References

[DEY+09]

Hamid Dehghani, Matthew E Eames, Phaneendra K Yalavarthy, Scott C Davis, Subhadra Srinivasan, Colin M Carpenter, Brian W Pogue, and Keith D Paulsen. Near infrared optical tomography using nirfast: algorithm for numerical model and image reconstruction. Communications in numerical methods in engineering, 25(6):711–732, 2009.

[FB09]

Qianqian Fang and David A Boas. Monte carlo simulation of photon migration in 3d turbid media accelerated by graphics processing units. Optics express, 17(22):20178–20190, 2009.

[Fis18]

Frank Fishburn. Tddr. 2018. URL: https://github.com/frankfishburn/TDDR/.

[FLVM19]

Frank A. Fishburn, Ruth S. Ludlum, Chandan J. Vaidya, and Andrei V. Medvedev. Temporal derivative distribution repair (tddr): a motion correction method for fnirs. NeuroImage, 184:171–179, 2019. URL: https://www.sciencedirect.com/science/article/pii/S1053811918308103, doi:https://doi.org/10.1016/j.neuroimage.2018.09.025.

[FPA+14]

Geng-Shen Fu, Ronald Phlypo, Matthew Anderson, Xi-Lin Li, and Tulay Adali. Blind Source Separation by Entropy Rate Minimization. IEEE Transactions on Signal Processing, 62(16):4245–4255, Aug 2014. URL: http://ieeexplore.ieee.org/document/6845364/ (visited on 2022-11-21), doi:10.1109/TSP.2014.2333563.

[GHLG15]

James S. Gao, Alexander G. Huth, Mark D. Lescroart, and Jack L. Gallant. Pycortex: an interactive surface visualizer for fmri. Frontiers in Neuroinformatics, 2015. URL: https://www.frontiersin.org/journals/neuroinformatics/articles/10.3389/fninf.2015.00023, doi:10.3389/fninf.2015.00023.

[HM22]

Nils Harmening and Daniel Miklody. MRIsegmentation. 11 2022. URL: https://github.com/harmening/MRIsegmentation, doi:10.5281/zenodo.7357674.

[HHC+98]

Colin J. Holmes, Rick Hoge, Louis Collins, Roger Woods, Arthur W. Toga, and Alan C. Evans. Enhancement of mr images using registration for signal averaging. Journal of Computer Assisted Tomography, 22(2):324–333, March 1998. URL: https://journals.lww.com/jcat/abstract/1998/03000/enhancement_of_mr_images_using_registration_for.32.aspx, doi:10.1097/00004728-199803000-00032.

[HDS+13]

Yu Huang, Jacek Dmochowski, Yuzhuo Su, Abhishek Datta, Chris Rorden, and Lucas Parra. Automated mri segmentation for individualized modeling of current flow in the human head. Journal of neural engineering, 10:066004, 10 2013. doi:10.1088/1741-2560/10/6/066004.

[HDFB09]

Theodore J. Huppert, Solomon G. Diamond, Maria A. Franceschini, and David A. Boas. Homer: a review of time-series analysis methods for near-infrared spectroscopy of the brain. Appl. Opt., 48(10):D280–D298, Apr 2009. URL: https://github.com/BUNPC/Homer3, doi:https://doi.org/10.1364/AO.48.00D280.

[JSBYucel18]

Sahar Jahani, Seyed K. Setarehdan, David A. Boas, and Meryem A. Yücel. Motion artifact detection and correction in functional near-infrared spectroscopy: a new hybrid method based on spline interpolation method and Savitzky–Golay filtering. Neurophotonics, 5(1):015003, 2018. doi:10.1117/1.NPh.5.1.015003.

[LA10a]

Xi-Lin Li and Tulay Adali. Blind spatiotemporal separation of second and/or higher-order correlated sources by entropy rate minimization. In 2010 IEEE International Conference on Acoustics, Speech and Signal Processing, 1934–1937. Dallas, TX, March 2010. IEEE. URL: http://ieeexplore.ieee.org/document/5495311/ (visited on 2024-04-17), doi:10.1109/ICASSP.2010.5495311.

