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