Software

Open source software packages covering quality assurance, gaze estimation and atlas label manipulation. Hopefully you’ll find some of this code useful. Let me know if you have comments, issues, feature requests, bug reports, etc through the relevant GitHub repository page.

MrGaze

Originally written for off-line analysis of infrared eye video recordings acquired in the magnet bore. Later extended for real-time eye tracking by Wolfgang Pauli (thanks Wolfgang!). The current release depends on MITs Pupil package for its user interface, but can be run offline from the command line too. GitHub

CBICQAlive

Simple command-line quality assurance software for in vivo human fMRI data. The software generates HTML reports with metrics, images and graphs relevant to in vivo fMRI work, including motion and signal outlier estimation. GitHub

Atlaskit

Collection of Python and Bash scripts for modifying and analyzing binary and multivalued 3D atlas label images. Developed originally for the probabilistic CIT168 amygdala atlas, which in turn depends heavily on ITK-SNAP and FSL. GitHub