diffusion-mri

There are 11 repositories under diffusion-mri topic.

• dipy / 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.

  diffusion-mridtitractographytractometryregistrationdenoisingspherical-harmonicsdkitrackingcontextual-enhancementneuroanatomyneuroimagingmedical-imagingmicrostructuremachine-learningpythonbundlessegmentationpatch2selfself-supervised-learning
  Language:Python 669

• PennLINC / qsiprep

  Preprocessing and reconstruction of diffusion MRI

  connectomicsdiffusion-mripipelinespythontractography
  Language:HTML 129

• StanfordMIMI / DDM2

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

  denoisingdiffusion-modelsdiffusion-mriiclriclr2023
  Language:Python 116

• AthenaEPI / dmipy

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

  diffusion-mrimicrostructure-estimationreproducible-researchnoddinoddi-binghamaxcaliberspherical-mean-techniquemulti-compartment-modelingmulti-shellmulti-echo-timemicroscopic-diffusion-imagingoptimizationconstrained-spherical-deconvolutionmulti-tissue-csdball-and-stickball-and-racketdiffusion-time-dependencemicrostructure-imaging-in-crossingsneuroscienceneuroimaging
  Language:Python 93
• KomaMRI.jl

  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.

  mrisimulationdiffusiondiffusion-mricardiacgpu-acceleration
  Language:Julia 89

• 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

  mriconnectomemultimodalimageprocessingbidsneuroimagingmicrostructureresting-statediffusion-mriawesome
  Language:Shell 75

• SlicerDMRI / SlicerDMRI

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

  diffusion-mri3d-slicermedical-image-computingneuroimaging3d-slicer-extensiontractography
  Language:C++ 73

• MIC-DKFZ / MITK-Diffusion

  MITK Diffusion - Official part of the Medical Imaging Interaction Toolkit

  diffusion-mridmrifiber-tractstractographymodellingdenoisingsegmentationregistrationdiffusion-tensorqballsbrainextractionbrainpeakmitk-diffusiondicomsupplement-181tractsegsimulationdiffusion-mri-simulationfiberfox
  Language:C++ 68

• 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.

  magnetic-resonance-imagingdiffusion-mripreprocessingbidsbids-apps
  Language:Python 62

• SlicerDMRI / whitematteranalysis

  White matter tractography clustering and more...

  diffusion-mritractographydmrineuroimagingwhite-matter
  Language:Python 61

• MASILab / Synb0-DISCO

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

  deep-learningdiffusion-mridistortion-correction
  Language:Python 54

• bids-apps / MRtrix3_connectome

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

  bidsbidsappdiffusion-mrimri
  Language:Python 45

• brain-life / encode

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

  multidimensional-arraysbrainbrain-connectomesencoding-connectomesmatlabwhite-matter-connectomesmbalifetractographydiffusion-mri
  Language:MATLAB 39

• francopestilli / life

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

  neuroimagingbrainneurosciencediffusion-mridiffusion-networkmriconnectomestatisticsneuroanatomy
  Language:MATLAB 35

• delucaal / MRIToolkit

  diffusion-mridmriinversion-recoveryivimrelaxometrymridiffusion-kurtosis-imagingdiffusion-tensor-imagingepi-correctioncsdtractographyfibertrackingclusteringwhitematterbrain
  Language:MATLAB 24

• SlicerDMRI / ORG-Atlases

  ORG Fiber Clustering White Matter Atlas

  atlasdiffusion-mridmrineuroimagingtractography
  24

• samuelstjean / nlsam

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

  diffusion-mrimachine-learningpythondenoising-algorithm
  Language:Python 23

• kerkelae / disimpy

  Massively parallel Monte Carlo diffusion MR simulator written in Python.

  diffusion-mrimonte-carlo-simulationgpu-computingcuda
  Language:Python 22

• DiffusionMRITool / dmritool

  DMRITool is an open souce toolbox for reconstruction, processing and visualization of diffusion MRI data (DWI, tensor, ODF,EAP, fibers etc.).

