T1w, BOLD | https://openneuro.org/datasets/ds000002/versions/00002 | |
| ds003 | single task, single run, in-plane T2, events, T1w, BOLD | https://openneuro.org/datasets/ds000003/versions/00001 | |
| ds005 | single task, multiple runs, in-plane T2, events, T1w, BOLD | https://openneuro.org/datasets/ds000005/versions/00001 | |
| ds006 | single task, multiple sessions, multiple runs, in-plane T2, events, T1w, BOLD | https://openneuro.org/datasets/ds000006/versions/00001 | |
| ds007 | single task, multiple runs, in-plane T2, events, T1w, BOLD | https://openneuro.org/datasets/ds000007/versions/00001 | |
| ds008 | multiple tasks, multiple runs, in-plane T2, events, T1w, BOLD | https://openneuro.org/datasets/ds000008/versions/00001 | |
| ds009 | multiple tasks, multiple runs, in-plane T2, events, T1w, BOLD | https://openneuro.org/datasets/ds000009/versions/00002 | |
| ds011 | multiple tasks, multiple runs, T1w, BOLD | https://openneuro.org/datasets/ds000011/versions/00001 | |
| ds051 | multiple tasks, multiple runs, T1w, BOLD, inplane T2 | https://openneuro.org/datasets/ds000051/versions/00001 | |
| ds052 | multiple tasks, multiple runs, T1w, BOLD, inplane T2 | https://openneuro.org/datasets/ds000052/versions/00001 | |
| ds101 | single task, multiple runs, T1w, BOLD | https://openneuro.org/datasets/ds000101/versions/00004 | |
| ds102 | single task, multiple runs, T1w, BOLD | https://openneuro.org/datasets/ds000102/versions/00001 | |
| ds105 | single task, multiple runs, T1w, BOLD | https://openneuro.org/datasets/ds000105/versions/00001 | |
| ds107 | single task, multiple runs, T1w, BOLD | https://openneuro.org/datasets/ds000107/versions/00001 | |
| ds108 | single task, multiple runs, T1w, BOLD | https://openneuro.org/datasets/ds000108/versions/00002 | |
| ds109 | multiple tasks, multiple runs, T1w, BOLD | https://openneuro.org/datasets/ds000109/versions/00001 | |
| ds110 | single task, multiple runs, T1w, BOLD, in plane T2 | https://openneuro.org/datasets/ds000110/versions/00001 | |
| ds113b | forrest gump watching, multiple sessions, multiple runs, T1w, T2w, BOLD, angiography, dwi, fieldmaps | https://openneuro.org/datasets/ds000113/versions/1.3.0 | |
| ds114 | multiple tasks, multiple runs, T1w, BOLD, DWI | https://openneuro.org/datasets/ds000114/versions/1.0.1 | |
| ds116 | multiple tasks, multiple runs, T1w, BOLD, inplane T2 | https://openneuro.org/datasets/ds000116/versions/00003 | |
| ds210 | multiple tasks, multiple runs, T1w, BOLD | https://openneuro.org/datasets/ds000210/versions/00002 | |
| hcp_example_bids | @robertoostenveld | https://bit.ly/2H0Z6Qt | |
| synthetic | @effigies | A synthetic dataset | mri |
| ds000001-fmriprep | @effigies | Common derivatives example | mri |
| 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 | 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 | mri | meg | eeg | https://openneuro.org/datasets/ds000117/ | ||
| ds000246 | @guiomar | Auditory dataset used for Brainstorm’s general online tutorial | mri | 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). | mri | meg | https://openneuro.org/datasets/ds000247/versions/00001 | |||
| ds000248 | @agramfort | MNE sample data: Data with visual and auditory stimuli | mri | meg | https://openneuro.org/datasets/ds000248/versions/00001 | |||
| eeg_cbm | @cpernet | Rest EEG. European Data Format (.edf) | mri | eeg | ||||
| eeg_ds000117 | @robertoostenveld | Multimodal (fMRI, MEG, EEG) stripped down to EEG with MRI anatomical scan and electrode coordinates. EEGLAB data format (.set, .fdt) | mri | eeg | https://openneuro.org/datasets/ds000117/ | |||
| eeg_rest_fmri | @cpernet | Resting state with simultaneous fMRI. BrainVision data format (.eeg, .vhdr, .vmrk) | mri | eeg | ||||
| ieeg_epilepsy | @ftadel | multiple sessions, tutorial | mri | ieeg | https://neuroimage.usc.edu/bst/getupdate.php?s=tutorial_epimap | |||
| ieeg_epilepsy_ecog | @ftadel | multiple sessions, tutorial | mri | ieeg | https://neuroimage.usc.edu/bst/getupdate.php?s=sample_ecog | |||
| ieeg_visual_multimodal | @irisgroen | mri | ieeg | |||||
| genetics_ukbb | @cpernet | multiple tasks, T1w, DTI, BOLD, genetic info | mri | genetics |