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  1. (hist) ‎Conventions used in this guide ‎[0 bytes]
  2. (hist) ‎How this guide is organized ‎[0 bytes]
  3. (hist) ‎PlugInDialogCT MD.java ‎[0 bytes]
  4. (hist) ‎PlugIn Algorithm Median (con't) ‎[0 bytes]
  5. (hist) ‎Skills you need to perform tasks in MIPAV ‎[0 bytes]
  6. (hist) ‎Volume 1, Basics ‎[0 bytes]
  7. (hist) ‎Volume 2, Algorithms ‎[0 bytes]
  8. (hist) ‎Where to find more information ‎[0 bytes]
  9. (hist) ‎Who should use this guide ‎[0 bytes]
  10. (hist) ‎Technical Information ‎[25 bytes]
  11. (hist) ‎MIPAV Script Running ‎[35 bytes]
  12. (hist) ‎MIPAV Script Recording ‎[42 bytes]
  13. (hist) ‎Figure 1 ‎[48 bytes]
  14. (hist) ‎Histogram ‎[70 bytes]
  15. (hist) ‎Algorithms used to draw VOI ‎[87 bytes]
  16. (hist) ‎DTI: Create List File ‎[92 bytes]
  17. (hist) ‎Subversion topics ‎[121 bytes]
  18. (hist) ‎Documentation of MIPAV contributions by Geometric Tools ‎[123 bytes]
  19. (hist) ‎Mosaic Registration ‎[207 bytes]
  20. (hist) ‎Histogram Cumulative ‎[242 bytes]
  21. (hist) ‎Visualizing Images: Displaying images using the surface renderer view ‎[256 bytes]
  22. (hist) ‎Making a MIPAV Algorithm Scriptable ‎[257 bytes]
  23. (hist) ‎Filters (Spatial): Kernel Regression ‎[276 bytes]
  24. (hist) ‎DTI Estimate tensor ‎[283 bytes]
  25. (hist) ‎Filters (Spatial): Haralick Texture ‎[284 bytes]
  26. (hist) ‎Combining scripts and other programs ‎[352 bytes]
  27. (hist) ‎Recording utilities usage with the history feature ‎[353 bytes]
  28. (hist) ‎Why can't I see the plugins I install in the menu? ‎[361 bytes]
  29. (hist) ‎Filters (Spatial): Local Normalization ‎[384 bytes]
  30. (hist) ‎Transform nonlinear ‎[385 bytes]
  31. (hist) ‎MIPAV FAQ ‎[470 bytes]
  32. (hist) ‎VOIs ‎[470 bytes]
  33. (hist) ‎Inverting the image ‎[482 bytes]
  34. (hist) ‎Quitting MIPAV ‎[495 bytes]
  35. (hist) ‎Sample images ‎[505 bytes]
  36. (hist) ‎Visualizing Images: Displaying images using the cine (movie) view ‎[523 bytes]
  37. (hist) ‎Viewing MIPAV news and updates ‎[661 bytes]
  38. (hist) ‎Saving a history of actions on images ‎[689 bytes]
  39. (hist) ‎Developing new tools using the API ‎[799 bytes]
  40. (hist) ‎3-D Surface Views ‎[866 bytes]
  41. (hist) ‎Copying images using the Clone command ‎[871 bytes]
  42. (hist) ‎Supported utilities ‎[874 bytes]
  43. (hist) ‎Muscle Segmentation ‎[883 bytes]
  44. (hist) ‎Load and save profile ‎[891 bytes]
  45. (hist) ‎Changing Image Datasets Using MIPAV Utilities ‎[937 bytes]
  46. (hist) ‎Video tutorials ‎[962 bytes]
  47. (hist) ‎Task 4, Transforming Talairach image and Talairach VOIs-1 to the original image ‎[1,028 bytes]
  48. (hist) ‎The SRB tab of the MIPAV options dialog box ‎[1,048 bytes]
  49. (hist) ‎Developing and using scripts ‎[1,056 bytes]
  50. (hist) ‎Mapping Brains in Talairach Space ‎[1,077 bytes]
  51. (hist) ‎Viewing the Talairach grid on Talairach images ‎[1,083 bytes]
  52. (hist) ‎MuscleSegmentation plugin ‎[1,101 bytes]
