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2D Histogram	3-D Surface Views	4 D tools
Adding image margins	Adding noise to images	Algorithms used to draw VOI
Allocating Memory in MIPAV	Analyzing Images	Autocorrelation Coefficients
Autocovariance Coefficients	Automatic de-Skulling	B-Spline Automatic Registration
B-Spline Automatic Registration Dialog box	BSpline registration: Detecting folding	Background
Barrel Distortion Correction	Browsing DICOM images	Building and compiling plug-in programs
Calculating VOI statistics	Calculating statistics on VOI groups	Calculating the volume of masks
Changing Image Contrast	Changing Image Datasets Using MIPAV Utilities	Changing the legends for functions
Choosing the default file types to display or save	Combining scripts and other programs	Connecting to SRB BIRN
Contributing code to MIPAV	Conventions used in this guide	Converting image datasets to different data types
Converting non-DICOM image files to DICOM format	Copying images using the Clone command	Correcting image spacing
Cost functions used in MIPAV algorithms	Creating a mask using the Paint Grow Segmentation method	Creating a self-contained plug-in frame
Creating new images	Crontab notes	Cropping images
Cumulative Histogram	Customizing MIPAV	Customizing the appearance of graphs - Modify graph dialog box
DESPOT Scripts	DICOM Conformance	DTI: Create List File
DTI Color Display	DTI Estimate tensor	DTI Pipeline
DTI Pipeline Tutorials	DTI pipeline interface	Data Download module
Data Repository tools	Data Upload module	Data Validation module
Degrees of freedom	Delineating volumes of interest (VOIs)	Detect folding
Developing Plugin Programs	Developing and using scripts	Developing new tools using the API
Developing plug-in programs	Displaying MIPAV Toolbars	Displaying and editing DICOM tag information
Displaying images	Displaying images using the default view	Documentation of MIPAV contributions by Geometric Tools
Eclipse installation and configuration documentation	Edge Detection: Zero X Laplacian	Edge Detection: Zero X Non-Maximum Suppression
Editing and deleting scripts	Examples	Examples of BSpline registration
Examples of MIPAV plug-ins	Extract Brain: Extract Brain Surface (BET)	Extract Brain: Extract Brain Surface (BSE)
Extract Surface (Marching Cubes)	FAQ: Customizing MIPAV	FAQ: How can I fix a "Cannot load Java Virtual Machine" error (memory limit set too high)?
FAQ: How can I view the debugging output of MIPAV?	FAQ: How do I setup and use Active stereo display in MIPAV?	FAQ: Trimmimg VOIs
FAQ: Trimming VOIs	FAQ: Understanding Changes in MIPAV	FAQ: Understanding Image Basics
FAQ: Understanding Memory	FAQ: Why do I get an exception when running MIPAV via X11 forwarding on Linux?	Face Anonymizer (BET)
Fast Fourier Transformation (FFT)	Figure 1	Filters (Frequency)
Filters (Spatial): Adaptive Noise Reduction	Filters (Spatial): Adaptive Path Smooth	Filters (Spatial): Coherence-Enhancing Diffusion
Filters (Spatial): Gaussian Blur	Filters (Spatial): Gradient Magnitude	Filters (Spatial): Haralick Texture
Filters (Spatial): Kernel Regression	Filters (Spatial): Local Normalization	Filters (Spatial): Mean
Filters (Spatial): Median	Filters (Spatial): Mode	Filters (Spatial): Nonlinear Noise Reduction
Filters (Spatial): Nonmaximum Suppression	Filters (Spatial): Regularized Isotropic (Nonlinear) Diffusion	Filters (Spatial): Slice Averaging
Filters (Spatial): Unsharp Mask	Filters (Spatial) Anisotropic Diffusion	Filters (Spatial) Laplacian
Filters (Spatial) Local Normalization	Filters (Wavelet): De-noising BLS GSM	Filters (Wavelet): Thresholding
Flipping images	Fuzzy C-Means: Multispectral and Single Channel Algorithms	Generating graphs
Getting Started Quickly with MIPAV	Getting Started with Eclipse	Glossary for MIPAV Help
Histogram	Histogram Cumulative	Histogram Equalization: Neighborhood Adaptive
Histogram Equalization: Regional Adaptive	Histogram Matching	Histogram summary
Hough Transform	How can I fix a "Cannot load Java Virtual Machine" error (memory limit set too high)?	How can I view the debugging output of MIPAV?
