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Preface

• Scope of this guide

Getting Started Quickly with MIPAV

1. Introducing MIPAV
   • • Platform Independence
     • Understanding MIPAV capabilities
     • Extensibility with Java plug-ins
     • Sampling of MIPAV's features
   • MIPAV mailing list
   • Viewing MIPAV News and Updates
   • Supported Formats
     • Graphical and file formats supported by MIPAV
     • Image formats' descriptions
     • MIPAV configuration files
     • Image files supported by MIPAV
2. Installing MIPAV
   • MIPAV system requirements
   • Installing MIPAV
   • Upgrading MIPAV
   • Uninstalling MIPAV
   • Quitting MIPAV
3. Getting Started Quickly with MIPAV
   • Starting MIPAV
   • MIPAV main window
   • Managing memory in MIPAV
   • Allocating Memory in MIPAV
   • Opening and loading image files
   • MIPAV toolbars
   • Displaying MIPAV Toolbars
   • Displaying images
     • Default View
     • Lightbox View
     • Cine View
     • Adjusting Magnification
     • Magnifying Regions within Images
     • Improving Image Contrast
   • Modifying image resolutions
   • Changing Image Contrast
     • Adjust Window and Level
     • Improving contrast by generating and modifying histograms
     • Using Lookup Table dialog box
     • Applying color to images using predefined LUTs
     • Comparing images using alphablending
     • Restoring images to their original appearance
   • Creating new images
     • Image dialog box
     • Annotating images with text
   • Saving and printing images
   • Volumes of Interest
     • Delineating volumes of interest (VOIs)
     • Calculating VOI statistics
     • VOI statistics dialog box
     • Reviewing VOI statistics
     • Calculating statistics on VOI groups
     • Generating graphs (intensity profiles)
   • Working with ImageJ
   • Customizing MIPAV
     • MIPAV Options dialog box
     • Showing and hiding the splash screen on start-up
     • Debugging MIPAV
     • Saving a history of actions on images
     • Choosing the default file types to display or save
     • Adding Shortcuts
     • MIPAV configuration files
   • Developing new tools using the API
   • Contacting MIPAV support
   • Joining MIPAV mailing list

   MIPAV Basics

4. Understanding Image Basics
5. Working with DICOM Images
   • Browsing DICOM images
   • Sending and retrieving DICOM images
   • Testing the connection
   • Posing queries and retrieving images
   • Receiving and sending image files
   • Displaying and editing DICOM tag information
   • Protecting patient privacy using Anonymize
   • Converting non-DICOM image files to DICOM format
6. Visualizing Images
   • Displaying images using the default view
     • Magnifying and minifying images
     • Viewing two images together
     • Changing image brightness and contrast using LUTs
   • Displaying images using the animate view
   • Displaying images using the cine (movie) view
   • Displaying images using the lightbox view
   • Displaying images using the link to another image view
   • Displaying images using the triplanar view
   • Displaying images using the triplanar-dual view
   • Displaying images using the surface plotter view
   • Displaying images using the surface renderer view
   • Displaying images using the volume shear view
   • Displaying images using the volume renderer view
7. Segmenting Images Using Contours and Masks
   • Using contours to segment a VOI
     • Modifying Contours
   • Generating masks
     • Creating a mask using the Paint Grow Segmentation method
   • Converting VOI contours to masks
   • Converting masks to VOI contours and paints
   • Advanced Paint and Power Paint tools
8. Analyzing Images
   • Calculating statistics for contoured VOIs
   • Calculating statistics on VOI groups
   • Calculating the volume of masks
   • Generating graphs
     • Customizing the appearance of graphs - Modify graph dialog box
     • Changing the legends for functions
9. Changing Image Datasets Using MIPAV Utilities
   • Standard tasks provided through commands on the Utilities menu
   • Recording utilities usage with the history feature
   • 4 D tools
   • Adding image margins
   • Copying images using the Clone command
   • Converting image datasets to different data types
   • Correcting image spacing
   • Cropping images
   • Masking (filling) images
   • Flipping images
   • Image Calculator
     • Image Calculator: OR
     • Image Calculator: Advanced image calculator options
   • Image Math
   • Inserting slices into image datasets
   • Inverting the image
   • Matching images
   • Maximum Intensity Projection
   • Adding noise to images
   • Pad
   • Quantify Mask
   • Replacing pixel/voxel value in images
   • Rotating images
   • Slice tools
   • Inserting slices into image datasets
   • Subtract VOI Background
   • Standard tasks provided through commands on the Utilities menu
10. Using Scripts (Macros) in MIPAV
    • Developing and using scripts
      • Setting up scripting
      • Planning scripts
      • Recording scripts
      • Running scripts
      • Editing and deleting scripts
      • Examples
    • Combining scripts and other programs
      • Using the mipav command
      • Using Shell scripting to lessen typing
11. Developing Plugin Programs
    • Understanding plug-in programs
    • Using the API documentation
    • Developing plug-in programs
    • Creating a self-contained plug-in frame
    • Examples of MIPAV plug-ins
      • Plug-in CT_MD, a typical plug-in program
        • PlugInAlgorithmCT_MD.java
        • Plug-in CT_MD.java
12. Technical Support