  diffusion-mriitkvtkmedical-image-computingcppsamplingreconstructionsimulationneuroimagingvisualization
  Language:C++ 21

• carpentries-incubator / SDC-BIDS-dMRI

  Introduction to dMRI

  antsbidscarpentries-incubatordiffusion-mridipydmridwifsllessonneuroimagingpre-alphaprogrammingpythontractography
  Language:Jupyter Notebook 20

• ShreyasFadnavis / patch2self

  Patch2Self Denoising - NeurIPS 2020 Spotlight Presentation

  self-supervised-learningmachine-learningdiffusion-mrimedical-imagingneurips-2020regression
  Language:Jupyter Notebook 20
• PyDesigner

  muscbridge / PyDesigner

  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

  dmridmriprepdiffusion-mridiffusion-mapsdwikurtosisdiffusion-preprocessingtractography
  Language:Python 19

• cabeen / qit

  A repository for the Quantitative Imaging Toolkit (QIT)

  neuroimagingvisualizationmodelingimage-analysisimage-processingdiffusion-mri
  Language:Java 18

• jonhrafe / MCDC_Simulator_public

  The Monte Carlo Diffusion and Collision simulator (MC/DC), is a C++ open-source Diffusion-Weighted Magnetic Resonance Imaging (DW-MRI) Monte Carlo Simulator.

  c-plus-plusdiffusion-mripythonsimulation
  Language:C++ 18

• NIRALUser / DTIPrep

  DTIPrep performs a "Study-specific Protocol" based automatic pipeline for DWI/DTI quality control and preparation

  3d-slicer-extensiondiffusion-mriquality-control
  Language:C++ 18
• SMI

  NYU-DiffusionMRI / SMI

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

  diffusion-mribiophysical-modelingparameter-estimationmachine-learning
  Language:MATLAB 17

• ruizengalways / FOD-Net

  FOD-Net: A Deep Learning Method for Fiber Orientation Distribution Angular Super Resolution

  deep-learningdiffusion-mrimedical-imagingconnectomicstractographymrtrix3fod
  Language:Python 17

• marksgraham / DW-POSSUM

  Simulate realistic diffusion-weighted MR data

  possumdiffusion-mrisimulation
  Language:Python 16

• jsjol / NOW

  NOW - Numerical Optimization of gradient Waveforms

  magnetic-resonance-imagingdiffusion-mridiffusion-trajectorydiffusion-trajectories
  Language:MATLAB 15

• chamberm / Detect

  Anomaly detection framework for Tractometry

  anomaly-detectiondiffusion-mripythontractometryvisualization
  Language:Python 14

• oliverchampion / IVIMNET

  This repository contains the code regarding our publication: Improved unsupervised physics-informed deep learning for intravoxel-incoherent motion modeling and evaluation in pancreatic cancer patients

  deep-learningdiffusion-mridwiivim
  Language:Python 14

• lamyj / erwin

  Quantitative MRI toolbox in Python

  quantitativemrifield-mappingcbfdiffusion-mrimotion-correctionmagnetization-transferquantitative-susceptibility-mappingsegmentationrelaxometrymrtrix3antsfslnifti
  Language:Python 11

• nipreps / eddymotion

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

  eddy-currdistortion-correctionheadmotionnipypedipydmriprepmachine-learningdiffusion-mri
  Language:Python 11
• MRtrix3Tissue

  3Tissue / MRtrix3Tissue

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

  diffusion-mridmri3-tissuecsd3-tissue-csdmrtrixmrtrix3tractography
  Language:C++ 10

• chamberm / fibernavigator

  FiberNavigator - Maxime Chamberland -

  visualizationdiffusion-mritractographyopenglglsl-shaders
  Language:C++ 10

• scilus / dmri-explorer

  A real-time diffusion MRI viewer for Linux and Windows using OpenGL 4.6.

  cppdiffusion-mrivisualizationopengl
  Language:C++ 9