Examples

• A note about the examples

Contents

• Examples

  • Quick Start

  • Preprocessing

  • Reconstruction

  • Contextual enhancement

  • Fiber tracking

  • Fiber tracking evaluation

  • Streamline analysis and connectivity

  • Registration

  • Segmentation

  • Simulations

  • Multiprocessing

  • File Formats

  • Visualization

  • Workflows

Quick Start

• Getting started with DIPY

• Introduction to Basic Tracking

Preprocessing

Gradients & Spheres

• Gradients and Spheres

Brain Extraction

• Brain segmentation with median_otsu

Basic SNR estimation

• SNR estimation for Diffusion-Weighted Images

Denoising

• Denoise images using Non-Local Means (NLMEANS)

• Denoise images using Local PCA via empirical thresholds

• Denoise images using the Marcenko-Pastur PCA algorithm

• Suppress Gibbs oscillations

Reslice

• Reslice diffusion datasets

Reconstruction

Constrained Spherical Deconvolution

• Reconstruction with Constrained Spherical Deconvolution

Fiber Orientation Estimated using Continuous Axially Symmetric Tensors

• Crossing invariant fiber response function with FORECAST model

Simple Harmonic Oscillator based Reconstruction and Estimation

• Continuous and analytical diffusion signal modelling with 3D-SHORE

• Calculate SHORE scalar maps

Mean Apparent Propagator (MAP)-MRI

• Continuous and analytical diffusion signal modelling with MAPMRI

Studying diffusion time-dependence using qt-dMRI

• Estimating diffusion time dependent q-space indices using qt-dMRI

Diffusion Tensor Imaging

• Reconstruction of the diffusion signal with the Tensor model

• Using the RESTORE algorithm for robust tensor fitting

Free-water Diffusion Tensor Imaging

• Using the free water elimination model to remove DTI free water contamination

Diffusion Kurtosis Imaging

• Reconstruction of the diffusion signal with the kurtosis tensor model

• Mean signal diffusion kurtosis imaging (MSDKI)

White Matter Tract Integrity Model

• Reconstruction of the diffusion signal with the WMTI model

Q-Ball Constant Solid Angle

• Reconstruct with Constant Solid Angle (Q-Ball)

Diffusion Spectrum Imaging

• Reconstruct with Diffusion Spectrum Imaging

• Calculate DSI-based scalar maps

Generalized Q-Sampling Imaging

• Reconstruct with Generalized Q-Sampling Imaging

DSI with Deconvolution

• DSI Deconvolution vs DSI

Sparse Fascicle Model

• Reconstruction with the Sparse Fascicle Model

Intravoxel incoherent motion (IVIM)

• Intravoxel incoherent motion

Statistical evaluation

• K-fold cross-validation for model comparison

Contextual enhancement

• Crossing-preserving contextual enhancement

• Fiber to bundle coherence measures

Fiber tracking

• Introduction to Basic Tracking

• An introduction to the Deterministic Maximum Direction Getter

• An introduction to the Probabilistic Direction Getter

• Bootstrap and Closest Peak Direction Getters Example

• Using Various Stopping Criterion for Tractography

• Particle Filtering Tractography

• Tracking with the Sparse Fascicle Model

Fiber tracking evaluation

• Linear fascicle evaluation (LiFE)

Streamline analysis and connectivity

• Connectivity Matrices, ROI Intersections and Density Maps

• Streamline length and size reduction

• Calculation of Outliers with Cluster Confidence Index

• Calculate Path Length Map

• Extracting AFQ tract profiles from segmented bundles

Registration

Image-based Registration

• Affine Registration in 3D

• Symmetric Diffeomorphic Registration in 2D

• Symmetric Diffeomorphic Registration in 3D

• Diffeomorphic Registration with binary and fuzzy images

Streamline-based Registration

• Direct Bundle Registration

Segmentation

Streamline Clustering

• Tractography Clustering with QuickBundles

• Enhancing QuickBundles with different metrics and features

• Tractography Clustering - Available Features

• Tractography Clustering - Available Metrics

Brain Segmentation

• Brain segmentation with median_otsu

Tissue Classification

• Tissue Classification of a T1-weighted Structural Image

Bundle Extraction

• Automatic Fiber Bundle Extraction with RecoBundles

Simulations

• MultiTensor Simulation

• DSI Deconvolution vs DSI

• DKI MultiTensor Simulation

Multiprocessing

• Parallel reconstruction using CSD

• Parallel reconstruction using Q-Ball

File Formats

• Read/Write streamline files

Visualization

• Advanced interactive visualization

• Simple volume slicing

• Visualize bundles and metrics on bundles

• Visualization of ROI Surface Rendered with Streamlines

Workflows

• Creating a new workflow.

• Creating a new combined workflow