Code related to the paper titled "The flattening of spacetime hierarchy of the DMT brain state is characterised by harmonic decomposition of spacetime (HADES) framework"
The Harmonic Decomposition of Spacetime (HADES) framework that characterises how different harmonic modes defined in space are expressed over time. Here applied to the DMT dataset
data/: folder containing data for the different steps of the HADES pipleine - decomposition, projections, dataset analysis and plottingutils/: folder containing matlab functions for the different steps of the HADES pipleine - decomposition, projections, dataset analysis and plottingresults/: folder containing various outputs for the different steps of the HADES pipleine - decomposition, projections, dataset analysis and plottingfigures/: folder containing figures for the different steps of the HADES pipleine - decomposition, projections, dataset analysis and plotting
p0_HADES_DMT_FMRI_main_projectFH.m: MATLAB script to project functional harmonics onto the timeseriesp1_HADES_DMT_spatiotemporal_analysis.m: MATLAB script to calculate the spatio-temporal analysisp2_HADES_DMT_dynamic_analysis_publication.m: MATLAB script to calculate dynamic analysisp3_HADES_DMT_latent_space_analysis_publication.m: MATLAB script to calculate latent space analysis analysis
s1_HCP_denseFC_2_vertices.m: MATLAB script to load the dense FCs2_HADES_basis_denseFC_vertex_on_HCP.m: MATLAB scripts to run the laplace decomposition on the dense FCs3_HADES_plotting_basis.m: MATLAB script to plot the functional harmonics on the cortical surface
Simply download the repository to get started. In order to run the code two additional files (Functional Harmonics (FHs) and projections of FHs to the DMT dataset) have to be downloaded from the OSF repository: https://osf.io/asntf/ you can find further instruction in the results folder.
HADES pipeline [p1-p4].
To run the code p1 uses the FHs projections on the fMRI resting-state data. The OSF repository provided the FHs projections onto the DMT dataset.
For personal use the appropriate dataset FHs projections should be provided in the cifti 64k vertices format.
Inside each code file, you'll find comments and documentation to guide you through usage. The repository serves as standalone for the HADES method. Please Consult the documentiaton for further guidance
Due to privacy the DMT data is only provided in terms of the FHs projections. The original data is available upon request from the authors of the experiment. To derive the Functional Harmonics, the dense functional connectome of the HCP dataset was used and can be accessed here. Important: Certain parts of generate_paper_figures.m and generate_paper_suppfigures.m rely on this OSF-hosted data. Ensure it's saved in the correct folders for smooth script execution.
The original empirical data stem from the Human Connectome Project. Refer to the provided link for comprehensive access, licensing, and usage terms.
Relevant toolboxes and repositories. Some MATLAB-based scripts rely on external packages. Copies are stored in utils/ for version compatibility. Visit the provided links for detailed information and support.
SPM12 - Statistical Parametric Mapping Toolbox
gifti - Freesurfer Toolbox
cifti - Human Connectome Workbench
spider plots - Chart Development Toolbox [version 1.3 (Nov 2019)]
colormaps - othercolor
Atasoy et al. scripts based on papers on Connectome Harmonics. (Atasoy2016, Atasoy2017, Atasoy2018)
Cabral et al. scripts based on papers on Leadin Eigenvector Analysis (LEiDA). (Cabral2017, Vohryzek2020)
Codes are tested on MATLAB versions R2023b.
[Article] J. Vohryzek,J. Cabral, C. Timmermann, S. Atasoy, L. Roseman, D.J. Nutt, R.L. Carhart-Harris, G. Deco, M.L. Kringelbach, The flattening of spacetime hierarchy of the DMT brain state is characterised by harmonic decomposition of spacetime (HADES) framework, NSR (2023) (DOI: 10.1093/nsr/nwae124)
[Preprint] J. Vohryzek,J. Cabral, C. Timmermann, S. Atasoy, L. Roseman, D.J. Nutt, R.L. Carhart-Harris, G. Deco, M.L. Kringelbach, Harmonic decomposition of spacetime (HADES) framework characterises the spacetime hierarchy of the DMT brain state, bioRxiv (2023) (DOI: 10.1101/2023.08.20.554019)
contact jakub.vohryzek@upf.edu