Generate a package-manager-friendly mouse brain atlases collection.

Ironsmith is a comprehensive, fully automated pipeline for creating and processing Quantitative Susceptibility Maps (QSM), extracting QSM based iron concentrations from subcortical and cortical brain regions and evaluating the quality of QSM data using SNR measures and assessment of outlier regions on phase images.

Gentoo Science Overlay

A modified FSL version for use with Slurm

Data and tools from the publication "Evolution of Cortical Geometry and its Link to Function, Behaviour and Ecology" by Schwartz et al. for mapping values defined on cortical surfaces between species based on their phylogenetic relationship

This reading list is centered around the practical application of linear dynamical systems models to predict neural data

The idea behind this website is to make available all the resources I have gathered/created over the years make other people's life easier.

Scripts and pipeline for the handling of scripts from DICOMS to 4DFP and then analysis.

Software for use at the University of Arizona SCAN Lab

An innovative and collaborative solution for setting up and executing Jupyter Notebooks on High-Performance Computing (HPC) clusters, tailored for neuroscience data processing workflows.

A Python distribution for neuroscience based on conda 🧠🐍

3D brain registration for LSFM

Scripts related to "White Matter Microstructure in Attention-Deficit/Hyperactivity Disorder: A Systematic Tractography Study in 654 Individuals"

Scripts related to "Longitudinal changes of ADHD symptoms in association with white matter microstructure: A tract-specific fixel-based analysis"

A simple script to deface (with use of fsl_deface) multiple T1/T2-weighetned files prepared according to the BIDS standard.

A Whole-Brain 3D Myeloarchitectonic Atlas: Mapping the Vogt-Vogt Legacy to the Cortical Surface

Alcohol study DTI Analyses

Pipeline for Cortical and Subcortical SC and FC

Common Docker Image for the Dosenbach and Greene Labs