Ali Khan's repositories
mdt-singularity
Singularity recipe for Microstructure Diffusion Toolbox (http://mdt-toolbox.readthedocs.io/en/latest/index.html)
fmriprep
fMRIprep is a functional magnetic resonance image pre-processing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to differences in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting.
surf_striatum
Pipeline for surface-based connectivity and morphometry in the striatum
scratch-the-dura
Begin to learn how to leverage Git, Docker, Jupyter, and various neuroinformatics tools for performing exciting science!
MP2RAGE-related-scripts
MP2RAGE Scripts - T1 map correction & Background noise removal
nipype
Workflows and interfaces for neuroimaging packages
global2017
webpage for Brainhack Global 2017
HippUnfolding
Code for unfolding of hippocampal grey matter using Laplacian equation. Requires manual labelling of the hippocampal 'dark band' and grey matter, as well as some surrounding structures (see associated publication for instructions)