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  1. 2D Histogram
  2. 3-D Surface Views
  3. 4 D tools
  4. Adding image margins
  5. Adding noise to images
  6. Algorithms used to draw VOI
  7. Allocating Memory in MIPAV
  8. Analyzing Images
  9. Autocorrelation Coefficients
  10. Autocovariance Coefficients
  11. Automatic de-Skulling
  12. B-Spline Automatic Registration
  13. B-Spline Automatic Registration Dialog box
  14. BSpline registration: Detecting folding
  15. Background
  16. Barrel Distortion Correction
  17. Browsing DICOM images
  18. Building and compiling plug-in programs
  19. Calculating VOI statistics
  20. Calculating statistics on VOI groups
  21. Calculating the volume of masks
  22. Changing Image Contrast
  23. Changing Image Datasets Using MIPAV Utilities
  24. Changing the legends for functions
  25. Combining scripts and other programs
  26. Connecting to SRB BIRN
  27. Contributing code to MIPAV
  28. Conventions used in this guide
  29. Converting image datasets to different data types
  30. Converting non-DICOM image files to DICOM format
  31. Copying images using the Clone command
  32. Correcting image spacing
  33. Cost functions used in MIPAV algorithms
  34. Creating a mask using the Paint Grow Segmentation method
  35. Creating a self-contained plug-in frame
  36. Creating new images
  37. Crontab notes
  38. Cropping images
  39. Cumulative Histogram
  40. Customizing MIPAV
  41. Customizing the appearance of graphs - Modify graph dialog box
  42. DICOM Conformance
  43. DTI: Create List File
  44. DTI Color Display
  45. DTI Estimate tensor
  46. DTI Pipeline
  47. DTI Pipeline Tutorials
  48. DTI pipeline interface
  49. Data Download module
  50. Data Repository tools
  51. Data Upload module
  52. Data Validation module
  53. Degrees of freedom
  54. Delineating volumes of interest (VOIs)
  55. Developing Plugin Programs
  56. Developing and using scripts
  57. Developing new tools using the API
  58. Developing plug-in programs
  59. Displaying MIPAV Toolbars
  60. Displaying and editing DICOM tag information
  61. Displaying images
  62. Documentation of MIPAV contributions by Geometric Tools
  63. Eclipse installation and configuration documentation
  64. Edge Detection: Zero X Laplacian
  65. Edge Detection: Zero X Non-Maximum Suppression
  66. Editing and deleting scripts
  67. Examples
  68. Examples of BSpline registration
  69. Examples of MIPAV plug-ins
  70. Extract Brain: Extract Brain Surface (BET)
  71. Extract Brain: Extract Brain Surface (BSE)
  72. Extract Surface (Marching Cubes)
  73. FAQ: Customizing MIPAV
  74. FAQ: How can I fix a "Cannot load Java Virtual Machine" error (memory limit set too high)?
  75. FAQ: How can I view the debugging output of MIPAV?
  76. FAQ: How do I setup and use Active stereo display in MIPAV?
  77. FAQ: Trimming VOIs
  78. FAQ: Understanding Changes in MIPAV
  79. FAQ: Understanding Image Basics
  80. FAQ: Understanding Memory
  81. FAQ: Why do I get an exception when running MIPAV via X11 forwarding on Linux?
  82. Face Anonymizer (BET)
  83. Fast Fourier Transformation (FFT)
  84. Figure 1
  85. Filters (Frequency)
  86. Filters (Spatial): Adaptive Noise Reduction
  87. Filters (Spatial): Adaptive Path Smooth
  88. Filters (Spatial): Coherence-Enhancing Diffusion
  89. Filters (Spatial): Gaussian Blur
  90. Filters (Spatial): Gradient Magnitude
  91. Filters (Spatial): Haralick Texture
  92. Filters (Spatial): Kernel Regression
  93. Filters (Spatial): Local Normalization
  94. Filters (Spatial): Mean
  95. Filters (Spatial): Median
  96. Filters (Spatial): Mode
  97. Filters (Spatial): Nonlinear Noise Reduction
  98. Filters (Spatial): Nonmaximum Suppression
  99. Filters (Spatial): Regularized Isotropic (Nonlinear) Diffusion
  100. Filters (Spatial): Slice Averaging
