MIPAV FAQ and MIPAV Help: Difference between pages

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== [[Preface]] ==
*[[Scope of this guide]]
== 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]]
**[[FAQ: Understanding Image Basics#FilesExtensions | Image files supported by MIPAV]]
<li  value="2">[[Installing mipav|Installing MIPAV]]
*[[MIPAV system requirements]]
*[[Installing mipav|Installing MIPAV]]
*[[Installing mipav#MipavUpgrade|Upgrading MIPAV]]
*[[Installing mipav#MipavUninstall|Uninstalling MIPAV]]
*[[Quitting 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]]
*[[Opening and loading image files]]
*[[MIPAV toolbars]]
*[[Displaying MIPAV Toolbars]]
*[[Displaying images]]
**[[Displaying images#DefaultView| Default View]]
**[[Displaying images#LightboxView| Lightbox View]]
**[[Displaying images#CineView| Cine View]]
**[[Displaying images#AdjustingMagnification| Adjusting Magnification]]
**[[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| Image dialog box]]
**[[Creating new images| Annotating images with text]]
*[[Saving and printing images]]
*[[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#MipavOptions | MIPAV Options dialog box]]
**[[Customizing MIPAV#SplashScreen | Showing and hiding the splash screen on start-up]]
**[[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="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]]
*[[Visualizing Images: Displaying images using the default view |Displaying images using the default view]]
**[[Visualizing Images:Displaying images using the default view: Magnifying and minifying images|Magnifying and minifying images]]
**[[Visualizing Images: Displaying images using the default view: Viewing two images together|Viewing two images together]]
**[[Visualizing Images: Displaying images using the default view:Changing image brightness and contrast using LUTs|Changing image brightness and contrast using LUTs]]
*[[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]]
*[[Visualizing Images: Displaying images using the lightbox view |Displaying images using the lightbox view]]
*[[Visualizing Images: Displaying images using the link to another image view|Displaying images using the link to another image view]]
*[[Visualizing Images: Displaying images using the triplanar view|Displaying images using the triplanar view]]
*[[Visualizing Images: Displaying images using the triplanar-dual view|Displaying images using the triplanar-dual view]]
*[[Visualizing Images: Displaying images using the surface plotter view|Displaying images using the surface plotter view]]
*[[Visualizing Images: Displaying images using the surface renderer view|Displaying images using the surface renderer view]]
*[[Visualizing Images: Displaying images using the surface renderer view|Displaying images using the volume shear view]]
*[[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]]
*[[Segmenting Images Using Contours and Masks: Using contours to segment a VOI|Using contours to segment a VOI]]
**[[Modifying Contours]]
*[[Segmenting Images Using Contours and Masks]]
**[[Segmenting Images Using Contours and Masks: Generating Masks|Generating masks]]
**[[Creating a mask using the Paint Grow Segmentation method]]
**[[Segmenting Images Using Contours and Masks:Converting VOI contours to masks|Converting VOI contours to masks]]
**[[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]]
*[[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]]
*[[Recording utilities usage with the history feature]]
*[[4 D tools]]
**[[4 D tools#Converting 3D to 4D images and vise versa|Converting 3D to 4D images and vise versa]]
**[[4 D tools#Convert 4D to RGB|Convert 4D to RGB]]
*[[Adding image margins]]
*[[Copying images using the Clone command]]
*[[Converting image datasets to different data types]]
*[[Correcting image spacing]]
**[[Correcting image spacing#UnderstandingContiguousPlanes|Understanding contiguous planes]]
**[[Correcting image spacing#UnderstandingImageSpacing|Understanding how MIPAV solves the image spacing problem]]
**[[Correcting image spacing#ViewImageAttributes|Image attributes]]
**[[Correcting image spacing#SaveDicomXml|Saving DICOM images as XML files]]
**[[Correcting image spacing#SaveOtherXml|Saving other (than DICOM) images as XML files]]
**[[Correcting image spacing#CorrectImageSpacing|Correcting image spacing]]
*[[Cropping images]]
*[[Masking (filling) images]]
*[[Flipping images]]
*[[Image Calculator]]
**[[Image Calculator: OR]]
**[[Image Calculator: Advanced image calculator options]]
**[[Image Calculator: Advanced image calculator options#Image Calculator-Bulk Images|Image Calculator: Bulk Images ]]
*[[Image Math]]
*[[Inserting slices into image datasets]]
*[[Inverting the image]]
*[[Matching images]]
*[[Maximum Intensity Projection]]
*[[Adding noise to images]]
*[[Pad]]
*[[Quantify Mask]]
*[[Replacing pixel/voxel value in images]]
*[[Rotating images]]
*[[Slice tools]]
