Site Map

• Index
• Events Archive
• Utilities
• Phantom Analysis Utility
• TORTOISE FAQ
• Change Data Type
• Download TORTOISE
• Acknowledgements
• Data
• Quick Start Guide
• Initial system setup
• 1.3.4 IDL VM
• Running TORTOISE Modules
• Data Import
• DIFF_CALC Loading
• Image Registration
• DIFF_CALC Fit
• Preprocessing Steps
• Preprocessing Steps: GE
• Preprocessing Steps: Phillips
• Quantitative MRI Group
• QMRI Group Members and Contributors
• QMRI Group Publications
• ISMRM 2009 Educational Materials
• ISMRM Software Comparison
• Posters and Presentations
• QMRI Acknowledgements
• DIFF_PREP
• DIFF_PREP Pipeline
• Transformation Files
• Fitting Options
• Legacy NIH_DMC Updates
• DIFF_PREP Update Notes
• NIHDMCS_04_25_2008
• NIHDMCS_05_30_2008
• NIHDMCS_V2
• NIHDMCS_V2.0.1
• NIHDMCS_V2.0.2
• NIHDMCS_V2.0.3
• NIHDMCS_V2.1
• 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
• IDL Utilities
• MRI Manager
• Starting Up and Software Overview
• Importing a Project/Study
• Exporting a Project/Study
• DIFF_CALC
• DIFF_CALC Software Guide
• 1. Introduction
• 1.1 Organization
• 1.2 About
• 1.3 Installation
• 1.3.1 System Requirements
• 1.3.2 Software Installation
• 1.3.3 Running DIFF_CALC
• 1.3.4 IDL VM
• 2. Software Overview
• 3. Usage
• 3.1 Configuration File
• 3.1.1 Optimize Configfile
• 3.1.1.1 Advanced Optimize Configfile
• 3.2 Main Software GUI
• 3.2.1 Load Listfile
• 3.2.2 Display Images
• 3.2.2.1 Inspect Entire Set
• 3.2.2.2 Delete Volume
• 3.2.3 Estimate Signal SD
• 3.2.4 Mask Raw Images
• 3.2.5 Quit
• 3.2.6 About TORTOISE
• 3.2.7 Process Tensor
• 3.2.7.1 RESTORE Options
• 3.2.7.2 iRESTORE Options
• 3.2.8 Compute Eigenvalues
• 3.2.9 Triplanar
• 3.2.9.1 Define ROI
• 3.2.10 ROI Utilities
• 3.2.10.1 Edit Options
• 3.2.10.2 Edit Color Options
• 3.2.10.3 Filter ROI Options
• 3.2.11 Export Images
• 3.2.11.1 Export to FSL
• 3.2.12 Save Session
• 3.2.13 Restore Session
• 3.2.14 Sensitize the Buttons
• DR-BUDDI
• DR-BUDDI Software Guide
• 1. Running the Module
• 2. Basic Settings
• 3. Advanced Settings
• 3.1 Initial Alignment
• 3.2 Deformation Initialization
• 3.3 DWI Type
• 3.4 B-value for Non-Diffusion Images
• 3.5 Use DWIs
• 3.6 Number of DWIs
• 3.7 Weighting of Volumes
• 3.8 Transform Type
• 3.9 Gaussian Kernel Size
• 3.10 Metric Modality
• 3.11 Cross Correlation
• 3.12 Metric Types
• 3.13 Number of Levels
• 3.14 Smoothing Kernels
• 3.15 Shrinking per Level
• 3.16 Restrict Deformation to Phase Encoding
• 3.17 Enforce Up and Down Symmetry
• 3.18 Steps
• 3.19 Final Image Resolution
• 3.20 Display Progress Window