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  1. Developing and using scripts
  2. Developing plug-in programs
  3. Documentation of MIPAV contributions by Geometric Tools
  4. Eclipse installation and configuration documentation
  5. Editing and deleting scripts
  6. Examples
  7. Examples of MIPAV plug-ins
  8. FAQ: Why do I get an exception when running MIPAV via X11 forwarding on Linux?
  9. Figure 1
  10. Generating graphs
  11. Getting Started with Eclipse
  12. Glossary for MIPAV Help
  13. Histogram
  14. How this guide is organized
  15. How to specify the script name of a plugin
  16. Image Calculator: OR
  17. Image overlays and composites
  18. Installing
  19. Installing a plug-in
  20. Introduction
  21. Inverting the image
  22. MIPAV FAQ
  23. MIPAV Help
  24. MIPAV Script Recording
  25. MIPAV Script Running
  26. MIPAV change list
  27. MIPAV change list 1.xx
  28. MIPAV change list 2.x
  29. MIPAV change list 3.x.x
  30. MIPAV change list 4.x.x
  31. MIPAV change list 5.x.x
  32. MIPAV change list pre-1.0
  33. MIPAV class
  34. MIPAV feature list
  35. Main Page
  36. Making a MIPAV Algorithm JISTable
  37. Making a MIPAV Algorithm Scriptable
  38. Mapping Brains in Talairach Space
  39. Matrix, Plot, LUT, VOI and Surface files
  40. Maximum Intensity Projection
  41. Modifying Contours
  42. MuscleSegmentation plugin
  43. Muscle Segmentation problems at UCSD
  44. Pad
  45. Planning scripts
  46. Plug-in CT MD, a typical plug-in program
  47. Plug-in CT MD.java
  48. PlugInAlgorithmCT MD.java
  49. PlugInDialogCT MD.java
  50. PlugIn Algorithm Median
  51. PlugIn Algorithm Median (con't)
  52. PlugIn Algorithm Median (con't, part 2)
  53. PlugIn Algorithm Median (con't, part 3)
  54. PlugIn Algorithm Median (con't, part 4)
  55. Preface
  56. Recording scripts
  57. Recording utilities usage with the history feature
  58. References
  59. Rotating images
  60. Saving a history of actions on images
  61. Scope of this guide
  62. Segmenting Images Using Contours and Masks:Converting VOI contours to masks
  63. Segmenting Images Using Contours and Masks: Converting masks to VOI contours and paints
  64. Segmenting Images Using Contours and Masks: Generating Masks
  65. Segmenting Images Using Contours and Masks: Using contours to segment a VOI
  66. Select Algorithms and Brain Tools for Talairach Transform
  67. Setting up scripting
  68. Skills you need to perform tasks in MIPAV
  69. Standard tasks provided through commands on the Utilities menu
  70. Subversion topics
  71. Supported utilities
  72. TRE Scripts
  73. Task 1, Performing a semimanual transformation on datasets to the Talairach coordinate system
  74. Task 2, Applying Talairach VOIs
  75. Task 3, Segmenting the original image
  76. Task 4, Transforming Talairach image and Talairach VOIs-1 to the original image
  77. Task 5, Copying Talairach VOIs to segmented images
  78. Task 6, Calculating statistics on VOIs
  79. Technical Information
  80. The SRB tab of the MIPAV options dialog box
  81. To show the splash screen
  82. Understanding Image Basics
  83. Understanding plug-in programs
  84. Using MIPAV for astronomical image processing
  85. Using Shell scripting to lessen typing
  86. Using the API documentation
  87. Using the mipav command
  88. VOIs
  89. Viewing the Talairach grid on Talairach images
  90. Visualizing Images
  91. Visualizing Images:Displaying images using the default view: Magnifying and minifying images
  92. Visualizing Images: Displaying images using the animate view
  93. Visualizing Images: Displaying images using the cine (movie) view
  94. Visualizing Images: Displaying images using the default view
  95. Visualizing Images: Displaying images using the default view: Viewing two images together
  96. Visualizing Images: Displaying images using the lightbox view
  97. Visualizing Images: Displaying images using the link to another image view
  98. Visualizing Images: Displaying images using the surface plotter view
  99. Visualizing Images: Displaying images using the surface renderer view
  100. Visualizing Images: Displaying images using the triplanar-dual view

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