MIPAV Algorithms

• Understanding MIPAV capabilities
• Developing new tools using the API
• Overview of MIPAV Algorithms
  • Cost functions used in MIPAV algorithms
  • Interpolation methods used in MIPAV
  • Degrees of freedom

• • Autocorrelation Coefficients
  • Autocovariance Coefficients
  • Barrel Distortion Correction

• • DTI Color Display
  • DTI Estimate tensor - under construction
  • DTI Pipeline - under construction

• • Edge Detection: Zero X Laplacian
  • Edge Detection: Zero X Non-Maximum Suppression

• • Extract Brain: Extract Brain Surface (BET)
  • Extract Brain: Extract Brain Surface (BSE)
  • Extract Surface (Marching Cubes)
  • Face Anonymizer (BET)

• • Fast Fourier Transformation (FFT)
  • Filters (Spatial): Adaptive Noise Reduction
  • Filters (Frequency)
  • Filters (Spatial): Adaptive Path Smooth
  • Filters (Spatial) Anisotropic Diffusion
  • Filters (Spatial): Coherence-Enhancing Diffusion
  • Filters (Spatial): Gaussian Blur
  • Filters (Spatial): Gradient Magnitude
  • Filters (Spatial): Haralick Texture
  • Filters (Spatial) Laplacian
  • 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 (Wavelet): De-noising BLS GSM
  • Filters (Wavelet): Thresholding
  • Fuzzy C-Means: Multispectral and Single Channel Algorithms

• • Histogram Equalization: Regional Adaptive
  • Histogram Equalization: Neighborhood Adaptive
  • Histogram Matching
  • 2D Histogram
  • Cumulative Histogram
  • Histogram summary
  • Image Calculator
  • Manual 2D Series
  • Mask

• • Microscopy Colocalization Orthogonal Regression
  • Microscopy: Fluorescence Resonance Energy Transfer (FRET)-Acceptor
  • Microscopy: FRAP (Fluorescence Recovery After Photobleaching)
  • Microscopy: Fluorescent Resonance Energy Transfer (FRET) Bleed Through and Efficiency
  • Microscopy: Blind Deconvolution

• • Midsagittal line alignment
  • Morphology
  • Reslice-Isotropic Voxels
  • Shading Correction: Inhomogeneity N3 Correction
  • Standard Deviation Threshold
  • Subsampling images
  • Threshold
  • Transform to power of 2

• • B-Spline Automatic Registration
    • Detect folding
    • User Dialogs in MIPAV
  • Optimized automatic registration 3D
  • Registration: Landmark-Least Squares
  • Registration: Landmark-TPSpline
  • Registration: Manual 2D Series
  • Registration: Midsagittal line alignment
  • Registration: Reslice-Isotropic Voxels
  • Registration: Time Series Optimized Automatic Registration

Glossary

Glossary for MIPAV Help

Appendices

1. References
2. DICOM Conformance
3. Supported Formats
   • Other formats supported by MIPAV
   • Understanding MIPAV-related files
4. Technical Information
5. PlugIn Algorithm Median
   • PlugIn Algorithm Median (con't, part 2)
   • PlugIn Algorithm Median (con't, part 3)
   • PlugIn Algorithm Median (con't, part 4)

Talairach

• Introduction
• Installing
• Mapping Brains in Talairach Space
  • 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
  • Viewing the Talairach grid on Talairach images

Frequently Asked Questions (FAQs)

• FAQ: Understanding Memory
• FAQ: Customizing MIPAV
• FAQ: Understanding Image Basics
• FAQ: Understanding Changes in MIPAV
• FAQ: Trimming VOIs

Publications

• Publications