Difference between revisions of "Wiki help testing"

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[[Optimized automatic registration 3D]]
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== [[Preface]] ==
 +
*[[Scope of this guide]]
 +
 
 +
== Recent changes in documentation ==
 +
 
 +
This section is reflects the recent changes in documentation. It is mostly for Olga to help her tracking changes. Please don't pay any special attention to it.
 +
 
 +
{{Special:RecentChanges/limit=10, hideminor, hidebots, hideliu}}
 +
 
 +
== Getting Started Quickly with MIPAV ==
 +
<ol type="1"><li  value="1">[[Introducing MIPAV]]
 +
**[[Introducing MIPAV#MipavPlatformIndependence | Platform Independence]]
 +
**[[Introducing MIPAV#MipavCapabilities | Understanding MIPAV capabilities]]
 +
**[[Introducing MIPAV#JavaPlugIns | Extensibility with Java plug-ins]]
 +
**[[Introducing MIPAV#MipavFeatures | Sampling of MIPAV's features]]
 +
*[[MIPAV mailing list]]
 +
*[[Installing mipav#MipavNews|Viewing MIPAV News and Updates]]
 +
 
 +
*[[Supported Formats]]
 +
**[[Supported Formats | Graphical and file formats supported by MIPAV]]
 +
**[[Image formats descriptions | Image formats' descriptions]]
 +
**[[MIPAV configuration files]]
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**[[FAQ: Understanding Image Basics#FilesExtensions | Image files supported by MIPAV]]
 +
 
 +
<li  value="2">[[Installing mipav|Installing MIPAV]]
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*[[MIPAV system requirements]]
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*[[Installing mipav|Installing MIPAV]]
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*[[Installing mipav#MipavUpgrade|Upgrading MIPAV]]
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*[[Installing mipav#MipavUninstall|Uninstalling MIPAV]]
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*[[Quitting MIPAV]]
 +
 
 +
<li  value="3">[[Getting Started Quickly with MIPAV]]
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*[[Getting Started Quickly with MIPAV#StartingMIPAV | Starting MIPAV]]
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*[[Getting Started Quickly with MIPAV#StartingMIPAV | MIPAV main window]]
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*[[Getting Started Quickly with MIPAV#ManagingMemoryResources | Managing memory in MIPAV]]
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*[[Allocating Memory in MIPAV]]
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*[[Opening and loading image files]]
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*[[MIPAV toolbars]]
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*[[Displaying MIPAV Toolbars]]
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*[[Displaying images]]
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**[[Displaying images#DefaultView| Default View]]
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**[[Displaying images#LightboxView| Lightbox View]]
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**[[Displaying images#CineView| Cine View]]
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**[[Displaying images#AdjustingMagnification| Adjusting Magnification]]
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**[[Displaying images#MagnifyingRegions| Magnifying Regions within Images]]
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**[[Displaying images#ImprovingContrast| Improving Image Contrast]]
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*[[Modifying image resolutions]]
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 +
*[[Changing Image Contrast]]
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**[[Changing Image Contrast|Adjust Window and Level]]
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**[[Changing Image Contrast|Improving contrast by generating and modifying histograms]]
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**[[Changing Image Contrast|Using Lookup Table dialog box]]
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**[[Changing Image Contrast#PredefinedLuts|Applying color to images using predefined LUTs]]
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**[[Changing Image Contrast|Comparing images using alphablending]]
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**[[Changing Image Contrast|Restoring images to their original appearance]]
 +
 
 +
*[[Creating new images]]
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**[[Creating new images| Image dialog box]]
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**[[Creating new images| Annotating images with text]]
 +
 
 +
*[[Saving and printing images]]
 +
 
 +
*[[Delineating volumes of interest (VOIs)| Volumes of Interest]]
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**[[Delineating volumes of interest (VOIs)]] 
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**[[Calculating VOI statistics]]
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**[[Calculating VOI statistics#VoiStatistics| VOI statistics dialog box]]
 +
**[[Reviewing VOI statistics]]
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**[[Calculating statistics on VOI groups]]
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**[[Reviewing VOI statistics|Generating graphs (intensity profiles)]] 
 +
 
 +
*[[ImageJ | Working with ImageJ]]
 +
*[[Customizing MIPAV]]
 +
**[[Customizing MIPAV#MipavOptions | MIPAV Options dialog box]]
 +
**[[Customizing MIPAV#SplashScreen | Showing and hiding the splash screen on start-up]]
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**[[Customizing MIPAV#DebuggingMipav | Debugging MIPAV]]
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**[[Customizing MIPAV#ActionsHistory | Saving a history of actions on images]]
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**[[Customizing MIPAV#DefaultFileTypes | Choosing the default file types to display or save]]
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**[[Customizing MIPAV#AddingShortcuts | Adding Shortcuts]]
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**[[MIPAV configuration files]]
 +
 
