Please cite this software as follows:

Kasper, L., Bollmann, S., Diaconescu, A.O., Hutton, C., Heinzle, J., 
Iglesias, S., Hauser, T.U., Sebold, M., Manjaly, Z.-M., Pruessmann, K.P., 
Stephan, K.E., 2017. The PhysIO Toolbox for Modeling Physiological Noise 
in fMRI Data. 
Journal of Neuroscience Methods 276, 56-72. 
doi:10.1016/j.jneumeth.2016.10.019

Please also cite the parent software collection TAPAS:

Fraessle, S., Aponte, E.A., Bollmann, S., Brodersen, K.H., Do, C.T., Harrison, O.K., 
Harrison, S.J., Heinzle, J., Iglesias, S., Kasper, L., Lomakina, E.I., Mathys, C., 
Mueller-Schrader, M., Pereira, I., Petzschner, F.H., Raman, S., Schoebi, D., 
Toussaint, B., Weber, L.A., Yao, Y., Stephan, K.E., 2021. 
TAPAS: an open-source software package for Translational Neuromodeling and Computational Psychiatry. 
Frontiers in Psychiatry 12, 857. 
https://doi.org/10.3389/fpsyt.2021.680811

If you use respiratory volume per time (RVT) regressors or preprocessing of respiratory traces, please also cite:

Harrison, S.J., Bianchi, S., Heinzle, J., Stephan, K.E., Iglesias, S., Kasper L., 2021.
A Hilbert-based method for processing respiratory timeseries.
NeuroImage, 117787. https://doi.org/10.1016/j.neuroimage.202...

For a detailed snippet to be included in the methods section of your manuscript, see the FAQ in the documentation.