Significance: Functional near-infrared spectroscopy (fNIRS), a well-established neuroimaging technique, enables monitoring cortical activation while subjects are unconstrained. However, motion artifact is a common type of noise that can hamper the interpretation of fNIRS data. Current methods that have been proposed to mitigate motion artifacts in fNIRS data are still dependent on expert-based knowledge and the post hoc tuning of parameters.

Aim: Here, we report a deep learning method that aims at motion artifact removal from fNIRS data while being assumption free. To the best of our knowledge, this is the first investigation to report on the use of a denoising autoencoder (DAE) architecture for motion artifact removal.

Approach: To facilitate the training of this deep learning architecture, we (i) designed a specific loss function and (ii) generated data to mimic the properties of recorded fNIRS sequences.

Results: The DAE model outperformed conventional methods in lowering residual motion artifacts, decreasing mean squared error, and increasing computational efficiency.

Conclusion: Overall, this work demonstrates the potential of deep learning models for accurate and fast motion artifact removal in fNIRS data.