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.

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.

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

iEEG datasets

MRI datasets

ASL datasets

qMRI datasets

PET datasets

Microscopy datasets

NIRS datasets

Multimodal datasets