MIPAV Help

• Scope of this guide

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
   • Segmenting Images Using Contours and Masks
     • 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
     • Converting 3D to 4D images and vise versa
     • Convert 4D to RGB
   • Adding image margins
   • Copying images using the Clone command
   • Converting image datasets to different data types
   • Correcting image spacing
     • Understanding contiguous planes
     • Understanding how MIPAV solves the image spacing problem
     • Image attributes
     • Saving DICOM images as XML files
     • Saving other (than DICOM) images as XML files
     • Correcting image spacing
   • Cropping images
   • Masking (filling) images
   • Flipping images
   • Image Calculator
     • Image Calculator: OR
     • Image Calculator: Advanced image calculator options
     • Image Calculator: Bulk Images
   • 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
     • Concatenating images
     • Extracting slices and volumes
     • Insert Missing Slices
     • Inserting slices into image datasets
     • Swap Slices and Volumes
   • 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
    • Extensibility with Java plug-ins
    • 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
    • Writing MIPAV plugins without MIPAV source code
    • Why can't I see the plugins I install in the menu?
12. Technical Support

• 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
  • Algorithms used to draw VOI

• • Autocorrelation Coefficients
  • Autocovariance Coefficients
  • Barrel Distortion Correction

• • DTI: Create List File
  • DTI Color Display
  • DTI Estimate tensor - under construction
  • DTI Pipeline

• • 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)

• • Filters (Frequency)
  • Fast Fourier Transformation (FFT)
  • Filters (Spatial): Adaptive Noise Reduction
  • 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 cumulative
  • Histogram Equalization: Regional Adaptive
  • Histogram Equalization: Neighborhood Adaptive
  • Histogram Matching
  • 2D Histogram
  • Histogram summary
  • Hough Transform
  • 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
    • Background Distance map
    • Close
    • Delete Objects
    • Dilate
    • Distance Map
    • Erode
    • Evaluate Segmentation
    • Fill holes
    • Find Edges
    • ID objects
    • Morphological Filter
    • Open
    • Particle Analysis
    • Skeletonize
    • Skeletonize 3D pot field
    • Ultimate erode
  • Muscle Segmentation
  • NEI Build macular pigment maps

• • Registration: B-Spline Automatic Registration
    • Detect folding
    • B-Spline Automatic Registration Dialog box
  • Registration: Optimized automatic registration 3D and 3.5D
  • 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
  • Reslice-Isotropic Voxels
  • Segmentation: Watershed
  • Shading Correction: Inhomogeneity N3 Correction
  • Standard Deviation Threshold
  • Subsampling images
  • Threshold
  • Transform
  • Transform to power of 2
  • Transform: Conformal Mapping Algorithms
  • Transform nonlinear
  • Volume Renderer

Glossary for MIPAV Help

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)

• 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

• Using Fluorescent Resonance Energy Transfer (FRET) algorithms in MIPAV

• FAQ: Understanding Memory
• FAQ: Customizing MIPAV
• FAQ: Understanding Image Basics
• FAQ: Understanding Changes in MIPAV
• FAQ: Trimming VOIs
• FAQ: How can I view the debugging output of MIPAV?
• FAQ: How can I fix a "Cannot load Java Virtual Machine" error (memory limit set too high)?
• FAQ: How do I setup and use Active stereo display in MIPAV?
• FAQ: Why can't I see the plugins I install in the menu?

• A video tutorial that explains how to load images into MIPAV and change the memory allocation - play.

• A video tutorial that explains how to do basic image display options - play.

• A video tutorial that explains how to convert VOIs into binary masks that can be read by other programs such as Matlab or ImageJ. It also explains how to calculate statistics over VOIs - play.

• A video tutorial that explains how to save and capture PDFs of images - play.

• A video tutorial that explains how to do basic image manipulations - play.

All tutorials are courtesy of MIPAVvideos.

• Publications

• Creating a Streamlined Pipeline Utility for the Analysis of Universal Diffusion Tensor Imaging Data, by Beth Tyrie, October 20, 2011, Media:TyrieDTIPostbacPresentation10-20PDF.pdf
• STREAMLINING THE ANALYSIS OF DIFFUSION TENSOR IMAGING FILES THROUGH THE CREATION OF A MASS IMAGE EDITOR by Sara Shen - the presentation given on August 07, 2013 on the summer students talk event at NIH/CIT/DCB, Media:SarahShenPresentation2013.pdf, Media:SarahShenPresentation2013.pptx‎

• Getting Started with MIPAV - a class conducted by Justin Senseney - Media:GettingstartedJS.ppt‎

• Introduction to Medical Image Processing in MIPAV
• Segmentation and Annotation of Medical Images in MIPAV
• Medical Image Visualization in MIPAV
• Medical Image Processing and Registration in MIPAV
• The Java Image Science Toolkit and Scripting in MIPAV
• Developing Java Plugins in MIPAV

• Talairach (presented by Pilou Bazin)