comet-toolbox 0.5

Dynamic functional connectivity toolbox for multiverse analysis

Comet - A toolbox for dynamic functional connectivity and multiverse analysis

About the toolbox

Please refer to the documentation for detailed information about the toolbox. The following README will only provide a very brief overview.

Please also note that the package is in an early stage of development, with frequent changes being made. If you intend to use this package at this stage, please feel free to contact me via the email address in the pyproject.toml file. Some features are also not yet tested, so there will be bugs (the question is just how many).

Installation and usage

It is recommended to use a dedicated Python environment (e.g. through conda) to mitigate the risk of potential version conflicts. Installation is possible through the Python Package Index (PyPI) or from the source code in this repository:

pip install comet-toolbox

Usage of the toolbox is then possible through either the GUI:

comet-gui

or (for more versatile usage) through the scripting API. For this, demo scripts are provided as starting points:

• Demo script for calculating dFC
• Demo script for performing multiverse analysis
• Demo script for multiverse analysis example from the preprint (+ additional visualizations)
• Demo script for graph analysis

Current features

Functional Connectivity	Graph Analysis	Multiverse Analysis
Continuous Sliding Window Correlation Jackknife Correlation Flexible Least Squares Spatial Distance Temporal Derivatives Phase Synchronization Leading Eigenvector Dynamics Wavelet Coherence Edge-centric connectivity State-Based SW Clustering Co-activation Patterns Discrete HMM Continuous HMM Windowless Static Pearson Correlation Partial Correlation Mutual Information	Optimized implementation Average Path Length Global Efficiency Nodal Efficiency Small-World Sigma Small-World Propensity Matching Index Standard Graph Functions Threshold Binarise Symmetrise Negative weights ... BCT Integration All BCT functions can be used seamlessly fory multiverse analysis Many BCT functions are available in the GUI	Simple Definition Forking paths as python dictionary Analysis pipeline template with decision points Generation Universes are created as individual scripts Modular approach Analysis Individual universes Entire multiverse (parallel) Visualization Multiverse summary Multiverse as a network Specification curve analysis

Current progress (roughly)

• Large set of dFC methods and graph measures
• Multiverse analysis framework
• Graphical user interface
• Documentation
• Tutorials for an easy start
• Complete testing suite
• GUI bugfixes and optimization
• Integrating over multiverse results
• Dynamic community measures