Projects in Awesome Lists tagged with diffusion-mri

https://github.com/dipy/dipy

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.

bundles contextual-enhancement denoising diffusion-mri dki dti machine-learning medical-imaging microstructure neuroanatomy neuroimaging patch2self python registration segmentation self-supervised-learning spherical-harmonics tracking tractography tractometry

Last synced: 21 Oct 2025

https://github.com/juliahealth/komamri.jl

Koma is a Pulseq-compatible framework to efficiently simulate Magnetic Resonance Imaging (MRI) acquisitions. The main focus of this package is to simulate general scenarios that could arise in pulse sequence development.

cardiac diffusion diffusion-mri gpu-acceleration mri simulation

Last synced: 29 Apr 2026

https://github.com/PennLINC/qsiprep

Preprocessing of diffusion MRI

bids denoising-images diffusion-mri distortion-correction motion-correction pipelines

Last synced: 29 Apr 2025

https://github.com/MICA-MNI/micapipe

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

awesome bids connectome diffusion-mri imageprocessing microstructure mri multimodal neuroimaging resting-state

Last synced: 29 Apr 2025

https://github.com/AthenaEPI/dmipy

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

axcaliber ball-and-racket ball-and-stick constrained-spherical-deconvolution diffusion-mri diffusion-time-dependence microscopic-diffusion-imaging microstructure-estimation microstructure-imaging-in-crossings multi-compartment-modeling multi-echo-time multi-shell multi-tissue-csd neuroimaging neuroscience noddi noddi-bingham optimization reproducible-research spherical-mean-technique

Last synced: 01 May 2025

https://github.com/mica-mni/micapipe

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

awesome bids connectome diffusion-mri imageprocessing microstructure mri multimodal neuroimaging resting-state

Last synced: 24 Jul 2025

https://github.com/masilab/synb0-disco

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

deep-learning diffusion-mri distortion-correction

Last synced: 16 Jan 2026

https://github.com/nipreps/dmriprep

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.

bids bids-apps diffusion-mri magnetic-resonance-imaging preprocessing

Last synced: 06 May 2025

https://github.com/bids-apps/MRtrix3_connectome

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

bids bidsapp diffusion-mri mri

Last synced: 29 Apr 2025

https://github.com/brain-life/encode

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

brain brain-connectomes diffusion-mri encoding-connectomes life matlab mba multidimensional-arrays tractography white-matter-connectomes

Last synced: 01 May 2025

https://github.com/kerkelae/disimpy

Massively parallel Monte Carlo diffusion MR simulator written in Python.

cuda diffusion-mri gpu-computing monte-carlo-simulation

Last synced: 12 Apr 2025

https://github.com/samuelstjean/nlsam

The reference implementation for the Non Local Spatial and Angular Matching (NLSAM) denoising algorithm for diffusion MRI

denoising-algorithm diffusion-mri machine-learning python

Last synced: 02 Mar 2026

https://github.com/carpentries-incubator/sdc-bids-dmri

Introduction to dMRI

ants bids carpentries-incubator diffusion-mri dipy dmri dwi fsl lesson neuroimaging pre-alpha programming python tractography

Last synced: 02 Sep 2025

https://github.com/masilab/cornn_tractography

Convolutional-recurrent neural networks approximate diffusion tractography from T1-weighted MRI and associated anatomical context

convolutional-recurrent-neural-network deep-learning diffusion-mri t1-weighted-mri tractography

Last synced: 16 Jan 2026

https://github.com/marksgraham/dw-possum

Simulate realistic diffusion-weighted MR data

diffusion-mri possum simulation

Last synced: 12 Jul 2025

https://github.com/nipreps/eddymotion

Open-source eddy-current and head-motion correction for dMRI.

diffusion-mri dipy distortion-correction dmriprep eddy-curr headmotion machine-learning nipype

Last synced: 28 Aug 2025

https://github.com/lamyj/erwin

Quantitative MRI toolbox in Python

ants cbf diffusion-mri field-mapping fsl magnetization-transfer motion-correction mri mrtrix3 nifti quantitative quantitative-susceptibility-mapping relaxometry segmentation

Last synced: 30 Apr 2025

https://github.com/cwatson/mri_library

Scripts for MRI preprocessing

brain diffusion-mri dti dwi hpc-applications mri neuroimaging pipeline slurm tractography

Last synced: 18 Feb 2026

https://github.com/GeodAIsics/TractLearn-WholeBrain

TractLearn is a Manifold Learning Toolbox for precision medicine. The first application is for Diffusion-Weighted MRI quantitative analysis.

diffusion-mri manifold-learning precision-medicine

Last synced: 01 May 2025

https://github.com/samuelstjean/autodmri

Automated characterization of noise distributions in diffusion MRI data

diffusion-mri python

Last synced: 10 Feb 2026

https://github.com/imeka/trk-io

TrackVis (*.trk) reader and writer

diffusion-mri rust trackvis trk

Last synced: 26 Jul 2025

https://github.com/bids-apps/ndmg

BIDS app for NeuroData's MRI to Graphs pipeline

bids bidsapp connectomics diffusion-mri docker-container singularity-container

Last synced: 29 May 2026

https://github.com/imperialcollegelondon/indi

INDI is a command line tool to process in-vivo cardiac diffusion tensor imaging.

cardiac diffusion-mri mri

Last synced: 13 Jul 2025

https://github.com/icon-lab/fd-net

Official repository for "FD-Net: An Unsupervised Deep Forward-Distortion Model for Susceptibility Artifact Correction in EPI"

deep-learning diffusion-mri distortion-correction echo-planar-imaging medical-imaging susceptibility unsupervised

Last synced: 12 Jun 2025

https://github.com/bids-apps/tracula

implements Freesurfer's TRACULA (TRActs Constrained by UnderLying Anatomy) tool for cross-sectional as well as longitudinal (multi session) input data.

bids bidsapp diffusion-mri

Last synced: 29 May 2026