  53. (hist) ‎Segmenting Images Using Contours and Masks: Converting masks to VOI contours and paints ‎[1,114 bytes]
  54. (hist) ‎Modifying image resolutions ‎[1,116 bytes]
  55. (hist) ‎Using Scripts (Macros) in MIPAV ‎[1,146 bytes]
  56. (hist) ‎To show the splash screen ‎[1,233 bytes]
  57. (hist) ‎Main Page ‎[1,273 bytes]
  58. (hist) ‎Developing Plugin Programs ‎[1,530 bytes]
  59. (hist) ‎Calculating the volume of masks ‎[1,533 bytes]
  60. (hist) ‎Task 5, Copying Talairach VOIs to segmented images ‎[1,566 bytes]
  61. (hist) ‎Image overlays and composites ‎[1,627 bytes]
  62. (hist) ‎TRE Scripts ‎[1,649 bytes]
  63. (hist) ‎Volume renderer GPU support listing ‎[1,719 bytes]
  64. (hist) ‎Testing the connection ‎[1,739 bytes]
  65. (hist) ‎FAQ: Why do I get an exception when running MIPAV via X11 forwarding on Linux? ‎[1,793 bytes]
  66. (hist) ‎FAQ: Understanding Changes in MIPAV ‎[1,823 bytes]
  67. (hist) ‎MIPAV feature list ‎[1,831 bytes]
  68. (hist) ‎Crontab notes ‎[1,849 bytes]
  69. (hist) ‎Visualizing Images: Displaying images using the default view ‎[1,921 bytes]
  70. (hist) ‎FAQ: How can I fix a "Cannot load Java Virtual Machine" error (memory limit set too high)? ‎[1,975 bytes]
  71. (hist) ‎Segmenting Images Using Contours and Masks:Converting VOI contours to masks ‎[1,992 bytes]
  72. (hist) ‎Displaying MIPAV Toolbars ‎[2,079 bytes]
  73. (hist) ‎Contributing code to MIPAV ‎[2,225 bytes]
  74. (hist) ‎Filters (Wavelet): De-noising BLS GSM ‎[2,380 bytes]
  75. (hist) ‎Muscle Segmentation problems at UCSD ‎[2,447 bytes]
  76. (hist) ‎Getting Started with Eclipse ‎[2,470 bytes]
  77. (hist) ‎Filters (Spatial): Slice Averaging ‎[2,675 bytes]
  78. (hist) ‎ImageJ ‎[2,733 bytes]
  79. (hist) ‎Transformation matrix ‎[2,775 bytes]
  80. (hist) ‎Setting up scripting ‎[2,782 bytes]
  81. (hist) ‎Cumulative Histogram ‎[2,796 bytes]
  82. (hist) ‎DTI Pipeline Tutorials ‎[2,826 bytes]
  83. (hist) ‎Degrees of freedom ‎[2,830 bytes]
  84. (hist) ‎Reslice-Isotropic Voxels ‎[2,947 bytes]
  85. (hist) ‎Eclipse installation and configuration documentation ‎[2,964 bytes]
  86. (hist) ‎MIPAV mailing list ‎[2,995 bytes]
  87. (hist) ‎Segmenting Images Using Contours and Masks ‎[3,083 bytes]
  88. (hist) ‎Visualizing Images: Displaying images using the link to another image view ‎[3,099 bytes]
  89. (hist) ‎Threshold ‎[3,105 bytes]
  90. (hist) ‎Understanding plug-in programs ‎[3,113 bytes]
  91. (hist) ‎Flipping images ‎[3,144 bytes]
  92. (hist) ‎Subsampling images ‎[3,146 bytes]
  93. (hist) ‎Autocorrelation Coefficients ‎[3,174 bytes]
  94. (hist) ‎Quantify Mask ‎[3,215 bytes]
  95. (hist) ‎Histogram summary ‎[3,231 bytes]
  96. (hist) ‎Task 6, Calculating statistics on VOIs ‎[3,316 bytes]
  97. (hist) ‎Editing and deleting scripts ‎[3,317 bytes]
  98. (hist) ‎Understanding MIPAV capabilities ‎[3,398 bytes]
  99. (hist) ‎Transform to power of 2 ‎[3,495 bytes]
  100. (hist) ‎Working with DICOM Images ‎[3,524 bytes]
  101. (hist) ‎References ‎[3,542 bytes]
  102. (hist) ‎How to specify the location of a plugin in the MIPAV menu ‎[3,688 bytes]