[LA10b]

Xi-Lin Li and Tülay Adali. Independent Component Analysis by Entropy Bound Minimization. IEEE Transactions on Signal Processing, 58(10):5151–5164, Oct 2010. URL: http://ieeexplore.ieee.org/document/5499122/ (visited on 2024-01-09), doi:10.1109/TSP.2010.2055859.

[LM21a]

Robert Luke and David McAlpine. fNIRS Finger Tapping Data in BIDS Format. September 2021. URL: https://github.com/rob-luke/BIDS-NIRS-Tapping, doi:10.5281/zenodo.5529797.

[LM21b]

Robert Luke and David McAlpine. fNIRS Finger Tapping Data in BIDS Format. September 2021. URL: https://github.com/rob-luke/BIDS-NIRS-Tapping, doi:10.5281/zenodo.5529797.

[MD12]

Behnam Molavi and Guy A Dumont. Wavelet-based motion artifact removal for functional near-infrared spectroscopy. Physiological Measurement, 33(2):259, 2012. doi:10.1088/0967-3334/33/2/259.

[OP01]

Robert Oostenveld and Peter Praamstra. The five percent electrode system for high-resolution eeg and erp measurements. Clinical Neurophysiology, 112(4):713–719, 2001. doi:https://doi.org/10.1016/S1388-2457(00)00527-7.

[PBO16]

Luca Pollonini, Heather Bortfeld, and John S. Oghalai. PHOEBE: a method for real time mapping of optodes-scalp coupling in functional near-infrared spectroscopy. Biomedical Optics Express, 7(12):5104, Dec 2016. URL: https://opg.optica.org/abstract.cfm?URI=boe-7-12-5104 (visited on 2022-11-21), doi:10.1364/BOE.7.005104.

[POA+14]

Luca Pollonini, Cristen Olds, Homer Abaya, Heather Bortfeld, Michael S. Beauchamp, and John S. Oghalai. Auditory cortex activation to natural speech and simulated cochlear implant speech measured with functional near-infrared spectroscopy. Hearing Research, 309:84–93, 2014. doi:https://doi.org/10.1016/j.heares.2013.11.007.

[SSE+20]

Arefeh Sherafati, Abraham Z. Snyder, Adam T. Eggebrecht, Karla M. Bergonzi, Tracy M. Burns-Yocum, Heather M. Lugar, Silvina L. Ferradal, Amy Robichaux-Viehoever, Christopher D. Smyser, Ben J. Palanca, Tamara Hershey, and Joseph P. Culver. Global motion detection and censoring in high-density diffuse optical tomography. Human Brain Mapping, 41(14):4093–4112, 2020. doi:https://doi.org/10.1002/hbm.25111.

[TDK+22]

Stephen Tucker, Jay Dubb, Sreekanth Kura, Alexander von Lühmann, Robert Franke, Jörn M. Horschig, Samuel Powell, Robert Oostenveld, Michael Lührs, Édouard Delaire, Zahra M. Aghajan, Hanseok Yun, Meryem A. Yücel, Qianqian Fang, Theodore J. Huppert, Blaise deB. Frederick, Luca Pollonini, David A. Boas, and Robert Luke. Introduction to the shared near infrared spectroscopy format. Neurophotonics, 10(1):013507, 2022. URL: https://doi.org/10.1117/1.NPh.10.1.013507, doi:10.1117/1.NPh.10.1.013507.

[YF20]

Shijie Yan and Qianqian Fang. Hybrid mesh and voxel based monte carlo algorithm for accurate and efficient photon transport modeling in complex bio-tissues. Biomedical Optics Express, 11(11):6262–6270, 2020.

[YNPKF18]

Leiming Yu, Fanny Nina-Paravecino, David Kaeli, and Qianqian Fang. Scalable and massively parallel monte carlo photon transport simulations for heterogeneous computing platforms. Journal of biomedical optics, 23(1):010504–010504, 2018.