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:

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