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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
- 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
- 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)
- 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
- 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: 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 (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 this guide is organized
- How to specify the location of a plugin in the MIPAV menu
- How to specify the script name of a plugin
- 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 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
- 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
- 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
- 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 capabilities
- Understanding plug-in programs
- 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
- 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