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csd

Matlab demonstration version of constrained spherical deconvolution

dhcp-release-notes

Notes for the dHCP data release

dstripe

This repository contains code and model weights for the method described in the paper "dStripe: slice artefact correction in diffusion MRI via constrained neural network" https://doi.org/10.1016/j.media.2021.102255

fixel_combat

This performs ComBat data harmonisation on fixel-based data.

git_collate_contributions

analyse contributions to a git repo, and produce a breakdown of commits, insertions and deletions per user

gmem

Simple tool to graph memory usage in terminal

jdtournier.github.io

a brief tutorial for users new to Unix

medphysstatscourse

Materials for the MedPhys Stats course

microstructure_simulations

Matlab code to run simple simulations of diffusion in cylinders - for demonstration purposes only

mrdegibbs3d

mrhub

Hub for open-source MR-related software

mrtrix-0.2

This is the legacy version of MRtrix. This version will only get updates for critical bug fixes. For any new developments, please use the newer MRtrix3 codebase.

mrtrix3

MRtrix provides a set of tools to perform various advanced diffusion MRI analyses, including constrained spherical deconvolution (CSD), probabilistic tractography, track-density imaging, and apparent fibre density

mrtrix3.github.io

Repository to hold the MRtrix3 website

mrtrix3_extras

A few odd but potentially useful commands

nd2tonii

Convert nd2 files from confocal microscope project to nifti

neonatal_acquisition_optimisation

Scripts used in optimisation of neonatal dMRI acquisition parameters

oop_tutorial

pipeline_scripting

A collection of bash helper functions to help with scripting neuroimaging pipelines

shard-recon

MRtrix3 module for motion correction and scattered slice reconstruction in multi-shell diffusion MRI.

simple_build

simple bash script to automatically build small C++ projects

staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

testing

The old MRtrix3 testing repo, now obsolete - do not use!

vu-meter

a simple mic level meter - useful to double-check mic levels when recording lectures!

vulkan_minimal_compute

Minimal Example of Using Vulkan for Compute Operations. Only ~400LOC.