Importing data from fNIRS devices

MNE includes various functions and utilities for reading NIRS data and optode locations.

NIRx (directory)

NIRx recordings can be read in using mne.io.read_raw_nirx(). The NIRx device stores data directly to a directory with multiple file types, MNE extracts the appropriate information from each file.

SNIRF (.snirf)

Data stored in the SNIRF format can be read in using mne.io.read_raw_snirf().

Warning

The SNIRF format has provisions for many different types of NIRS recordings. MNE currently only supports continuous wave data stored in the .snirf format.

BOXY (.txt)

BOXY recordings can be read in using mne.io.read_raw_boxy(). The BOXY software and ISS Imagent I and II devices are frequency domain systems that store data in a single .txt file containing what they call (with MNE’s name for that type of data in parens):

• DC

  All light collected by the detector (fnirs_cw_amplitude)

• AC

  High-frequency modulated light intensity (fnirs_fd_ac_amplitude)

• Phase

  Phase of the modulated light (fnirs_fd_phase)

DC data is stored as the type fnirs_cw_amplitude because it collects both the modulated and any unmodulated light, and hence is analogous to what is collected by continuous wave systems such as NIRx. This helps with conformance to SNIRF standard types.

These raw data files can be saved by the acquisition devices as parsed or unparsed .txt files, which affects how the data in the file is organised. MNE will read either file type and extract the raw DC, AC, and Phase data. If triggers are sent using the digaux port of the recording hardware, MNE will also read the digaux data and create annotations for any triggers.

Storing of optode locations

NIRs devices consist of light sources and light detectors. A channel is formed by source-detector pairs. MNE stores the location of the channels, sources, and detectors.

Warning

Information about device light wavelength is stored in channel names. Manual modification of channel names is not recommended.

Estimated memory usage: 8 MB