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Table Of Contents
Examples
Quick Start
Preprocessing
Gradients & Spheres
Brain Extraction
SNR estimation
Denoising
Reslice
Reconstruction
Constrained Spherical Deconvolution
Simple Harmonic Oscillator based Reconstruction and Estimation
Diffusion Tensor Imaging
Q-Ball Constant Solid Angle
Diffusion Spectrum Imaging
Generalized Q-Sampling Imaging
DSI with Deconvolution
Sparse Fascicle Model
Statistical evaluation
Fiber tracking (NEW - Experimental)
Fiber tracking
Fiber tracking validation (NEW)
Streamline analysis and connectivity
Registration (NEW)
Image-based Registration
Streamline-based Registration
Segmentation
Streamline Clustering
Brain Segmentation
Simulations
Multiprocessing
File Formats
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A note about the examples
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Examples
¶
A note about the examples
Contents
Examples
Quick Start
Preprocessing
Reconstruction
Fiber tracking (NEW - Experimental)
Fiber tracking
Fiber tracking validation (NEW)
Streamline analysis and connectivity
Registration (NEW)
Segmentation
Simulations
Multiprocessing
File Formats
Quick Start
¶
Getting started with Dipy
Tracking Quick Start
Preprocessing
¶
Gradients & Spheres
¶
Gradients and Spheres
Brain Extraction
¶
Brain segmentation with median_otsu
SNR estimation
¶
SNR estimation for Diffusion-Weighted Images
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
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 (NEW)
¶
Linear fascicle evaluation (LiFE)
Streamline analysis and connectivity
¶
Connectivity Matrices, ROI Intersections and Density Maps
Streamline length and size reduction
Registration (NEW)
¶
Image-based Registration
¶
Symmetric Diffeomorphic Registration in 2D
Symmetric Diffeomorphic Registration in 3D
Streamline-based Registration
¶
Direct Bundle Registration
Segmentation
¶
Streamline Clustering
¶
Tractography Clustering with QuickBundles
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
Navigation
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