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ai-flares

brain-coloring

Brain colouring program with Blender

compartmentalanalysis_gui

Matlab Graphic User Interface (GUI) for compartmental analysis of various compartmental systems for the FDG uptake in murine models

connect_metrics

MATLAB code for brain connectivity graph theory built on top of Brain Connectivity Toolbox

dipy

DIPY is the paragon 3D/4D+ imaging library in Python. Contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medical images. Additionally, it contains specialized methods for computational anatomy including diffusion, perfusion and structural imaging.

disease-progression-modelling.github.io

Website

dpm-website-tutorial

Repository of data for running the GPPM-DS tutorial available on the DPM website (disease-progression-modelling.github.io/pages/main.html)

graph-neural-pde

Graph Neural PDEs

hcp-dmri-connectome

MRtrix scripts to generate dense weighted structural connectomes from the Human Connectome Project "minimally pre-processed" diffusion MRI data

hi-gcn

Code of hi-GCN

mechanistic-profiles

Code for building mechanistic profiles of neurological diseases from grey matter volumetric information.

ms-predictive-enrichment

Code for the paper by Falet et al. (2022) "Estimating treatment effect for individuals with progressive multiple sclerosis using deep learning"

neuron_2019

opendata

Data made openly available by the Neuroanatomy and Connectivity Research Group

parametric_compartmentalanalysis

Matlab Graphic User Interface (GUI) for parametric compartmental analysis of kidneys and tumor for the FDG uptake in murine models

pipelines

Neuroimgaing data processing pipelines used in the lab

quicknat_pytorch

PyTorch Implementation of QuickNAT and Bayesian QuickNAT, a fast brain MRI segmentation framework with segmentation Quality control using structure-wise uncertainty

quicknatv2

Fast Whole Brain Segmentation (Layers, codes and Pre-trained Models)

shap

A game theoretic approach to explain the output of any machine learning model.

sparse_bayesian_imaging_rhessi

Sequential Monte Carlo algorithm approximating posterior distributions for solar flares imaging from RHESSI visibilities

ssm

Bayesian learning and inference for state space models

surfdist

For calculating exact geodesic distances on cortical surface meshes

torchio

Medical imaging toolkit for deep learning