Software

All software is open-source and freely distributed on my gitbhub page . We try to document the code as thoroughly as possible but sometimes we can fall behind.

Automated Fiber Quantification (AFQ)

AFQ is designed to automatically identify major fiber tracts and quantify tissue properties along their trajectories. The result is a "Tract Profile" of MRI parameters that can be used to study white matter tissue properties in healthy brains or quantify abnormalities in diseased brains. In the future we hope to be able to automatically identify abnormalities in an individual and quantify that individual's risk for various functional consequences. For example the images below show a quantitative comparison between diffusion measurements in a child born preterm with ventricular dilation compare to a normative sample of typically developing children. The software can be downloaded from my github site and I try to maintain a detailed users manual. The software is described in a recent PLoS ONE paper where we apply it to identify developmental abnormalities and predict developmental outcomes in children born prematurely.

3D Visualization Cerebral White Matter Movie

High quality three dimensional visualization is essential for analyzing and understanding brain circuits. I have written a software package for building models of an individual's cortical surface and white matter tracts and interactively visualizing the functional and structural properties of these circuits in 3D. This code is included in the AFQ software package and can be downloaded from my github site.