Multi-platform, free open source software for visualization and image computing.

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.

A Reproducible Workflow for Structural and Functional Connectome Ensemble Learning

Graph theory analysis of brain MRI data

Easy and comprehensive assessment of predictive power, with support for neuroimaging features

Diffusion MRI analysis and visualization in 3D Slicer open source medical imaging platform.

Preprocessing and reconstruction of diffusion MRI

Method for encoding brain connectomes in multidimensional arrays (tensors).

Magnetic resonance imaging and tractography with R

MITK Diffusion - Official part of the Medical Imaging Interaction Toolkit

Scripts for MRI preprocessing

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

Cloud Based Interactive Visualization of Tractography Brain Connectome (CIVILITY) is an interactive visualization tool of brain connectome in the web.

Python tool for spatially normalizing diffusion MRI data

Automatic Tractography Tool

OG 2019 - Project 04: Novel neuronavigation to guide brain stimulation

This repository extracts the tractograpic feature, other first-order features and the state-of-the-art feature from the stroke lesion. A random forest regressor is used with one type of feature to predict the modified Rankin Scale of stroke patients.

Runs mrtrix3 ACT (Anatomically Constrained Tractography) using either single- or multi-shell diffusion-weighted MRI data.

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

A collection of jupyter notebooks designed to provide a comprehensive exploration of concepts related to white matter segmentation.

This is a set of tools associated with automatically segmenting tractography datasets using a combination of two complementary approaches: streamlines included in a fascicle model are identified based on 1) anatomical connectivity priors based on Freesurfer-derived regions of interest (ROIs) in the subject’s native space and 2) shape priors based on 3D streamline bundle atlases applied using Recobundles. The code for a methodology generating bundle atlases is also included, as well as useful command-line helper scripts such as identification of outliers, filtering, and merging functions.

We provide a method to extract the tractographic features from structural MR images for patients with brain tumor

Run the recommended preprocessing procedure provided by mrtrix3. The options available mostly reflect the optimal DESIGNER pipeline that was recently proposed. This App runs for >15 on topup if both PA and AP dwi files are provided. It detects bvecs flipping (dwigradcheck) and update the gradient table accordingly.

TRAMPOLINO (TRActography Meta-Pipeline cOmmand LINe tOol) is a CLI for brain tractography. It leverages Nipype to offer an immediate way to reconstruct an orientation distribution function, use it to track the streamlines and eventually filter them, all using existing software toolboxes.

Connectivity-based parcellation

Source files for my PhD thesis "Brain functional connectivity and its aberrations in mouse models of autism"

LiFE-GPU-opt software is an optimized implementation of the compute-intensive matrix operations of the LiFE algorithm for GPUs.