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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
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 (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
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