Difference between revisions of "Wiki help testing"

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=[[Preface]]=
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== [[Preface]] ==
 
*[[Scope of this guide]]
 
*[[Scope of this guide]]
  
−
=MIPAV Help Volume 1: MIPAV Basics =
+
== 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]]
 
<ol type="1"><li  value="1">[[Introducing MIPAV]]
−
*[[Understanding MIPAV capabilities]]
+
**[[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]]
 
*[[MIPAV mailing list]]
−
*[[Developing new tools using the API]]
+
*[[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]]
 +
**[[FAQ: Understanding Image Basics#FilesExtensions | Image files supported by MIPAV]]
  
 
<li  value="2">[[Installing mipav|Installing MIPAV]]
 
<li  value="2">[[Installing mipav|Installing MIPAV]]
 
*[[MIPAV system requirements]]
 
*[[MIPAV system requirements]]
 
*[[Installing mipav|Installing MIPAV]]
 
*[[Installing mipav|Installing MIPAV]]
−
*[[Installing mipav#MipavNews|Viewing MIPAV News  and Updates]]
+
*[[Installing mipav#MipavUpgrade|Upgrading MIPAV]]
−
 
+
*[[Installing mipav#MipavUninstall|Uninstalling MIPAV]]
−
 
+
*[[Quitting MIPAV]]
  
 
<li  value="3">[[Getting Started Quickly with MIPAV]]
 
<li  value="3">[[Getting Started Quickly with MIPAV]]
 +
*[[Getting Started Quickly with MIPAV#StartingMIPAV | Starting MIPAV]]
 +
*[[Getting Started Quickly with MIPAV#StartingMIPAV | MIPAV main window]]
 +
*[[Getting Started Quickly with MIPAV#ManagingMemoryResources | Managing memory in MIPAV]]
 
*[[Allocating Memory in MIPAV]]
 
*[[Allocating Memory in MIPAV]]
−
*[[Allocating Memory in MIPAV|Opening and loading image files]]  
+
*[[Opening and loading image files]]  
 
*[[MIPAV toolbars]]
 
*[[MIPAV toolbars]]
 
*[[Displaying MIPAV Toolbars]]
 
*[[Displaying MIPAV Toolbars]]
−
*[[Displaying images using the default view]]
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*[[Displaying images]]
−
*[[Using the right mouse button]]
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**[[Displaying images#DefaultView| Default View]]
−
*[[Using the right mouse button|Selecting views]]  
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**[[Displaying images#LightboxView| Lightbox View]]
−
*[[Using the right mouse button|Adjusting magnification]]
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**[[Displaying images#CineView| Cine View]]
−
*[[Using the right mouse button|Improving contrast, adding color, etc.]]  
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**[[Displaying images#AdjustingMagnification| Adjusting Magnification]]
−
*[[Using the right mouse button|Comparing images using alphablending]]  
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**[[Displaying images#MagnifyingRegions| Magnifying Regions within Images]]
 +
**[[Displaying images#ImprovingContrast| Improving Image Contrast]]
 +
*[[Modifying image resolutions]]
 +
 
 +
*[[Changing Image Contrast]]
 +
**[[Changing Image Contrast|Adjust Window and Level]]
 +
**[[Changing Image Contrast|Improving contrast by generating and modifying histograms]]  
 +
**[[Changing Image Contrast|Using Lookup Table dialog box]]
 +
**[[Changing Image Contrast#PredefinedLuts|Applying color to images using predefined LUTs]]
 +
**[[Changing Image Contrast|Comparing images using alphablending]]  
 +
**[[Changing Image Contrast|Restoring images to their original appearance]]
 +
 
 
*[[Creating new images]]  
 
*[[Creating new images]]  
−
*[[Creating new images|Delineating volumes of interest (VOIs)]]  
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**[[Creating new images| Image dialog box]]  
−
*[[Creating new images|Annotating images with text]]
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**[[Creating new images| Annotating images with text]]
−
*[[Creating new images|Calculating VOI statistics]]  
+
 
−
*[[Reviewing the statistics]]  
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*[[Saving and printing images]]
−
*[[Reviewing the statistics|Generating graphs (intensity profiles)]]   
+
 
−
*[[Reviewing the statistics|Saving and printing images]]
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*[[Delineating volumes of interest (VOIs)| Volumes of Interest]]
 +
**[[Delineating volumes of interest (VOIs)]] 
 +
**[[Calculating VOI statistics]]
 +
**[[Calculating VOI statistics#VoiStatistics| VOI statistics dialog box]]
 +
**[[Reviewing VOI statistics]]  
 +
**[[Calculating statistics on VOI groups]]
 +
**[[Reviewing VOI statistics|Generating graphs (intensity profiles)]]   
 +
 