  101. Filters (Spatial): Unsharp Mask
  102. Filters (Spatial) Anisotropic Diffusion
  103. Filters (Spatial) Laplacian
  104. Filters (Wavelet): De-noising BLS GSM
  105. Filters (Wavelet): Thresholding
  106. Flipping images
  107. Fuzzy C-Means: Multispectral and Single Channel Algorithms
  108. Generating graphs
  109. Getting Started Quickly with MIPAV
  110. Getting Started with Eclipse
  111. Glossary for MIPAV Help
  112. Histogram
  113. Histogram Cumulative
  114. Histogram Equalization: Neighborhood Adaptive
  115. Histogram Equalization: Regional Adaptive
  116. Histogram Matching
  117. Histogram summary
  118. Hough Transform
  119. How this guide is organized
  120. How to specify the location of a plugin in the MIPAV menu
  121. How to specify the script name of a plugin
  122. ImageJ
  123. Image Calculator
  124. Image Calculator: Advanced image calculator options
  125. Image Calculator: OR
  126. Image Math
  127. Image formats descriptions
  128. Image overlays and composites
  129. Image submission plug-in
  130. Inserting slices into image datasets
  131. Installing
  132. Installing a plug-in
  133. Installing mipav
  134. Interpolation methods used in MIPAV
  135. Introducing MIPAV
  136. Introduction
  137. Inverting the image
  138. Load and save profile
  139. MIPAV FAQ
  140. MIPAV Help
  141. MIPAV Script Recording
  142. MIPAV Script Running
  143. MIPAV change list
  144. MIPAV change list 1.xx
  145. MIPAV change list 2.x
  146. MIPAV change list 3.x.x
  147. MIPAV change list 4.x.x
  148. MIPAV change list 5.x.x
  149. MIPAV change list pre-1.0
  150. MIPAV class
  151. MIPAV configuration files
  152. MIPAV feature list
  153. MIPAV mailing list
  154. MIPAV system requirements
  155. MIPAV toolbars
  156. Main Page
  157. Making a MIPAV Algorithm JISTable
  158. Making a MIPAV Algorithm Scriptable
  159. Manual 2D Series
  160. Map IDs
  161. Mapping Brains in Talairach Space
  162. Mask
  163. Masking (filling) images
  164. Matching images
  165. Matrix, Plot, LUT, VOI and Surface files
  166. Maximum Intensity Projection
  167. Microscopy: Blind Deconvolution
  168. Microscopy: FRAP (Fluorescence Recovery After Photobleaching)
  169. Microscopy: Fluorescence Resonance Energy Transfer (FRET)-Acceptor
  170. Microscopy: Fluorescent Resonance Energy Transfer (FRET) Bleed Through and Efficiency
  171. Microscopy Colocalization Orthogonal Regression
  172. Midsagittal line alignment
  173. Modifying Contours
  174. Modifying image resolutions
  175. Morphology
  176. Mosaic Registration
  177. MuscleSegmentation plugin
  178. Muscle Segmentation
  179. Muscle Segmentation problems at UCSD
  180. NEIRetinalRegistration
  181. Opening and loading image files
  182. Optimized automatic registration 3D
  183. Pad
  184. Planning scripts
  185. Plug-in CT MD, a typical plug-in program
  186. Plug-in CT MD.java
  187. PlugInAlgorithmCT MD.java
  188. PlugInDialogCT MD.java
  189. PlugIn Algorithm Median
  190. PlugIn Algorithm Median (con't)
  191. PlugIn Algorithm Median (con't, part 2)
  192. PlugIn Algorithm Median (con't, part 3)
  193. PlugIn Algorithm Median (con't, part 4)
  194. Posing queries and retrieving images
  195. Preface
  196. Prostate segmentation and surface reconstruction
  197. Protecting patient privacy using Anonymize
  198. Publications
  199. Quantify Mask
  200. Quitting MIPAV
  201. Receiving and sending image files
  202. Recording scripts
  203. Recording utilities usage with the history feature
  204. References
  205. Registration: Landmark-Least Squares
  206. Registration: Landmark-TPSpline
  207. Registration: Manual 2D Series
  208. Registration: Time Series Optimized Automatic Registration
  209. Replacing pixel/voxel value in images
  210. Reslice-Isotropic Voxels
  211. Reviewing VOI statistics
  212. Rotating images
