References
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Please cite **TMFC_denoise** as:
 - Ruslan Masharipov. (2025). TMFC denoise (v1.4.4) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.17176264
 - <Toolbox paper in review...>

If you use the **TMFC toolbox**, please cite:
 - Masharipov, R., Knyazeva, I., Korotkov, A., Cherednichenko, D., & Kireev, M. (2024). Comparison of whole-brain task-modulated functional connectivity methods for fMRI task connectomics. Communications Biology, 7(1). https://doi.org/10.1038/s42003-024-07088-3

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**Other sources**

Statistical Parametric Mapping (SPM):
 - Penny, W., Friston, K., Ashburner, J., Kiebel, S., & Nichols, T. (2011). Statistical Parametric Mapping: The Analysis of Functional Brain Images. Academic Press.

Robust weighted least squares (rWLS):
 - Diedrichsen, J., & Shadmehr, R. (2005). Detecting and adjusting for artifacts in fMRI time series data. NeuroImage, 27(3), 624–634. https://doi.org/10.1016/j.neuroimage.2005.04.039

Head motion parameter (HMP) expansions:
 - Friston, K. J., Williams, S., Howard, R., Frackowiak, R. S. J., & Turner, R. (1996). Movement‐Related effects in fMRI time‐series. Magnetic Resonance in Medicine, 35(3), 346–355. https://doi.org/10.1002/mrm.1910350312
 - Satterthwaite, T. D., Elliott, M. A., Gerraty, R. T., Ruparel, K., Loughead, J., Calkins, M. E., Eickhoff, S. B., Hakonarson, H., Gur, R. C., Gur, R. E., & Wolf, D. H. (2012). An improved framework for confound regression and filtering for control of motion artifact in the preprocessing of resting-state functional connectivity data. NeuroImage, 64, 240–256. https://doi.org/10.1016/j.neuroimage.2012.08.052
 - Van Dijk, K. R., Sabuncu, M. R., & Buckner, R. L. (2012). The influence of head motion on intrinsic functional connectivity MRI. NeuroImage, 59(1), 431–438. https://doi.org/10.1016/j.neuroimage.2011.07.044

Framewise displacement (FD):
 - Power, J. D., Barnes, K. A., Snyder, A. Z., Schlaggar, B. L., & Petersen, S. E. (2012). Spurious but systematic correlations in functional connectivity MRI networks arise from subject motion. NeuroImage, 59(3), 2142–2154. https://doi.org/10.1016/j.neuroimage.2011.10.018

Spike regression (SpikeReg):
 - Lemieux, L., Salek-Haddadi, A., Lund, T. E., Laufs, H., & Carmichael, D. (2007). Modelling large motion events in fMRI studies of patients with epilepsy. Magnetic Resonance Imaging, 25(6), 894–901. https://doi.org/10.1016/j.mri.2007.03.009
 - Satterthwaite, T. D., Elliott, M. A., Gerraty, R. T., Ruparel, K., Loughead, J., Calkins, M. E., Eickhoff, S. B., Hakonarson, H., Gur, R. C., Gur, R. E., & Wolf, D. H. (2012). An improved framework for confound regression and filtering for control of motion artifact in the preprocessing of resting-state functional connectivity data. NeuroImage, 64, 240–256. https://doi.org/10.1016/j.neuroimage.2012.08.052

Anatomical component correction (aCompCor):
 - Behzadi, Y., Restom, K., Liau, J., & Liu, T. T. (2007). A component based noise correction method (CompCor) for BOLD and perfusion based fMRI. NeuroImage, 37(1), 90–101. https://doi.org/10.1016/j.neuroimage.2007.04.042
 - Muschelli, J., Nebel, M. B., Caffo, B. S., Barber, A. D., Pekar, J. J., & Mostofsky, S. H. (2014). Reduction of motion-related artifacts in resting state fMRI using aCompCor. NeuroImage, 96, 22–35. https://doi.org/10.1016/j.neuroimage.2014.03.028

Pre-orthogonalization of tissue-specific signals before aCompCor:
 - Mascali, D., Moraschi, M., DiNuzzo, M., Tommasin, S., Fratini, M., Gili, T., Wise, R. G., Mangia, S., Macaluso, E., & Giove, F. (2021). Evaluation of denoising strategies for task‐based functional connectivity: Equalizing residual motion artifacts between rest and cognitively demanding tasks. Human Brain Mapping, 42(6), 1805–1828. https://doi.org/10.1002/hbm.25332

Derivative of Root Mean Square Variance Over Voxels (DVARS):
 - Power, J. D., Barnes, K. A., Snyder, A. Z., Schlaggar, B. L., & Petersen, S. E. (2012). Spurious but systematic correlations in functional connectivity MRI networks arise from subject motion. NeuroImage, 59(3), 2142–2154. https://doi.org/10.1016/j.neuroimage.2011.10.018
 - Muschelli, J., Nebel, M. B., Caffo, B. S., Barber, A. D., Pekar, J. J., & Mostofsky, S. H. (2014). Reduction of motion-related artifacts in resting state fMRI using aCompCor. NeuroImage, 96, 22–35. https://doi.org/10.1016/j.neuroimage.2014.03.028

WM and CSF Signal Regression (Phys):
 - Fox, M. D., Snyder, A. Z., Vincent, J. L., Corbetta, M., Van Essen, D. C., & Raichle, M. E. (2005). The human brain is intrinsically organized into dynamic, anticorrelated functional networks. Proceedings of the National Academy of Sciences, 102(27), 9673–9678. https://doi.org/10.1073/pnas.0504136102
 - Parkes, L., Fulcher, B., Yücel, M., & Fornito, A. (2017). An evaluation of the efficacy, reliability, and sensitivity of motion correction strategies for resting-state functional MRI. NeuroImage, 171, 415–436. https://doi.org/10.1016/j.neuroimage.2017.12.073

Global Signal Regression (GSR):
 - Fox, M. D., Snyder, A. Z., Vincent, J. L., Corbetta, M., Van Essen, D. C., & Raichle, M. E. (2005). The human brain is intrinsically organized into dynamic, anticorrelated functional networks. Proceedings of the National Academy of Sciences, 102(27), 9673–9678. https://doi.org/10.1073/pnas.0504136102
 - Murphy, K., Birn, R. M., Handwerker, D. A., Jones, T. B., & Bandettini, P. A. (2008). The impact of global signal regression on resting state correlations: Are anti-correlated networks introduced? NeuroImage, 44(3), 893–905. https://doi.org/10.1016/j.neuroimage.2008.09.036
 - Fox, M. D., Zhang, D., Snyder, A. Z., & Raichle, M. E. (2009). The global signal and observed anticorrelated resting state brain networks. Journal of Neurophysiology, 101(6), 3270–3283. https://doi.org/10.1152/jn.90777.2008
 - Chen, G., Chen, G., Xie, C., Ward, B. D., Li, W., Antuono, P., & Li, S.-J. (2012). A method to determine the necessity for global signal regression in resting-state fMRI studies. Magnetic Resonance in Medicine, 68(6), 1828–1835. https://doi.org/10.1002/mrm.24201
 - Murphy, K., & Fox, M. D. (2016). Towards a consensus regarding global signal regression for resting state functional connectivity MRI. NeuroImage, 154, 169–173. https://doi.org/10.1016/j.neuroimage.2016.11.052