PhysIO-Live

This repository contains a Live-Script demo of the TAPAS PhysIO toolbox for physiological (cardiac and respiratory) noise modelling and correction of fmri data.

How to work with this repository

There are three ways to work with this repository:

• Run online

• Run locally on your machine

• View on

To clone this repository and run it locally on your machine:

1. Clone this repository recursively. This way, all dependent libraries, e.g., SPM and TAPAS PhysIO are automatically installed as well.

git clone --recursive https://github.com/likeajumprope/PhysIO-Live

• Note: Check that the libs subfolder is not empty, and e.g,. libs/tapas contains files.

2. Get the data.

For this live demo, we use the Forrest Gump data set. Here we use the audio perception sub data set (see also here) The following files need to be downloaded into the results/sub-01 folder:

• sub-01/ses-audiotoryperception/func/sub-01_ses-auditoryperception_task-auditoryperception_run-01_bold.nii.gz (unpack)
• sub-01/ses-forestgump/anat/sub-01_ses-forrestgump_T1w.nii.gz (unpack)
• sub-01_ses-auditoryperception_func_sub-01_ses-auditoryperception_task-auditoryperception_run-01_physio.tsv
• recording-cardresp_physio.json

To make the download easier, you can also just open teh terminal run the file get_files.sh in the misc folder:

misc my-username$ ./get_files.sh

Move all those files into the results/sub-01 folder. Your folder structure should look like the following:

Now your folders are ready to go!

3. Adapt the environment variables in main.mlx (matlab version > 2019a) or in main.m

The two files main.mlx and main.m are identical and ensure the usability of this tutorial for matlab versions that do not support .mlx files.

Debugging - common issues

• Make sure every step is run out of the results/>subjectID< folder!
• Make sure tapas, spm/matlabbatch are on the path. Any "cannot find/open file" error is usually due to the relevant folder not being on the path.
• Some operations take some time. A wheel of doom when hovering over the batch editor indicates that the process is still running!
• When cloning the repository, pulling the wikidocs of TAPAS Physio might fail. Don't worry about that, the demo is fully functional!

Literature

Please cite this software (PhysIO) 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.2021.117787

(C) 2023 Johanna Bayer, supervised by Lars Kasper, supported by Mathworks Inc.