How do I setup and use Active stereo display in MIPAV?	How this guide is organized	How to fix a "Cannot load Java Virtual Machine" error (memory limit set too high)
How to specify location of plugin in MIPAV GUI	How to specify the location of a plugin in the MIPAV menu	How to specify the script name of a plugin
How to view the debugging output of a MIPAV install	ImageJ	Image Calculator
Image Calculator: Advanced image calculator options	Image Calculator: OR	Image Math
Image formats descriptions	Image overlays and composites	Image submission plug-in
Inserting slices into image datasets	Installing	Installing MIPAV
Installing a plug-in	Installing mipav	Interpolation methods used in MIPAV
Introducing MIPAV	Introduction	Inverting the image
Load and save profile	MIPAV FAQ	MIPAV Help
MIPAV Script Recording	MIPAV Script Running	MIPAV change list
MIPAV change list 1.xx	MIPAV change list 2.x	MIPAV change list 3.x.x
MIPAV change list 4.x.x	MIPAV change list 5.x.x	MIPAV change list pre-1.0
MIPAV class	MIPAV configuration files	MIPAV feature list
MIPAV mailing list	MIPAV system requirements	MIPAV toolbars
Main Page	Making a MIPAV Algorithm JISTable	Making a MIPAV Algorithm Scriptable
Manual 2D Series	Map IDs	Mapping Brains in Talairach Space
Mask	Masking (filling) images	Matching images
Matrix, Plot, LUT, VOI and Surface files	Matrix, Plot, VOI and Surface files	Matrix file
Maximum Intensity Projection	Microscopy: Blind Deconvolution	Microscopy: FRAP (Fluorescence Recovery After Photobleaching)
Microscopy: Fluorescence Resonance Energy Transfer (FRET)-Acceptor	Microscopy: Fluorescent Resonance Energy Transfer (FRET) Bleed Through and Efficiency	Microscopy Colocalization Orthogonal Regression
Midsagittal line alignment	Modifying Contours	Modifying image resolutions
Morphology	Mosaic Registration	MuscleSegmentation plugin
Muscle Segmentation	Muscle Segmentation problems at UCSD	NEIRetinalRegistration
Opening and loading image files	Optimized automatic registration 3D	Other formats supported by MIPAV
Pad	Planning scripts	Plug-in CT MD, a typical plug-in program
Plug-in CT MD.java	PlugInAlgorithmCT MD.java	PlugInDialogCT MD.java
PlugIn Algorithm Median	PlugIn Algorithm Median (con't)	PlugIn Algorithm Median (con't, part 2)
PlugIn Algorithm Median (con't, part 3)	PlugIn Algorithm Median (con't, part 4)	Posing queries and retrieving images
Preface	Prostate segmentation and surface reconstruction	Protecting patient privacy using Anonymize
Publications	Quantify Mask	Quitting MIPAV
Receiving and sending image files	Recording scripts	Recording utilities usage with the history feature
References	Registration: Landmark-Least Squares	Registration: Landmark-TPSpline
Registration: Manual 2D Series	Registration: Time Series Optimized Automatic Registration	Replacing pixel/voxel value in images
Reslice-Isotropic Voxels	Reviewing VOI statistics	Reviewing the statistics
Rotating images	Running scripts	Sample images
Saving a history of actions on images	Saving and printing images	Scope of this guide
Segmenting Images Using Contours and Masks	Segmenting Images Using Contours and Masks:Converting VOI contours to masks	Segmenting Images Using Contours and Masks: Advanced paint and Power Paint tools
Segmenting Images Using Contours and Masks: Converting masks to VOI contours and paints	Segmenting Images Using Contours and Masks: Generating Masks	Segmenting Images Using Contours and Masks: Using contours to segment a VOI
Select Algorithms and Brain Tools for Talairach Transform	Sending and retrieving DICOM images	Setting up scripting
Shading Correction: Inhomogeneity N3 Correction	Skills you need to perform tasks in MIPAV	Slice tools
Standard Deviation Threshold	Standard tasks provided through commands on the Utilities menu	Subsampling images
Subtract VOI Background	Subversion topics	Supported Formats
Supported algorithms	Supported file formats	Supported utilities
Swap slices and swap volumes	TRE Scripts	Task 1, Performing a semimanual transformation on datasets to the Talairach coordinate system
Task 2, Applying Talairach VOIs	Task 3, Segmenting the original image	Task 4, Transforming Talairach image and Talairach VOIs-1 to the original image
Task 5, Copying Talairach VOIs to segmented images	Task 6, Calculating statistics on VOIs	Technical Information
Technical Support	Testing the connection	The SRB tab of the MIPAV options dialog box
Threshold	To show the splash screen	Transform
Transform: Conformal Mapping Algorithms	Transform nonlinear	Transform to power of 2
Transformation matrix	Understanding Image Basics	Understanding MIPAV-related files
Understanding MIPAV capabilities	Understanding plug-in programs	User Dialogs in MIPAV
Using MIPAV Algorithms	Using MIPAV for astronomical image processing	Using Scripts (Macros) in MIPAV
Using Shell scripting to lessen typing	Using the API documentation	Using the mipav command
Using the right mouse button	VOIs	Video tutorials
Viewing MIPAV news and updates	Viewing the Talairach grid on Talairach images	Visualizing Images
Visualizing Images:Displaying images using the default view: Magnifying and minifying images	Visualizing Images: Displaying images using the animate view	Visualizing Images: Displaying images using the cine (movie) view
Visualizing Images: Displaying images using the default view	Visualizing Images: Displaying images using the default view:Changing image brightness and contrast using LUTs	Visualizing Images: Displaying images using the default view: Viewing two images together
Visualizing Images: Displaying images using the lightbox view	Visualizing Images: Displaying images using the link to another image view	Visualizing Images: Displaying images using the surface plotter view
Visualizing Images: Displaying images using the surface renderer view	Visualizing Images: Displaying images using the triplanar-dual view	Visualizing Images: Displaying images using the triplanar view
Volume 1, Basics	Volume 2, Algorithms	Volume Renderer
Volume renderer GPU support listing	Watershed	Where to find more information
Who should use this guide	Why can't I see the plugins I install in the menu?	Wiki help testing
Working with DICOM Images	Writing MIPAV plugins without MIPAV source code	Writing MIPAV plugins without access to MIPAV source code

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