Software

We love open science! Check out our Lab’s GitHub page for the latest in software tools developed in the lab. Here are some highlights:

Eigenmode-based brain mapping and modelling

Tools for extracting and applying geometric eigenmodes to model brain dynamics
These tools can be used to extract geometric eigenmodes of the cortical surface (in two dimensions) or subcortical volumes (in three dimensions), and use those modes to reconstruct different types of neural activity data or simulate wave models of dynamics
Code | Paper

Mode-based morphometry
This toolbox leverages structural eigenmodes of the brain to understand variations in cortical morphometry (e.g., grey matter volume, surface area, cortical thickness, etc) associated with age, cognition, disease or some other variable. The approach is more accurate and reliable than conventional methods.
Code | Paper

MRI Preprocessing

Evaluating preprocessing pipelines for diffusion MRI
Code for estimating various quality control metrics of diffusion MRI studies.
Code | Paper

Diffuse Cluster Estimation and Removal (DiCER)
A method for identifying and removing widespread signal deflections from functional MRI data.
Code | Paper

Evaluating preprocessing pipelines for functional MRI
Code for estimating various quality control metrics for resting-state functional MRI studies.
Code | Paper

Transcriptomic analyses

Enrichment analysis for transcriptional atlas data
Code for performing appropriate statistical inference during Gene Ontology (GO) enrichment analysis of brain-wide transcriptional atlas data.
Code | Paper

Optimized processing pipelines for transcriptomic data
Code and resources for appropriate processing of gene expression measures in the Allen Human Brain Atlas.
Code | Paper

Connectome mapping

Network-based statistic
A toolbox for performing statistical inference in connectome-wide association analyses.
Code | Paper

Correlational psychophysiological interactions (cPPI)
A toolbox for estimating task-related functional connectivity in large-scale brain networks.
Code | Paper

Network visualization

NeuroMarvl
A web-based tool for easily visualising brain network data (Beta version). Should be used with Google Chrome.
Website

BrainConn
R-based tool for plotting brain network data.
Code

Modeling

Models of brain network wiring
A set of tools for specifying and evaluating generative network models of human connectomes mapped with diffusion MRI.
Code | Paper

Models of brain network dynamics
Tools for fitting and evaluating large-scale models of brain network fMRI dynamics
Code | Paper