  103. (hist) ‎Technical Support ‎[3,777 bytes]
  104. (hist) ‎Filters (Spatial): Regularized Isotropic (Nonlinear) Diffusion ‎[3,952 bytes]
  105. (hist) ‎FAQ: Trimming VOIs ‎[4,063 bytes]
  106. (hist) ‎Pad ‎[4,107 bytes]
  107. (hist) ‎Examples of BSpline registration ‎[4,231 bytes]
  108. (hist) ‎FAQ: How can I view the debugging output of MIPAV? ‎[4,289 bytes]
  109. (hist) ‎Volume Renderer ‎[4,341 bytes]
  110. (hist) ‎Barrel Distortion Correction ‎[4,342 bytes]
  111. (hist) ‎Filters (Spatial): Unsharp Mask ‎[4,345 bytes]
  112. (hist) ‎MIPAV system requirements ‎[4,368 bytes]
  113. (hist) ‎Allocating Memory in MIPAV ‎[4,434 bytes]
  114. (hist) ‎Filters (Spatial): Gradient Magnitude ‎[4,448 bytes]
  115. (hist) ‎How to specify the script name of a plugin ‎[4,458 bytes]
  116. (hist) ‎Filters (Spatial): Nonmaximum Suppression ‎[4,569 bytes]
  117. (hist) ‎Planning scripts ‎[4,609 bytes]
  118. (hist) ‎Replacing pixel/voxel value in images ‎[4,664 bytes]
  119. (hist) ‎FAQ: Customizing MIPAV ‎[4,725 bytes]
  120. (hist) ‎Installing a plug-in ‎[4,729 bytes]
  121. (hist) ‎Supported algorithms ‎[4,751 bytes]
  122. (hist) ‎Filters (Spatial): Nonlinear Noise Reduction ‎[4,837 bytes]
  123. (hist) ‎Task 1, Performing a semimanual transformation on datasets to the Talairach coordinate system ‎[4,976 bytes]
  124. (hist) ‎Autocovariance Coefficients ‎[5,037 bytes]
  125. (hist) ‎Masking (filling) images ‎[5,063 bytes]
  126. (hist) ‎Installing mipav ‎[5,100 bytes]
  127. (hist) ‎Filters (Wavelet): Thresholding ‎[5,133 bytes]
  128. (hist) ‎Scope of this guide ‎[5,252 bytes]
  129. (hist) ‎Mask ‎[5,294 bytes]
  130. (hist) ‎Image Math ‎[5,474 bytes]
  131. (hist) ‎Installing ‎[5,615 bytes]
  132. (hist) ‎Data Upload module ‎[5,724 bytes]
  133. (hist) ‎Rotating images ‎[5,760 bytes]
  134. (hist) ‎Data Download module ‎[5,995 bytes]
  135. (hist) ‎MIPAV class ‎[6,004 bytes]
  136. (hist) ‎Registration: Landmark-TPSpline ‎[6,092 bytes]
  137. (hist) ‎Reviewing VOI statistics ‎[6,209 bytes]
  138. (hist) ‎FAQ: How do I setup and use Active stereo display in MIPAV? ‎[6,239 bytes]
  139. (hist) ‎Watershed ‎[6,255 bytes]
  140. (hist) ‎Filters (Spatial) Laplacian ‎[6,638 bytes]
  141. (hist) ‎Histogram Matching ‎[6,675 bytes]
  142. (hist) ‎Midsagittal line alignment ‎[6,736 bytes]
  143. (hist) ‎Image Calculator: Advanced image calculator options ‎[6,968 bytes]
  144. (hist) ‎Subtract VOI Background ‎[7,015 bytes]
  145. (hist) ‎Matching images ‎[7,017 bytes]
  146. (hist) ‎Cropping images ‎[7,068 bytes]
  147. (hist) ‎Adding noise to images ‎[7,164 bytes]
  148. (hist) ‎Delineating volumes of interest (VOIs) ‎[7,200 bytes]
  149. (hist) ‎Adding image margins ‎[7,226 bytes]
  150. (hist) ‎Filters (Spatial) Anisotropic Diffusion ‎[7,321 bytes]
  151. (hist) ‎BSpline registration: Detecting folding ‎[7,348 bytes]
  152. (hist) ‎MIPAV toolbars ‎[7,384 bytes]
  153. (hist) ‎Saving and printing images ‎[7,458 bytes]
  154. (hist) ‎Task 2, Applying Talairach VOIs ‎[7,482 bytes]
  155. (hist) ‎Filters (Spatial): Mean ‎[7,485 bytes]