 +
*[[Developing new tools using the API]]
 +
 
 +
*[[Technical Support | Contacting MIPAV support]]
 +
*[[MIPAV mailing list | Joining MIPAV mailing list]]
 +
 
 +
== MIPAV Basics ==
 +
<li  value="4">[[Understanding Image Basics]]
 +
 
 +
<li  value="5">[[Working with DICOM Images]]
 +
*[[Browsing DICOM images|Browsing DICOM images]]
 +
*[[Sending and retrieving DICOM images|Sending and retrieving DICOM images ]]
 +
*[[Testing the connection|Testing the connection ]]
 +
*[[Posing queries and retrieving images|Posing queries and retrieving images]]
 +
*[[Receiving and sending image files|Receiving and sending image files]]
 +
*[[Displaying and editing DICOM tag information|Displaying and editing DICOM tag information]]
 +
*[[Protecting patient privacy using Anonymize|Protecting patient privacy using Anonymize]]
 +
*[[Converting non-DICOM image files to DICOM format|Converting non-DICOM image files to DICOM format]]
 +
 
 +
<li  value="6">[[Visualizing Images]]
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*[[Visualizing Images: Displaying images using the default view |Displaying images using the default view]]
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**[[Visualizing Images:Displaying images using the default view: Magnifying and minifying images|Magnifying and minifying images]]
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**[[Visualizing Images: Displaying images using the default view: Viewing two images together|Viewing two images together]]
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**[[Visualizing Images: Displaying images using the default view:Changing image brightness and contrast using LUTs|Changing image brightness and contrast using LUTs]]
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*[[Visualizing Images: Displaying images using the animate view |Displaying images using the animate view]]
 +
*[[Visualizing Images: Displaying images using the cine (movie) view|Displaying images using the cine (movie) view]]
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*[[Visualizing Images: Displaying images using the lightbox view |Displaying images using the lightbox view]]
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*[[Visualizing Images: Displaying images using the link to another image view|Displaying images using the link to another image view]]
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*[[Visualizing Images: Displaying images using the triplanar view|Displaying images using the triplanar view]]
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*[[Visualizing Images: Displaying images using the triplanar-dual view|Displaying images using the triplanar-dual view]]
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*[[Visualizing Images: Displaying images using the surface plotter view|Displaying images using the surface plotter view]]
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*[[Visualizing Images: Displaying images using the surface renderer view|Displaying images using the surface renderer view]]
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*[[Visualizing Images: Displaying images using the surface renderer view|Displaying images using the volume shear view]]
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*[[Visualizing Images: Displaying images using the surface renderer view|Displaying images using the volume renderer view]]
 +
 
 +
<li  value="7">[[Segmenting Images Using Contours and Masks]]
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*[[Segmenting Images Using Contours and Masks: Using contours to segment a VOI|Using contours to segment a VOI]]
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**[[Modifying Contours]]
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*[[Segmenting Images Using Contours and Masks: Generating Masks|Generating masks]]
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**[[Creating a mask using the Paint Grow Segmentation method]]
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*[[Segmenting Images Using Contours and Masks:Converting VOI contours to masks|Converting VOI contours to masks]]
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*[[Segmenting Images Using Contours and Masks: Converting masks to VOI contours and paints |Converting masks to VOI contours and paints]]
 +
*[[Segmenting Images Using Contours and Masks: Advanced paint and Power Paint tools|Advanced Paint and Power Paint tools]]
 +
 
 +
<li  value="8">[[Analyzing Images]]
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*[[Analyzing Images|Calculating statistics for contoured VOIs ]]
 +
*[[Calculating statistics on VOI groups|Calculating statistics on VOI groups]]
 +
*[[Calculating the volume of masks|Calculating the volume of masks ]]
 +
*[[Generating graphs|Generating graphs]]
 +
**[[Customizing the appearance of graphs - Modify graph dialog box]]
 +
**[[Changing the legends for functions]]
 +
 
 +
<li  value="9">[[Changing Image Datasets Using MIPAV Utilities]]
 +
*[[Standard tasks provided through commands on the Utilities menu]]
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*[[Recording utilities usage with the history feature]]
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*[[4 D tools]]
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*[[Adding image margins]]
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*[[Copying images using the Clone command]]
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*[[Converting image datasets to different data types]]
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*[[Correcting image spacing]]
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*[[Cropping images]]
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*[[Masking (filling) images]]
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*[[Flipping images]]
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*[[Image Calculator]]
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**[[Image Calculator: OR]]
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**[[Image Calculator: Advanced image calculator options]]
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*[[Image Math]]
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*[[Inserting slices into image datasets]]
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*[[Inverting the image]]
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*[[Matching images]]
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*[[Maximum Intensity Projection]]
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*[[Adding noise to images]]
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*[[Pad]]
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*[[Quantify Mask]]
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*[[Replacing pixel/voxel value in images]]
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*[[Rotating images]]
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*[[Slice tools]]
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*[[Inserting slices into image datasets]]
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*[[Subtract VOI Background]]
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*[[Standard tasks provided through commands on the Utilities menu]]
 +
 
 +
<li  value="10">[[Using Scripts (Macros) in MIPAV]]
 +
*[[Developing and using scripts]]
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**[[Setting up scripting]]
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**[[Planning scripts]]
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**[[Recording scripts]]
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**[[Running scripts]]
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**[[Editing and deleting scripts]]
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**[[Examples]]
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*[[Combining scripts and other programs]]
 +
**[[Using the mipav command]]
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**[[Using Shell scripting to lessen typing]]
 +
 
 +
<li  value="11">[[Developing Plugin Programs]]
 +
*[[Understanding plug-in programs]]
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*[[Using the API documentation]]
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*[[Developing plug-in programs]]
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*[[Creating a self-contained plug-in frame]]
 +
*[[Examples of MIPAV plug-ins]]
 +
**[[Plug-in CT_MD, a typical plug-in program]]
 +
***[[PlugInAlgorithmCT_MD.java]]
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***[[Plug-in CT_MD.java]]
 +
 
 +
<li  value="12">[[Technical Support]]</ol>
 +
 
 +
== MIPAV Algorithms ==
 +
*[[Understanding MIPAV capabilities]]
 +
*[[Developing new tools using the API]]
 +
*[[Using MIPAV Algorithms | Overview of MIPAV Algorithms]]
 +
**[[Cost functions used in MIPAV algorithms]]
 +
**[[Interpolation methods used in MIPAV]]
 +
**[[Degrees of freedom]]
 +
<div id="AutoCorrelation"></div>
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**[[Autocorrelation Coefficients]]
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**[[Autocovariance Coefficients]]
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**[[Barrel Distortion Correction]]
 +
<div id="DtiAlgorithms"></div>
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**[[DTI Color Display]]
 +
**[[DTI Estimate tensor | DTI Estimate tensor - under construction]]
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**[[DTI Pipeline]]
 +
<div id="EdgeDetection"></div>
 +
**[[Edge Detection: Zero X Laplacian]]
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**[[Edge Detection: Zero X Non-Maximum Suppression]]
 +
<div id="ExtractSurface"></div>
 +
**[[Extract Brain: Extract Brain Surface (BET)]]
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**[[Extract Brain: Extract Brain Surface (BSE)]]
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**[[Extract Surface (Marching Cubes)]]
 +
**[[Face Anonymizer (BET)]]
 +
<div id="FilterAlgorithms"></div>
 +
**[[Fast Fourier Transformation (FFT)]]
 +
**[[Filters (Spatial): Adaptive Noise Reduction]]
 +
**[[Filters (Frequency)]]
 +
**[[Filters (Spatial): Adaptive Path Smooth]]
 +
**[[Filters (Spatial) Anisotropic Diffusion]]
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**[[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]]
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**[[Filters (Spatial): Nonmaximum Suppression]]
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**[[Filters (Spatial): Regularized Isotropic (Nonlinear) Diffusion]]
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**[[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]]
 +
<div id="HistogramAlgorithms"></div>
 +
**[[Histogram Equalization: Regional Adaptive]]
 +
**[[Histogram Equalization: Neighborhood Adaptive]]
 +
**[[Histogram Matching]]
 +
**[[2D Histogram]]
 +
**[[Cumulative Histogram]]
 +
**[[Histogram summary]]
 +
**[[Image Calculator]]
 +
**[[Manual 2D Series]]
 +
**[[Mask]]
 +
<div id="MicroscopyAlgorithms"></div>
 +
**[[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]]
 +
<div id="TransformationAlgorithms"></div>
 +
**[[Midsagittal line alignment]]
 +
**[[Morphology]]
 +
**[[Reslice-Isotropic Voxels]]
 +
**[[Shading Correction: Inhomogeneity N3 Correction]]
 +
**[[Standard Deviation Threshold]]
 +
**[[Subsampling images]]
 +
**[[Threshold]]
 +
**[[Transform to power of 2]]
 +
<div id="RegistrationAlgorithms"></div>
 +
**[[B-Spline Automatic Registration | Registration: B-Spline Automatic Registration ]]
 +
***[[Detect folding]]
 +
***[[User Dialogs in MIPAV]]
 +
**[[Optimized automatic registration 3D | Registration: Optimized automatic registration 3D and 3.5D]]
 +
**[[Registration: Landmark-Least Squares]]
 +
**[[Registration: Landmark-TPSpline]]
 +
**[[Registration: Manual 2D Series]]
 +
**[[Midsagittal line alignment | Registration: Midsagittal line alignment]]
 +
**[[Reslice-Isotropic Voxels | Registration: Reslice-Isotropic Voxels]]
 +
**[[Registration: Time Series Optimized Automatic Registration]]
 +
**[[Volume Renderer]]
 +
 
 +
== Glossary ==
 +
[[Glossary for MIPAV Help]]
 +
 
 +
== Appendices ==
 +
<ol type="A"><li  value="1">[[References]]
 +
<li  value="B">[[DICOM Conformance]]
 +
<li  value="C">[[Supported Formats]]
 +
*[[Other formats supported by MIPAV ]]
 +
*[[Understanding MIPAV-related files]]
 +
 
 +
 
 +
<li  value="D">[[Technical Information]]
 +
<li  value="E"> [[PlugIn Algorithm Median]]
 +
*[[PlugIn Algorithm Median (con't, part 2)]]
 +
*[[PlugIn Algorithm Median (con't, part 3)]]
 +
*[[PlugIn Algorithm Median (con't, part 4)]]
 +
</ol>
 +
 
 +
== Talairach ==
 +
*[[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]]
 +
 
 +
== Frequently Asked Questions (FAQs) ==
 +
*[[FAQ: Understanding Memory]]
 +
*[[FAQ: Customizing MIPAV]]
 +
*[[FAQ: Understanding Image Basics]]
 +
*[[FAQ: Understanding Changes in MIPAV]]
 +
*[[FAQ: Trimming VOIs]]
 +
 
 +
== Videos ==
 +
 
 +
*A video tutorial that explains how to load images into MIPAV and change the memory allocation - [http://www.youtube.com/embed/npSYWYJa530 play].
 +
 
 +
*A video tutorial that explains how to do basic image display options - [http://www.youtube.com/watch?v=02vUrfSaGWE&feature=relmfu 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 - [http://www.youtube.com/watch?v=uCr-Zlxu454&feature=relmfu play].
 +
 
 +
* A video tutorial that explains how to save and capture PDFs of images - [http://www.youtube.com/watch?v=Zfh5nKITbkA&feature=relmfu play].
 +
 
 +
* A video tutorial that explains how to do basic image manipulations - [http://www.youtube.com/watch?v=uCr-Zlxu454&feature=relmfu play].
 +
 
 +
All tutorials are courtesy of [http://www.youtube.com/user/MIPAVvideos MIPAVvideos].
 +
 
 +
== Publications ==
 +
* [[Publications]]

Latest revision as of 15:42, 12 June 2012

Preface

Recent changes in documentation

This section is reflects the recent changes in documentation. It is mostly for Olga to help her tracking changes. Please don't pay any special attention to it.

No changes during the given period matching these criteria.

Getting Started Quickly with MIPAV

  1. Introducing MIPAV
  2. Installing MIPAV
  3. Getting Started Quickly with MIPAV

    MIPAV Basics

  4. Understanding Image Basics
  5. Working with DICOM Images
  6. Visualizing Images
  7. Segmenting Images Using Contours and Masks
  8. Analyzing Images
  9. Changing Image Datasets Using MIPAV Utilities
  10. Using Scripts (Macros) in MIPAV
  11. Developing Plugin Programs
  12. Technical Support

MIPAV Algorithms

Glossary

Glossary for MIPAV Help

Appendices

  1. References
  2. DICOM Conformance
  3. Supported Formats
  4. Technical Information
  5. PlugIn Algorithm Median

Talairach

Frequently Asked Questions (FAQs)

Videos

  • 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

Retrieved from "http://mipav.cit.nih.gov/pubwiki/index.php?title=Wiki_help_testing&oldid=43142"