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processFNIRS2 (pf2)

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processFNIRS2 (pf2)

An open-source MATLAB toolbox for reproducible neuroergonomics research

processFNIRS2 handle fNIRS workflows from raw device files through group-level statistics and figures. The same modular components used to clean and convert one recording can be assembled into reproducible pipelines for a complete study.

Import and preprocess

pf2 imports data natively fNIR/Biopac, SNIRF, Hitachi ETG, Artinis, and NIRX systems and supports BIDS-NIRS with SNIRF compatability. Preprocessing includes seven motion-correction methods, short-channel regression, and global-signal regression. A headless quality-control pipeline supports automated workflows. Auxiliary recordings such as heart rate, accelerometer, EDA, and EEG signals retain explicit signal types and can be used as nuisance regressors or covariates.

Analyze

For activation studies, pf2 provides GLM estimation with AR-IRLS and first-level contrasts. It also includes functional connectivity, hyperscanning and inter-brain synchrony, and graph-theoretic network measures. Group analyses can use linear mixed-effects models and growth-curve analysis.

Visualize and share

Results can be displayed as 2D topographies, 3D cortical renders, connectomes, or diffuse optical tomography images. pf2 exports data to SNIRF, BIDS-NIRS, and HDF5 tensors. It can be run through a GUI, from the command line, or headlessly for batch and reproducible workflows.

Benchmarked on the FRESH datasets. Across 22 pipeline variants, pf2 activation maps were highly correlated with results from Cedalion, MNE-NIRS, and AnalyzIR (r = 0.87 to 0.96). Its individual-level results also fell within the distribution reported by the FRESH teams. In this benchmark, pf2 produced results consistent with established fNIRS analysis toolboxes.

Get pf2: github.com/adriancurtin/processFNIRS2 · Documentation: docs · Free and open-source under GPLv3

Curtin, A. & Ayaz, H. (2026). processFNIRS2: An Open-Source MATLAB Toolbox Validated on the FRESH fNIRS Benchmark. 6th International Neuroergonomics Conference, Boston University, Boston, MA.