Software

We have used a number of in-house developed tools in our work, including the two R packages described here.

VertexWiseR

This R package contains a suite of tools to extract, manipulate, analyze, and visualize cortical surface and hippocampal vertex-wise data. This R package is designed to be easy for beginners and it also contains advanced functionalities such as hippocampal surface analyses, meta-analytic decoding, threshold-free cluster enhancement, and mixed effects models that would appeal to experienced researchers. This R package is now available on CRAN (you simply install.packages("VertexWiseR)) and it accompanying paper is now published at Imaging Neuroscience

Do check out the following examples to get started:

  1. Extracting surface data
  2. Example analyses 1
  3. Example analyses 2

FCtools R package

A collection of in-house R functions for post-processing, analyzing and visualizing brain connectivity data

  1. Working with HCP data
    • generating download lists for HCP data: extract_links
    • post-processing and extracting FC matrices from HCP-preprocessed fMRI data: extractFC()
  2. Working with fMRIprep preprocessed data
    • Extracting head motion data from fMRIprep preprocessed directories: extract_headmotion()
    • Vectorizing and concatenating a cohort of participants FC matrices into a single N (number of subjects) x E (number of edges) matrix: vectorizeFC()
  3. Analyses
    • A faster and more efficient analysis of Network-based statistics: NBS()
    • Intersubject similarity analysis: intersubject_similarity()
    • Connectome-based prediction modelling: cpm.train(), cpm.train.cv(), cpm.predict(), cpm.train(), cpm.lesion()
  4. Visualization of FC
    • Connectogram vizConnectogram(), chord diagram vizChord() and heatmap vizHeatmap()
    • Glassbrain plot vizGlassbrain() (New!)