**[[Slice tools#Concatenating images|Concatenating images]]
**[[Slice tools#Extracting slices.2Fvolumes| Extracting slices and volumes]]
**[[Slice tools#Insert Missing Slices|Insert Missing Slices]]
**[[Inserting slices into image datasets]]
** [[Swap slices and swap volumes| Swap Slices and Volumes]]
*[[Subtract VOI Background]]
*[[Standard tasks provided through commands on the Utilities menu]]
<li  value="10">[[Using Scripts (Macros) in MIPAV]]
*[[Developing and using scripts]]
**[[Setting up scripting]]
**[[Planning scripts]]
**[[Recording scripts]]
**[[Running scripts]]
**[[Editing and deleting scripts]]
**[[Examples]]
*[[Combining scripts and other programs]]
**[[Using the mipav command]]
**[[Using Shell scripting to lessen typing]]
<li  value="11">[[Developing Plugin Programs]]
*[[Understanding plug-in programs]]
*[[Introducing MIPAV#Extensibility with Java plug-ins| Extensibility with Java plug-ins]]
*[[Using the API documentation]]
*[[Developing plug-in programs]]
*[[Creating a self-contained plug-in frame]]
*[[Examples of MIPAV plug-ins]]
**[[Plug-in CT_MD, a typical plug-in program]]
***[[PlugInAlgorithmCT_MD.java]]
***[[Plug-in CT_MD.java]]
*[[Writing MIPAV plugins without MIPAV source code]]
*[[Why can't I see the plugins I install in the menu?]]
<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]]
**[[Algorithms used to draw VOI]]
<div id="AutoCorrelation"></div>
**[[Autocorrelation Coefficients]]
**[[Autocovariance Coefficients]]
**[[Barrel Distortion Correction]]
<div id="DtiAlgorithms"></div>
**[[DTI: Create List File]]
**[[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 Non-Maximum Suppression]]
<div id="ExtractSurface"></div>
**[[Extract Brain: Extract Brain Surface (BET)]]
**[[Extract Brain: Extract Brain Surface (BSE)]]
**[[Extract Surface (Marching Cubes)]]
**[[Face Anonymizer (BET)]]
<div id="FilterAlgorithms"></div>
**[[Filters (Frequency)]]
**[[Fast Fourier Transformation (FFT)]]
**[[Filters (Spatial): Adaptive Noise Reduction]]
**[[Filters (Spatial): Adaptive Path Smooth]]
**[[Filters (Spatial) Anisotropic Diffusion]]
**[[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]]
**[[Filters (Spatial): Nonmaximum Suppression]]
**[[Filters (Spatial): Regularized Isotropic (Nonlinear) Diffusion]]
**[[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>
**[[Cumulative Histogram|Histogram cumulative]]
**[[Histogram Equalization: Regional Adaptive]]
**[[Histogram Equalization: Neighborhood Adaptive]]
**[[Histogram Matching]]
**[[2D Histogram]]
**[[Histogram summary]]
**[[Hough Transform]]
**[[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]]
***[[Morphology#Background Distance map|Background Distance map]]
***[[Morphology#Close|Close]]
***[[Morphology#Delete Objects| Delete Objects]]
***[[Morphology#Dilate|Dilate]]
***[[Morphology#Distance Map|Distance Map]]
***[[Morphology#Erode|Erode]]
***[[Morphology#Evaluate Segmentation|Evaluate Segmentation]]
***[[Morphology#Fill holes|Fill holes]]
***[[Morphology#Find Edges|Find Edges]]
***[[Morphology#ID objects|ID objects]]
***[[Morphology#Morphological Filter|Morphological Filter]]
***[[Morphology#Open|Open]]
***[[Morphology#Particle Analysis|Particle Analysis]]
***[[Morphology#Skeletonize|Skeletonize]]
***[[Morphology#Skeletonize 3D pot field|Skeletonize 3D pot field]]
***[[Morphology#Ultimate erode|Ultimate erode]]
**[[Muscle Segmentation]]
**[[NEIRetinalRegistration | NEI Build macular pigment maps]]
<div id="RegistrationAlgorithms"></div>
**[[B-Spline Automatic Registration | Registration: B-Spline Automatic Registration ]]
***[[Detect folding]]
***[[User Dialogs in MIPAV|B-Spline Automatic Registration Dialog box]]
**[[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]]
**[[Reslice-Isotropic Voxels]]
**[[Watershed|Segmentation: Watershed]]
**[[Shading Correction: Inhomogeneity N3 Correction]]
**[[Standard Deviation Threshold]]
**[[Subsampling images]]
**[[Threshold]]
**[[Transform]]
**[[Transform to power of 2]]
**[[Transform: Conformal Mapping Algorithms]]
**[[Transform nonlinear]]
**[[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]]
== Using FRET in MIPAV ==
* [http://mipav.cit.nih.gov/documentation/techguides/TechGuide3_UsingFRET.pdf Using Fluorescent Resonance Energy Transfer (FRET) algorithms in MIPAV]
== Frequently Asked Questions (FAQs) ==
* [[FAQ: Understanding Memory]]
* [[FAQ: Understanding Memory]]
* [[FAQ: Customizing MIPAV]]
* [[FAQ: Customizing MIPAV]]
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* [[FAQ: How can I fix a "Cannot load Java Virtual Machine" error (memory limit set too high)?]]
* [[FAQ: How can I fix a "Cannot load Java Virtual Machine" error (memory limit set too high)?]]
* [[FAQ: How do I setup and use Active stereo display in MIPAV?]]
* [[FAQ: How do I setup and use Active stereo display in MIPAV?]]
* [[FAQ: Why do I get an exception when running MIPAV via X11 forwarding on Linux?]]
*[[Why can't I see the plugins I install in the menu?| FAQ: Why can't I see the plugins I install in the menu?]]
 
== 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]]
 
== Presentations and Classes ==
 
=== Recent presentations ===
*Creating a Streamlined Pipeline Utility for the Analysis of Universal Diffusion Tensor Imaging Data, by Beth Tyrie, October 20, 2011, [[Media:TyrieDTIPostbacPresentation10-20PDF.pdf]]
* STREAMLINING THE ANALYSIS OF DIFFUSION TENSOR IMAGING FILES THROUGH THE CREATION OF A MASS IMAGE EDITOR by Sara Shen - the presentation given on August 07, 2013 on the summer students talk event at NIH/CIT/DCB, [[Media:SarahShenPresentation2013.pdf]], [[Media:SarahShenPresentation2013.pptx‎]]
 
=== Fall 2012 classes ===
 
* Getting Started with MIPAV - a class conducted by Justin Senseney - [[Media:GettingstartedJS.ppt‎]]
 
=== Spring/Summer 2012 classes:===
* [http://mipav.cit.nih.gov/documentation/presentations/gettingstarted.pdf Introduction to Medical Image Processing in MIPAV]
* [http://mipav.cit.nih.gov/documentation/presentations/SegAnno.pdf Segmentation and Annotation of Medical Images in MIPAV]
* [http://mipav.cit.nih.gov/documentation/presentations/visualization.pdf Medical Image Visualization in MIPAV]
* [http://mipav.cit.nih.gov/documentation/presentations/algorithms.pdf Medical Image Processing and Registration in MIPAV]
* [http://mipav.cit.nih.gov/documentation/presentations/scripting.pdf The Java Image Science Toolkit and Scripting in MIPAV]
* [http://mipav.cit.nih.gov/documentation/presentations/plugins.pdf Developing Java Plugins in MIPAV]
 
=== Previous classes ===
* [http://mipav.cit.nih.gov/documentation/presentations/talairach.pdf Talairach (presented by Pilou Bazin)]

Revision as of 19:26, 10 September 2013

Preface

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

Using FRET in MIPAV

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

Presentations and Classes

Recent presentations

Fall 2012 classes

Spring/Summer 2012 classes:

Previous classes

Retrieved from "https://mipav.cit.nih.gov/pubwiki/index.php?title=MIPAV_FAQ&oldid=307"