 +
*[[ImageJ | Working with ImageJ]]
 
*[[Customizing MIPAV]]
 
*[[Customizing MIPAV]]
−
*[[To show the splash screen]]
+
**[[Customizing MIPAV#MipavOptions | MIPAV Options dialog box]]
−
*[[Choosing the default file types to display or save]]  
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**[[Customizing MIPAV#SplashScreen | Showing and hiding the splash screen on start-up]]
−
*[[Choosing the default file types to display or save|Quitting MIPAV]]
+
**[[Customizing MIPAV#DebuggingMipav | Debugging MIPAV]]
 +
**[[Customizing MIPAV#ActionsHistory | Saving a history of actions on images]]
 +
**[[Customizing MIPAV#DefaultFileTypes | Choosing the default file types to display or save]]
 +
**[[Customizing MIPAV#AddingShortcuts | Adding Shortcuts]]
 +
**[[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="4">[[Understanding Image Basics]]
  
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*[[Flipping images]]  
 
*[[Flipping images]]  
 
*[[Image Calculator]]  
 
*[[Image Calculator]]  
−
**[[Image Calculator: OR ]]
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**[[Image Calculator: OR]]
 
**[[Image Calculator: Advanced image calculator options]]
 
**[[Image Calculator: Advanced image calculator options]]
 
*[[Image Math]]
 
*[[Image Math]]
 +
*[[Inserting slices into image datasets]]
 
*[[Inverting the image]]  
 
*[[Inverting the image]]  
 
*[[Matching images]]
 
*[[Matching images]]
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<li  value="12">[[Technical Support]]</ol>
 
<li  value="12">[[Technical Support]]</ol>
  
−
= MIPAV Help Volume 2: Algorithms=
+
== MIPAV Algorithms ==
 
*[[Understanding MIPAV capabilities]]
 
*[[Understanding MIPAV capabilities]]
−
**[[Understanding MIPAV capabilities]]
+
*[[Developing new tools using the API]]
−
**[[Developing new tools using the API]]
+
*[[Using MIPAV Algorithms | Overview of MIPAV Algorithms]]
−
*[[Using MIPAV Algorithms]]
+
**[[Cost functions used in MIPAV algorithms]]
−
**[[B-Spline Automatic Registration]]
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**[[Interpolation methods used in MIPAV]]
−
***[[Detect folding]]
+
**[[Degrees of freedom]]
−
***[[User Dialogs in MIPAV]]
+
<div id="AutoCorrelation"></div>
−
 
+
**[[Autocorrelation Coefficients]]
 +
**[[Autocovariance Coefficients]]
 +
**[[Barrel Distortion Correction]]
 +
<div id="DtiAlgorithms"></div>
 
**[[DTI Color Display]]
 
**[[DTI Color Display]]
 +
**[[DTI Estimate tensor | DTI Estimate tensor - under construction]]
 +
**[[DTI Pipeline]]
 +
<div id="EdgeDetection"></div>
 
**[[Edge Detection: Zero X Laplacian]]
 
**[[Edge Detection: Zero X Laplacian]]
 
**[[Edge Detection: Zero X Non-Maximum Suppression]]
 
**[[Edge Detection: Zero X Non-Maximum Suppression]]
 +
<div id="ExtractSurface"></div>
 
**[[Extract Brain: Extract Brain Surface (BET)]]
 
**[[Extract Brain: Extract Brain Surface (BET)]]
 
**[[Extract Brain: Extract Brain Surface (BSE)]]
 
**[[Extract Brain: Extract Brain Surface (BSE)]]
 +
**[[Extract Surface (Marching Cubes)]]
 
**[[Face Anonymizer (BET)]]
 
**[[Face Anonymizer (BET)]]
 +
<div id="FilterAlgorithms"></div>
 
**[[Fast Fourier Transformation (FFT)]]
 
**[[Fast Fourier Transformation (FFT)]]
 
**[[Filters (Spatial): Adaptive Noise Reduction]]
 
**[[Filters (Spatial): Adaptive Noise Reduction]]
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**[[Filters (Spatial): Gaussian Blur]]
 
**[[Filters (Spatial): Gaussian Blur]]
 
**[[Filters (Spatial): Gradient Magnitude]]
 
**[[Filters (Spatial): Gradient Magnitude]]
 +
**[[Filters (Spatial): Haralick Texture]]
 
**[[Filters (Spatial) Laplacian]]
 
**[[Filters (Spatial) Laplacian]]
−
**[[Filters (Spatial) Local Normalization]]
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**[[Filters (Spatial): Local Normalization]]
 
**[[Filters (Spatial): Mean]]
 
**[[Filters (Spatial): Mean]]
 
**[[Filters (Spatial): Median]]
 
**[[Filters (Spatial): Median]]
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**[[Filters (Spatial): Slice Averaging]]
 