  156. (hist) ‎Making a MIPAV Algorithm JISTable ‎[7,538 bytes]
  157. (hist) ‎Receiving and sending image files ‎[7,728 bytes]
  158. (hist) ‎Visualizing Images ‎[7,750 bytes]
  159. (hist) ‎Getting Started Quickly with MIPAV ‎[7,765 bytes]
  160. (hist) ‎Filters (Spatial): Mode ‎[7,782 bytes]
  161. (hist) ‎Writing MIPAV plugins without MIPAV source code ‎[7,800 bytes]
  162. (hist) ‎Filters (Spatial): Median ‎[7,966 bytes]
  163. (hist) ‎Maximum Intensity Projection ‎[8,015 bytes]
  164. (hist) ‎Running scripts ‎[8,046 bytes]
  165. (hist) ‎Face Anonymizer (BET) ‎[8,136 bytes]
  166. (hist) ‎2D Histogram ‎[8,235 bytes]
  167. (hist) ‎Data Repository tools ‎[8,247 bytes]
  168. (hist) ‎Filters (Spatial): Gaussian Blur ‎[8,340 bytes]
  169. (hist) ‎Creating new images ‎[8,609 bytes]
  170. (hist) ‎Registration: Landmark-Least Squares ‎[8,864 bytes]
  171. (hist) ‎Edge Detection: Zero X Laplacian ‎[8,992 bytes]
  172. (hist) ‎Filters (Spatial): Adaptive Noise Reduction ‎[9,430 bytes]
  173. (hist) ‎Filters (Spatial): Coherence-Enhancing Diffusion ‎[9,557 bytes]
  174. (hist) ‎Cost functions used in MIPAV algorithms ‎[10,137 bytes]
  175. (hist) ‎Image Calculator: OR ‎[10,167 bytes]
  176. (hist) ‎Opening and loading image files ‎[10,187 bytes]
  177. (hist) ‎DTI Pipeline ‎[10,284 bytes]
  178. (hist) ‎Correcting image spacing ‎[10,481 bytes]
  179. (hist) ‎Calculating VOI statistics ‎[10,492 bytes]
  180. (hist) ‎Introduction ‎[10,566 bytes]
  181. (hist) ‎Displaying images ‎[10,610 bytes]
  182. (hist) ‎Using the API documentation ‎[10,652 bytes]
  183. (hist) ‎Histogram Equalization: Regional Adaptive ‎[10,934 bytes]
  184. (hist) ‎Connecting to SRB BIRN ‎[10,981 bytes]
  185. (hist) ‎Background ‎[11,205 bytes]
  186. (hist) ‎Task 3, Segmenting the original image ‎[11,497 bytes]
  187. (hist) ‎Extract Brain: Extract Brain Surface (BSE) ‎[11,555 bytes]
  188. (hist) ‎FAQ: Understanding Memory ‎[11,641 bytes]
  189. (hist) ‎Filters (Frequency) ‎[12,012 bytes]
  190. (hist) ‎Visualizing Images:Displaying images using the default view: Magnifying and minifying images ‎[12,109 bytes]
  191. (hist) ‎Visualizing Images: Displaying images using the default view: Viewing two images together ‎[12,300 bytes]
  192. (hist) ‎Posing queries and retrieving images ‎[12,369 bytes]
  193. (hist) ‎Analyzing Images ‎[12,393 bytes]
  194. (hist) ‎Edge Detection: Zero X Non-Maximum Suppression ‎[12,573 bytes]
  195. (hist) ‎Displaying and editing DICOM tag information ‎[12,600 bytes]
  196. (hist) ‎Creating a mask using the Paint Grow Segmentation method ‎[12,609 bytes]
  197. (hist) ‎Using the mipav command ‎[12,625 bytes]
  198. (hist) ‎Filters (Spatial): Adaptive Path Smooth ‎[12,630 bytes]
  199. (hist) ‎Standard Deviation Threshold ‎[12,796 bytes]
  200. (hist) ‎Browsing DICOM images ‎[12,874 bytes]
  201. (hist) ‎Data Validation module ‎[12,984 bytes]
  202. (hist) ‎Introducing MIPAV ‎[13,038 bytes]
  203. (hist) ‎Supported file formats ‎[13,059 bytes]
