braindynamicslab/tda-metpro

System requirements: This software was made and tested on a desktop computer (Mac OS) running Matlab 2019+

Installation guide:

1. Just go the main folder in Matlab and run the bdl_taskfMRI_postfMRIPrep_v1_MetPro file to postprocess fMRIPrep output and get parcellated data as Input for Mapper.

2. Run monique_mapper_Sep21_2021.m file to run Mapper on the data and to extract participation coefficient etc for the main results in the paper. This file also implements the modeling framework.

License: The work is covered under the BSD 3-Clause Clear License More information here - https://choosealicense.com/licenses/bsd-3-clause-clear/

Cite/References: Please cite the following papers if you use this code:

1. Saggar, M., Bruno, J., Gaillard, C., Claudino, L., & Ernst, M. (2022). Neural resources shift under Methylphenidate: A computational approach to examine anxiety-cognition interplay. NeuroImage, 264, 119686. https://doi.org/10.1016/j.neuroimage.2022.119686

2. Saggar, M., Shine, J.M., Liégeois, R. et al. Precision dynamical mapping using topological data analysis reveals a hub-like transition state at rest. Nat Commun 13, 4791 (2022). https://doi.org/10.1038/s41467-022-32381-2

3. Geniesse, C., Sporns, O., Petri, G., Saggar, M. (2019). Generating dynamical neuroimaging spatiotemporal representations (DyNeuSR) using topological data analysis. Network Neuroscience. http://dx.doi.org/10.1162/netn_a_00093

4. Saggar, M., Sporns, O., Gonzalez-Castillo, J., Bandettini, P.A., Carlsson, G., Glover, G., Reiss, A.L. (2018) Towards a new approach to visualize and quantify brain's dynamical organization using topological data analysis. Nature Communications. http://dx.doi.org/10.1038/s41467-018-03664-4

5. Saggar, Manish. "Systems and Methods for Mapping Neuronal Circuitry and Clinical Applications Thereof." U.S. Patent Application 16/171,255, filed April 25, 2019