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    • Overview
    • Tutorials
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    • CLI / Workflows
    • API
    • CLI API

    • Latest

    • DIPY Workshop 2024

    • Past

    • DIPY Workshop 2023
    • DIPY Workshop 2022
    • DIPY Workshop 2021
    • DIPY Workshop 2020
    • DIPY Workshop 2019

    • News

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Section Navigation

  • Quick Start
    • Getting started with DIPY
    • Introduction to Basic Tracking
  • Preprocessing
    • Reslice diffusion datasets
    • Between-volumes Motion Correction on DWI datasets
    • Noise estimation using PIESNO
    • Denoise images using Non-Local Means (NLMEANS)
    • Brain segmentation with median_otsu
    • Patch2Self: Self-Supervised Denoising via Statistical Independence
    • Denoise images using Local PCA via empirical thresholds
    • Gradients and Spheres
    • Denoise images using Adaptive Soft Coefficient Matching (ASCM)
    • SNR estimation for Diffusion-Weighted Images
    • Denoise images using the Marcenko-Pastur PCA algorithm
    • Suppress Gibbs oscillations
  • Reconstruction
    • Applying positivity constraints to Q-space Trajectory Imaging (QTI+)
    • Reconstruct with Diffusion Spectrum Imaging
    • Reconstruction of the diffusion signal with the correlation tensor model
    • DSI Deconvolution vs DSI
    • Calculate SHORE scalar maps
    • Continuous and analytical diffusion signal modelling with 3D-SHORE
    • Reconstruct with Generalized Q-Sampling Imaging
    • Reconstruct with Constant Solid Angle (Q-Ball)
    • Reconstruction with the Sparse Fascicle Model
    • Calculate DSI-based scalar maps
    • Reconstruction of the diffusion signal with the kurtosis tensor model
    • Reconstruct with Q-space Trajectory Imaging (QTI)
    • K-fold cross-validation for model comparison
    • Reconstruction of the diffusion signal with the Tensor model
    • Crossing invariant fiber response function with FORECAST model
    • Local reconstruction using the Histological ResDNN
    • Reconstruction of the diffusion signal with the WMTI model
    • Using the RESTORE algorithm for robust tensor fitting
    • Signal Reconstruction Using Spherical Harmonics
    • Using the free water elimination model to remove DTI free water contamination
    • Intravoxel incoherent motion
    • Reconstruction with Constrained Spherical Deconvolution
    • Reconstruction with Multi-Shell Multi-Tissue CSD
    • Continuous and analytical diffusion signal modelling with MAP-MRI
    • Mean signal diffusion kurtosis imaging (MSDKI)
    • Reconstruction with Robust and Unbiased Model-BAsed Spherical Deconvolution
    • Estimating diffusion time dependent q-space indices using qt-dMRI
  • Contextual Enhancement
    • Fiber to bundle coherence measures
    • Crossing-preserving contextual enhancement
  • Fiber Tracking
    • Surface seeding for tractography
    • An introduction to the Deterministic Maximum Direction Getter
    • Parallel Transport Tractography
    • Tracking with Robust Unbiased Model-BAsed Spherical Deconvolution (RUMBA-SD)
    • Bootstrap and Closest Peak Direction Getters Example
    • Tracking with the Sparse Fascicle Model
    • Introduction to Basic Tracking
    • An introduction to the Probabilistic Direction Getter
    • Particle Filtering Tractography
    • Linear fascicle evaluation (LiFE)
    • Using Various Stopping Criterion for Tractography
  • Streamlines Analysis and Connectivity
    • BUAN Bundle Shape Similarity Score
    • BUAN Bundle Assignment Maps Creation
    • Extracting AFQ tract profiles from segmented bundles
    • Streamline length and size reduction
    • Calculation of Outliers with Cluster Confidence Index
    • Calculate Path Length Map
    • Connectivity Matrices, ROI Intersections and Density Maps
  • Registration
    • Groupwise Bundle Registration
    • Direct Bundle Registration
    • Symmetric Diffeomorphic Registration in 3D
    • Symmetric Diffeomorphic Registration in 2D
    • Diffeomorphic Registration with binary and fuzzy images
    • Nonrigid Bundle Registration with BundleWarp
    • Applying image-based deformations to streamlines
    • Affine Registration with Masks
    • Affine Registration in 3D
  • Segmentation
    • Brain segmentation with median_otsu
    • Tractography Clustering with QuickBundles
    • Tissue Classification of a T1-weighted Structural Image
    • Tractography Clustering - Available Metrics
    • Fast Streamline Search
    • Enhancing QuickBundles with different metrics and features
    • Tractography Clustering - Available Features
    • Automatic Fiber Bundle Extraction with RecoBundles
  • Simulation
    • DSI Deconvolution vs DSI
    • DKI MultiTensor Simulation
    • MultiTensor Simulation
  • Multiprocessing
    • Parallel reconstruction using Q-Ball
    • Parallel reconstruction using CSD
  • File Formats
    • Read/Write streamline files
  • Visualization
    • Visualization of ROI Surface Rendered with Streamlines
    • Visualize bundles and metrics on bundles
    • Simple volume slicing
    • Advanced interactive visualization
  • Workflows
    • Creating a new workflow.
    • Creating a new combined workflow
  • Examples
  • DIPY

Visualization#

Visualization of ROI Surface Rendered with Streamlines

Visualization of ROI Surface Rendered with Streamlines

Visualize bundles and metrics on bundles

Visualize bundles and metrics on bundles

Simple volume slicing

Simple volume slicing

Advanced interactive visualization

Advanced interactive visualization

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Read/Write streamline files

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Visualization of ROI Surface Rendered with Streamlines

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  • The department of Intelligent Systems Engineering of Indiana University
  • The National Institute of Biomedical Imaging and Bioengineering, NIH
  • The Gordon and Betty Moore Foundation and the Alfred P. Sloan Foundation, through the University of Washington eScience Institute Data Science Environment
  • Google supported DIPY through the Google Summer of Code Program (2015-2024)
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