  204. (hist) ‎Registration: Time Series Optimized Automatic Registration ‎[13,195 bytes]
  205. (hist) ‎MIPAV change list ‎[13,440 bytes]
  206. (hist) ‎Publications ‎[13,715 bytes]
  207. (hist) ‎Recording scripts ‎[13,937 bytes]
  208. (hist) ‎Transform: Conformal Mapping Algorithms ‎[14,028 bytes]
  209. (hist) ‎Generating graphs ‎[14,117 bytes]
  210. (hist) ‎Preface ‎[14,389 bytes]
  211. (hist) ‎Standard tasks provided through commands on the Utilities menu ‎[14,457 bytes]
  212. (hist) ‎Microscopy: Fluorescence Resonance Energy Transfer (FRET)-Acceptor ‎[14,493 bytes]
  213. (hist) ‎MIPAV change list 2.x ‎[14,558 bytes]
  214. (hist) ‎Wiki help testing ‎[14,733 bytes]
  215. (hist) ‎Customizing the appearance of graphs - Modify graph dialog box ‎[14,848 bytes]
  216. (hist) ‎Histogram Equalization: Neighborhood Adaptive ‎[15,207 bytes]
  217. (hist) ‎NEIRetinalRegistration ‎[15,302 bytes]
  218. (hist) ‎Transform ‎[15,713 bytes]
  219. (hist) ‎4 D tools ‎[15,728 bytes]
  220. (hist) ‎Segmenting Images Using Contours and Masks: Advanced paint and Power Paint tools ‎[15,821 bytes]
  221. (hist) ‎Image Calculator ‎[15,887 bytes]
  222. (hist) ‎Segmenting Images Using Contours and Masks: Using contours to segment a VOI ‎[16,108 bytes]
  223. (hist) ‎Protecting patient privacy using Anonymize ‎[16,510 bytes]
  224. (hist) ‎Using Shell scripting to lessen typing ‎[16,629 bytes]
  225. (hist) ‎Slice tools ‎[16,701 bytes]
  226. (hist) ‎Fuzzy C-Means: Multispectral and Single Channel Algorithms ‎[16,822 bytes]
  227. (hist) ‎Prostate segmentation and surface reconstruction ‎[16,936 bytes]
  228. (hist) ‎Extract Surface (Marching Cubes) ‎[17,131 bytes]
  229. (hist) ‎Changing Image Contrast ‎[17,424 bytes]
  230. (hist) ‎Automatic de-Skulling ‎[17,465 bytes]
  231. (hist) ‎Changing the legends for functions ‎[17,614 bytes]
  232. (hist) ‎Shading Correction: Inhomogeneity N3 Correction ‎[17,988 bytes]
  233. (hist) ‎Interpolation methods used in MIPAV ‎[18,143 bytes]
  234. (hist) ‎Extract Brain: Extract Brain Surface (BET) ‎[18,799 bytes]
  235. (hist) ‎Swap slices and swap volumes ‎[18,934 bytes]
  236. (hist) ‎MIPAV Help ‎[18,937 bytes]
  237. (hist) ‎Inserting slices into image datasets ‎[19,241 bytes]
  238. (hist) ‎Supported Formats ‎[20,244 bytes]
  239. (hist) ‎Visualizing Images: Displaying images using the triplanar view ‎[20,796 bytes]
  240. (hist) ‎Modifying Contours ‎[21,279 bytes]
  241. (hist) ‎Microscopy: Blind Deconvolution ‎[21,388 bytes]
  242. (hist) ‎MIPAV change list 3.x.x ‎[21,749 bytes]
  243. (hist) ‎FAQ: Understanding Image Basics ‎[21,814 bytes]
  244. (hist) ‎Understanding Image Basics ‎[22,342 bytes]
  245. (hist) ‎Calculating statistics on VOI groups ‎[22,640 bytes]
  246. (hist) ‎Using MIPAV for astronomical image processing ‎[22,670 bytes]
  247. (hist) ‎Image submission plug-in ‎[22,717 bytes]
  248. (hist) ‎Customizing MIPAV ‎[22,845 bytes]
  249. (hist) ‎Using MIPAV Algorithms ‎[23,150 bytes]
  250. (hist) ‎Fast Fourier Transformation (FFT) ‎[23,356 bytes]

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