CBPtools: a Python package for regional connectivity-based parcellation

Brain Structure & Function
Niels ReuterKaustubh R Patil

Abstract

Regional connectivity-based parcellation (rCBP) is a widely used procedure for investigating the structural and functional differentiation within a region of interest (ROI) based on its long-range connectivity. No standardized software or guidelines currently exist for applying rCBP, making the method only accessible to those who develop their own tools. As such, there exists a discrepancy between the laboratories applying the procedure each with their own software solutions, making it difficult to compare and interpret the results. Here, we outline an rCBP procedure accompanied by an open source software package called CBPtools. CBPtools is a Python (version 3.5+) package that allows users to run an extensively evaluated rCBP analysis workflow on a given ROI. It currently supports two modalities: resting-state functional connectivity and structural connectivity based on diffusion-weighted imaging, along with support for custom connectivity matrices. Analysis parameters are customizable and the workflow can be scaled to a large number of subjects using a parallel processing environment. Parcellation results with corresponding validity metrics are provided as textual and graphical output. Thus, CBPtools provides a simple plug-an...Continue Reading

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Citations

Jul 24, 2020·Neuroscience Bulletin·Xiaojin LiuKaustubh R Patil
May 18, 2020·Brain Structure & Function·Hiromasa Takemura, Michel Thiebaut de Schotten

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Methods Mentioned

BETA
SMA

Software Mentioned

R
Mango
SciPy
NumPy
SLURM
snakemake
scikit
FSL
cbptools
NiBabel

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