Welcome to ConWhAt’s documentation!

ConWhAt is a tool for studying the effects of white matter damage on brain networks.

The code is hosted on github: https://github.com/JohnGriffiths/ConWhAt/

It is written in python and draws strongly on the powerful functionality provided by other neuroimaging analysis tools in the nipy ecosystem for manipulation and visualization of nifti images and tractography streamlines.

The primary intended mode of interaction is through jupyter notebooks and python / bash scripting. Notebooks versions of some of the following documentation pages can be viewed at https://github.com/JohnGriffiths/ConWhAt/doc/examples

( Please note: the software and atlases are still in beta, and future versions may include major front and/or backend changes )

About ConWhAt

• Overview
• Ontology & Representation
• ConWhAt Atlases

Getting Started

• Installation
• Downloading atlases
• Exploring the atlases

Analyses of Brain Lesions

• Defining a Lesion
• Compute lesion overlap

Other Applications

• Connectivity-based decomposition of white matter tracts
• Setting up TVB simulations from ConWhAt outputs