**[[Filters (Spatial): Slice Averaging]]
 
**[[Filters (Spatial): Unsharp Mask]]
 
**[[Filters (Spatial): Unsharp Mask]]
 +
**[[Filters (Wavelet): De-noising BLS GSM]]
 
**[[Filters (Wavelet): Thresholding]]
 
**[[Filters (Wavelet): Thresholding]]
 
**[[Fuzzy C-Means: Multispectral and Single Channel Algorithms]]
 
**[[Fuzzy C-Means: Multispectral and Single Channel Algorithms]]
 +
<div id="HistogramAlgorithms"></div>
 
**[[Histogram Equalization: Regional Adaptive]]
 
**[[Histogram Equalization: Regional Adaptive]]
 
**[[Histogram Equalization: Neighborhood Adaptive]]
 
**[[Histogram Equalization: Neighborhood Adaptive]]
 
**[[Histogram Matching]]
 
**[[Histogram Matching]]
 
**[[2D Histogram]]
 
**[[2D Histogram]]
 +
**[[Cumulative Histogram]]
 
**[[Histogram summary]]
 
**[[Histogram summary]]
 +
**[[Image Calculator]]
 
**[[Manual 2D Series]]
 
**[[Manual 2D Series]]
−
**[[Extract Surface (Marching Cubes)]]
 
 
**[[Mask]]
 
**[[Mask]]
 +
<div id="MicroscopyAlgorithms"></div>
 
**[[Microscopy Colocalization Orthogonal Regression]]
 
**[[Microscopy Colocalization Orthogonal Regression]]
 
**[[Microscopy: Fluorescence Resonance Energy Transfer (FRET)-Acceptor]]
 
**[[Microscopy: Fluorescence Resonance Energy Transfer (FRET)-Acceptor]]
 
**[[Microscopy: FRAP (Fluorescence Recovery After Photobleaching)]]
 
**[[Microscopy: FRAP (Fluorescence Recovery After Photobleaching)]]
 +
**[[Microscopy: Fluorescent Resonance Energy Transfer (FRET) Bleed Through and Efficiency]]
 
**[[Microscopy: Blind Deconvolution]]
 
**[[Microscopy: Blind Deconvolution]]
 +
<div id="TransformationAlgorithms"></div>
 
**[[Midsagittal line alignment]]
 
**[[Midsagittal line alignment]]
 
**[[Morphology]]
 
**[[Morphology]]
−
**[[Optimized automatic registration 3D]]
 
−
**[[Registration: Landmark-Least Squares]]
 
−
**[[Registration: Landmark-TPSpline]]
 
−
**[[Registration: Manual 2D Series]]
 
−
**[[Registration: Time Series Optimized Automatic Registration]]
 
 
**[[Reslice-Isotropic Voxels]]
 
**[[Reslice-Isotropic Voxels]]
 
**[[Shading Correction: Inhomogeneity N3 Correction]]
 
**[[Shading Correction: Inhomogeneity N3 Correction]]
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**[[Threshold]]
 
**[[Threshold]]
 
**[[Transform to power of 2]]
 
**[[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 ==
 
[[Glossary for MIPAV Help]]
 
[[Glossary for MIPAV Help]]
  
−
=Appendices=
+
== Appendices ==
 
<ol type="A"><li  value="1">[[References]]
 
<ol type="A"><li  value="1">[[References]]
 
<li  value="B">[[DICOM Conformance]]
 
<li  value="B">[[DICOM Conformance]]
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*[[Other formats supported by MIPAV ]]
 
*[[Other formats supported by MIPAV ]]
 
*[[Understanding MIPAV-related files]]
 
*[[Understanding MIPAV-related files]]
−
*[[Matrix file]]
+
 
−
*[[MIPAV Surface file ]]
+
  
 
<li  value="D">[[Technical Information]]
 
<li  value="D">[[Technical Information]]
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</ol>
 
</ol>
  
−
=Talairach=
+
== Talairach ==
 
*[[Introduction]]
 
*[[Introduction]]
 
*[[Installing]]
 
*[[Installing]]
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**[[Viewing the Talairach grid on Talairach images]]
 
**[[Viewing the Talairach grid on Talairach images]]
  
−
=Frequently Asked Questions (FAQ)=
+
== Frequently Asked Questions (FAQs) ==
 
*[[FAQ: Understanding Memory]]
 
*[[FAQ: Understanding Memory]]
 
*[[FAQ: Customizing MIPAV]]
 
*[[FAQ: Customizing MIPAV]]
 
*[[FAQ: Understanding Image Basics]]
 
*[[FAQ: Understanding Image Basics]]
 
*[[FAQ: Understanding Changes in MIPAV]]
 
*[[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"