DIPY is the paragon 3D/4D+ medical 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.

Koma is a GPU-accelerated, Pulseq-compatible framework for simulating Magnetic Resonance Imaging (MRI) acquisitions. The primary focus of this package is to simulate the wide range of scenarios encountered during pulse sequence development.

[ICLR2023] Official repository of DDM2: Self-Supervised Diffusion MRI Denoising with Generative Diffusion Models

Preprocessing of diffusion MRI

The open source toolbox for reproducible diffusion MRI-based microstructure estimation

micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below

MITK Diffusion - Official part of the Medical Imaging Interaction Toolkit

Distortion correction of diffusion weighted MRI without reverse phase-encoding scans or field-maps

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

White matter tractography clustering and more...

dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.

Generate subject connectomes from raw BIDS data & perform inter-subject connection density normalisation, using the MRtrix3 software package.

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

Please use the new version of LiFE: www.github.com/brain-life/encode

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

ORG Fiber Clustering White Matter Atlas

Massively parallel Monte Carlo diffusion MR simulator written in Python.

Toolbox for parameter estimation of the Standard Model of diffusion in white matter

[ICLR 2025] Official code of the paper "Self-Supervised Diffusion MRI Denoising via Iterative and Stable Refinement"