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Data format and organization

File Format: SNIRF

The Society for fNIRS has proposed SNIRF (Shared Near InfraRed File) to be adopted as the official file format for fNIRS (CW-, TD-, FD-), DCS, fluorescence and bioluminescence measurements and imaging.
SNIRF includes both data and metadata, and is a standard, open-source HDF5 (Hierarchical Data Format version 5) format with .snirf extension supported by many APIs in many languages (C, C++, MATLAB, Python, etc.).

Official specifications (release v1.0): https://github.com/fNIRS/snirf

SNIRF readers/writers:
– Homer 3 (MATLAB): https://github.com/BUNPC/Homer3/wiki/Standalone-SNIRF-loading-and-saving
– EasyH5 (MATLAB): https://github.com/fangq/easyh5
– JSNIRF (MATLAB): https://github.com/fangq/jsnirfy
– MNE (Python): https://mne.tools
– ICNNA (MATLAB): https://github.com/forihuelaespina/ICNNA

NOTE: SNIRF allows to store multiple runs, but BIDS (see below) requires only one recording per file.

Dataset Sharing Format: BIDS

Brain Imaging Data Structure (BIDS) defines a hierarchical organization of neuroimaging and behavioral data that facilitates data sharing and streamlines data processing (see Luke et al., 2025 for further details).

fNIRS-BIDS specifications: https://bids-specification.readthedocs.io/en/stable/modality-specific-files/near-infrared-spectroscopy.html

Folder structure:

  • *_nirs.snirf: Single-subject, single-run SNIRF recording
  • *_nirs.json: Sidecar JSON-formatted metadata including task name, sampling frequency, number of channels, sources, detectors (required), headgear, manufacturer, source and detector types, atlas, short channels information (recommended)
  • *_events.tsv: Tabular file describing the experimental task onset, duration (required), type, response time, value, presentation software information (recommended). May be accompanied by a JSON data dictionary for describing all columns.
  • *_channels.tsv: Tabular file describing channel name, type, source, detector, wavelength, unit (required), sampling frequency, orientation, short channel, measured wavelength, etc. (optional).
  • *_optodes.tsv: Tabular file describing optode name, type, location (required), description, hardware type (optional)
  • *_coordsystem.json: JSON file specifying the fiducials, the location of anatomical landmarks, and the coordinate system and units in which the position of optodes and landmarks is expressed.

BIDSify your Dataset: If you would like to convert your dataset in BIDS format, here is a webinar detailing a free tool to do that!

BIDS Converters and Utility Tools: multi-language applications for converting datasets to/from BIDS, performing quality assurance (QT-NIRS), etc. https://bids.neuroimaging.io/benefits.html

BIDS Validator: online or local JavaScript application that checks the compliance with the latest BIDS specification. https://bids-standard.github.io/bids-validator/

BIDS Apps: container for running analytical pipelines locally, in the cloud, or on HPC. http://fnirs-apps.org/overview/

BIDS Examples: https://tinyurl.com/ydotew8q

Data Sharing Platforms: