Data Organization

OpenfMRI strives to be a neuroimaging data sharing platform that provides curated datasets in a way that maximizes their long term availability and reuse. To this end, OpenfMRI has adopted the Brain Imaging Data Structure (BIDS) format as its standard format for shared, curated datasets.

Brain Imaging Data Structure (BIDS)

BIDS is an exciting neuroimaging data organization format developed within the International Neuroinformatics Coordinating Facility and in the collaboration with many scientists working in the neuroimaging field. The goal of BIDS is to define a powerful, flexible, and consistent framework for integrating the diverse types of experimental data routinely acquired in neuroimaging studies.

Provisions are included in BIDS to accommodate these data types:

Subject-level variables (gender, age, handedness, etc.),

Longitudinal and multi-session studies,

Structural, anatomical imaging data (MPRAGE, T1-weighted, T2-weighted, and many more),

Resting state and task-based fMRI data (including specifying event onsets and durations),

Diffusion-weighted imaging data (including DTI, HARDI, DSI, etc. along with B-values and gradient directionality),

Field maps for correcting for B0 inhomogeneity in echo-planar imaging sequences along with the necessary information to apply them,

Physiological (pulse, respiration, etc.) monitoring output acquired during MRI experiments,

Behavioral data collected without MRI, and

Standardized metadata to describe the conditions and parameters of the experiment data.

Please see the official BIDS format specification for more information and details.

BIDS Tools and Utilities

Open source tools are available now, and more are in development for working with BIDS datasets (including datasets available from OpenfMRI):

bids-validator: A validator written in JavaScript that scans a BIDS dataset and produces warnings or errors when things seem to deviate from the specification.

BIDS-examples: A set of reduced-size (zero file size) datasets already in BIDS format for example purposes and to test the bids-validator.

bids-utils: A repository that will contain new utilities and tools that work with BIDS datasets.

dcm2niix: Supports creation of BIDS-compatible scan metadata .json files with TR, TE, slice timings and other necessary parameters during DICOM to NIfTI conversion.

heudiconv: A flexible DICOM converter for organizing brain imaging data into structured directory layouts.

Submitting Data to OpenfMRI

All curated data sets available from OpenfMRI will be organized in BIDS format. If you plan to submit data to OpenfMRI for sharing, please consider submitting it in BIDS format to streamline the curation and publishing process. Our data curation staff can assist you with converting your existing data into BIDS format prior to submission.

Old OpenfMRI Data Organization

Information regarding how data was organized on OpenfMRI prior to the BIDS standard can be found here.