A Reproducible Workflow for Structural and Functional Connectome Ensemble Learning

MITK Diffusion - Official part of the Medical Imaging Interaction Toolkit

Connectome Mapper 3 is a BIDS App that implements full anatomical, diffusion, resting/state functional MRI, and recently EEG processing pipelines, from raw T1 / DWI / BOLD , and preprocessed EEG data to multi-resolution brain parcellation with corresponding connection matrices.

White matter tractography clustering and more...

ORG Fiber Clustering White Matter Atlas

Introduction to dMRI

A hands-free DTI, DKI, FBI and FBWM preprocessing pipeline. Information on algorithms and preprocessing steps are available at https://www.biorxiv.org/content/10.1101/2021.10.20.465189v1 A video tutorial on PyDesigner and its usage is now available at https://www.youtube.com/watch?v=mChQFuQqX3k

KUL/UZ NeuroImaging Suite. A set of tools for brain and spine MRI analysis.

MRtrix3Tissue adds capabilities for 3-Tissue CSD modelling and analysis to a complete version of MRtrix3.

Automated tractography using MRTrix3 CSD based on subject-specific parcellations from FreeSurfer and MultiScaleBrainParcellator

Source code for FiberStars, a visualization tool for comparing dMRI data of multiple subjects.

Tractography learning

ElikoPy is Python library aiming at easing the processing of diffusion imaging for microstructural analysis.

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

Reconstruction of preprocessed q-space images (dMRI)

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

This repo contains preprocessing scripts used in the lab, organized (mainly) by imaging modality.

experiments with diffusion image registration

FENRI (Fiber Orientations from Explicit Neural Representations) Implementation Repository, presented at the ISBI 2024 conference