  213. Running scripts
  214. Sample images
  215. Saving a history of actions on images
  216. Saving and printing images
  217. Scope of this guide
  218. Segmenting Images Using Contours and Masks
  219. Segmenting Images Using Contours and Masks:Converting VOI contours to masks
  220. Segmenting Images Using Contours and Masks: Advanced paint and Power Paint tools
  221. Segmenting Images Using Contours and Masks: Converting masks to VOI contours and paints
  222. Segmenting Images Using Contours and Masks: Generating Masks
  223. Segmenting Images Using Contours and Masks: Using contours to segment a VOI
  224. Select Algorithms and Brain Tools for Talairach Transform
  225. Sending and retrieving DICOM images
  226. Setting up scripting
  227. Shading Correction: Inhomogeneity N3 Correction
  228. Skills you need to perform tasks in MIPAV
  229. Slice tools
  230. Standard Deviation Threshold
  231. Standard tasks provided through commands on the Utilities menu
  232. Subsampling images
  233. Subtract VOI Background
  234. Subversion topics
  235. Supported Formats
  236. Supported algorithms
  237. Supported file formats
  238. Supported utilities
  239. Swap slices and swap volumes
  240. TRE Scripts
  241. Task 1, Performing a semimanual transformation on datasets to the Talairach coordinate system
  242. Task 2, Applying Talairach VOIs
  243. Task 3, Segmenting the original image
  244. Task 4, Transforming Talairach image and Talairach VOIs-1 to the original image
  245. Task 5, Copying Talairach VOIs to segmented images
  246. Task 6, Calculating statistics on VOIs
  247. Technical Information
  248. Technical Support
  249. Testing the connection
  250. The SRB tab of the MIPAV options dialog box
  251. Threshold
  252. To show the splash screen
  253. Transform
  254. Transform: Conformal Mapping Algorithms
  255. Transform nonlinear
  256. Transform to power of 2
  257. Transformation matrix
  258. Understanding Image Basics
  259. Understanding MIPAV capabilities
  260. Understanding plug-in programs
  261. Using MIPAV Algorithms
  262. Using MIPAV for astronomical image processing
  263. Using Scripts (Macros) in MIPAV
  264. Using Shell scripting to lessen typing
  265. Using the API documentation
  266. Using the mipav command
  267. VOIs
  268. Video tutorials
  269. Viewing MIPAV news and updates
  270. Viewing the Talairach grid on Talairach images
  271. Visualizing Images
  272. Visualizing Images:Displaying images using the default view: Magnifying and minifying images
  273. Visualizing Images: Displaying images using the animate view
  274. Visualizing Images: Displaying images using the cine (movie) view
  275. Visualizing Images: Displaying images using the default view
  276. Visualizing Images: Displaying images using the default view:Changing image brightness and contrast using LUTs
  277. Visualizing Images: Displaying images using the default view: Viewing two images together
  278. Visualizing Images: Displaying images using the lightbox view
  279. Visualizing Images: Displaying images using the link to another image view
  280. Visualizing Images: Displaying images using the surface plotter view
  281. Visualizing Images: Displaying images using the surface renderer view
  282. Visualizing Images: Displaying images using the triplanar-dual view
  283. Visualizing Images: Displaying images using the triplanar view
  284. Volume 1, Basics
  285. Volume 2, Algorithms
  286. Volume Renderer
  287. Volume renderer GPU support listing
  288. Watershed
  289. Where to find more information
  290. Who should use this guide
  291. Why can't I see the plugins I install in the menu?
  292. Wiki help testing
  293. Working with DICOM Images
  294. Writing MIPAV plugins without MIPAV source code

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