DIFF_PREP Software Guide

1. Introduction

• 1.1 Welcome
• 1.1.1 Document Organization
• 1.1.2 About
• 1.2 Installation
• 1.2.1 System Requirements
• 1.2.2 Software Installation

2. Software Overview

• 2.1 Overall Algorithm
• 2.2 Motion Distortion Correction
• 2.3 Eddy Current Distortion Correction
• 2.4 EPI Distortion Correction
• 2.5 Other Features
• 2.5.1 Image Resampling
• 2.5.2 Automatic Noise Computation
• 2.5.3 Image Cropping
• 2.5.4 Brain Masking

3. Usage

• 3.1 Running the Software
• 3.1.1 Data Format
• 3.1.2 Data Description File
• 3.1.2.1 Sample Data Description File
• 3.1.3 From Command Line
• 3.1.4 With GUI
• 3.1.4.1 Import Tools
• 3.2 Registration Settings
• 3.2.1 Sample Registration Settings File
• 3.2.2 DWI-B0 Registration (1)
• 3.2.3 DWI-B0 Registration (2)
• 3.2.4 Smoothing
• 3.2.5 Smoothing Algorithm
• 3.2.6 Gaussian Variance
• 3.2.7 Kappa
• 3.2.8 Automatic Noise Computation
• 3.2.9 Automatic Kappa
• 3.2.10 Verbose
• 3.2.11 NBINS
• 3.2.12 DWI Final Voxelsize (mm)
• 3.2.13 Structural Final Voxelsize (mm)
• 3.2.14 Mask with bet2
• 3.2.15 ITK Structural Registration
• 3.2.16 Initial Global Search
• 3.2.17 Initial Upsampling
• 3.2.18 Upsampling Factor
• 3.2.19 Upsampling Method
• 3.2.20 Scale Signal Factor
• 3.2.21 Working FOV
• 3.2.22 Correction for B0 Distortion with B-Splines
• 3.2.23 BSpline Grid Size
• 3.2.24 write_extra_files
• 3.2.25 Affine Correction for Subsequent B0s
• 3.2.26 Image Format
• 3.2.27 Output Endianism
• 3.2.28 Write Noise Variance
• 3.2.29 Compute Noise Correlation
• 3.2.30 Start Stop Steps (1)
• 3.2.31 Start Stop Steps (2)
• 3.2.32 keep_step4_output
• 3.2.33 keep_deformation_field
• 3.2.34 save_template
• 3.2.35 write_fsl_output
• 3.2.36 keep_intermediate_data
• 3.3 Optimization Settings