Examples

• A note about the examples

Contents

• Examples
  • Quick Start
  • Preprocessing
  • Reconstruction
  • Fiber tracking (NEW - Experimental)
  • Fiber tracking
  • Fiber tracking validation
  • Streamline analysis and connectivity
  • Registration
  • Segmentation
  • Simulations
  • Multiprocessing
  • File Formats
  • Visualization

Quick Start

• Getting started with Dipy
• Tracking Quick Start

Preprocessing

Gradients & Spheres

• Gradients and Spheres

Brain Extraction

• Brain segmentation with median_otsu

Basic SNR estimation

• SNR estimation for Diffusion-Weighted Images

Robust noise estimation with PIESNO

• Noise estimation using PIESNO

Denoising

• Denoise images using Non-Local Means (NLMEANS)

Reslice

• Reslice diffusion datasets

Reconstruction

Constrained Spherical Deconvolution

• Reconstruction with Constrained Spherical Deconvolution

Simple Harmonic Oscillator based Reconstruction and Estimation

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

Diffusion Tensor Imaging

• Reconstruction of the diffusion signal with the Tensor model
• Using the RESTORE algorithm for robust tensor fitting

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

Statistical evaluation

• K-fold cross-validation for model comparison

Fiber tracking (NEW - Experimental)

• Introduction to Basic Tracking
• An introduction to the Probabilistic Direction Getter
• An introduction to the Deterministic Maximum Direction Getter
• Using Various Tissue Classifiers for Tractography
• Tracking with the Sparse Fascicle Model

Fiber tracking

• Deterministic Tracking with EuDX on Tensor Fields
• Deterministic Tracking with EuDX on ODF Peaks

Fiber tracking validation

• Linear fascicle evaluation (LiFE)

Streamline analysis and connectivity

• Connectivity Matrices, ROI Intersections and Density Maps
• Streamline length and size reduction

Registration

Image-based Registration

• Affine Registration in 3D
• Symmetric Diffeomorphic Registration in 2D
• Symmetric Diffeomorphic Registration in 3D

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

Simulations

• MultiTensor Simulation
• DSI Deconvolution vs DSI

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
• Create a minimalistic user interface