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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 (DSI)
    • Reconstruction of the diffusion signal with the correlation tensor model (CTI)
    • DSI Deconvolution (DSID) vs DSI
    • Calculate SHORE scalar maps
    • Reconstruct with Generalized Q-Sampling Imaging
    • Continuous and analytical diffusion signal modelling with 3D-SHORE
    • Reconstruct with Constant Solid Angle (Q-Ball)
    • Reconstruction with the Sparse Fascicle Model (SFM)
    • Calculate DSI-based scalar maps
    • Reconstruction of the diffusion signal with the kurtosis tensor model (DKI)
    • Reconstruct with Q-space Trajectory Imaging (QTI)
    • Reconstruction of the diffusion signal with DTI (single tensor) model
    • K-fold cross-validation for model comparison
    • Crossing invariant fiber response function with FORECAST model
    • Local reconstruction using the Histological ResDNN
    • Reconstruction of the diffusion signal with the WMTI model (DKI-MICRO)
    • Using the RESTORE algorithm for robust tensor fitting
    • Using the free water elimination model to remove DTI free water contamination
    • Signal Reconstruction Using Spherical Harmonics
    • Reconstruction with Multi-Shell Multi-Tissue CSD
    • Continuous and analytical diffusion signal modelling with MAP-MRI
    • Reconstruction with Constrained Spherical Deconvolution model (CSD)
    • Intravoxel incoherent motion (IVIM)
    • Reconstruction of Bingham Functions from ODFs
    • Mean signal diffusion kurtosis imaging (MSDKI)
    • Reconstruction with Robust and Unbiased Model-BAsed Spherical Deconvolution (RUMBA)
    • Estimating diffusion time dependent q-space indices using qt-dMRI
  • Contextual Enhancement
    • Crossing-preserving contextual enhancement
    • Fiber to bundle coherence measures
  • Fiber Tracking
    • Surface seeding for tractography
    • Parallel Transport Tractography
    • An introduction to the Deterministic Tractography
    • Bootstrap and Closest Peak Direction Getters Example
    • Tracking with Robust Unbiased Model-BAsed Spherical Deconvolution (RUMBA-SD)
    • Tracking with the Sparse Fascicle Model
    • Introduction to Basic Tracking
    • Particle Filtering Tractography
    • An introduction to the Probabilistic 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
    • Calculation of Outliers with Cluster Confidence Index
    • Streamline length and size reduction
    • Calculate Path Length Map
    • Connectivity Matrices, ROI Intersections and Density Maps
  • Registration
    • Groupwise Bundle Registration
    • Direct Bundle Registration
    • Diffeomorphic Registration with binary and fuzzy images
    • Symmetric Diffeomorphic Registration in 3D
    • Symmetric Diffeomorphic Registration in 2D
    • 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
    • Tissue Classification using Diffusion MRI with DAM
    • 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 (DSID) vs DSI
    • DKI MultiTensor Simulation
    • MultiTensor Simulation
  • Multiprocessing
    • Parallel reconstruction using Q-Ball
    • Parallel reconstruction using CSD
    • An introduction to the Fast Tracking Module
    • Tractography on the DiSCo Phantom
  • 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
  • Multiprocessing

Multiprocessing#

Parallel reconstruction using Q-Ball

Parallel reconstruction using Q-Ball

Parallel reconstruction using CSD

Parallel reconstruction using CSD

An introduction to the Fast Tracking Module

An introduction to the Fast Tracking Module

Tractography on the DiSCo Phantom

Tractography on the DiSCo Phantom

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MultiTensor Simulation

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Parallel reconstruction using Q-Ball

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