Difference between revisions of "MIPAV Help"

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**[[Slice tools#Extracting slices.2Fvolumes| Extracting slices and volumes]]
 
**[[Slice tools#Extracting slices.2Fvolumes| Extracting slices and volumes]]
 
**[[Slice tools#Insert Missing Slices|Insert Missing Slices]]
 
**[[Slice tools#Insert Missing Slices|Insert Missing Slices]]
*[[Inserting slices into image datasets]]  
+
**[[Inserting slices into image datasets]]
 +
** [[Swap slices and swap volumes| Swap Slices and Volumes]]
 
*[[Subtract VOI Background]]
 
*[[Subtract VOI Background]]
 
*[[Standard tasks provided through commands on the Utilities menu]]
 
*[[Standard tasks provided through commands on the Utilities menu]]
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**[[Face Anonymizer (BET)]]
 
**[[Face Anonymizer (BET)]]
 
<div id="FilterAlgorithms"></div>
 
<div id="FilterAlgorithms"></div>
 +
**[[Filters (Frequency)]]
 
**[[Fast Fourier Transformation (FFT)]]
 
**[[Fast Fourier Transformation (FFT)]]
 
**[[Filters (Spatial): Adaptive Noise Reduction]]
 
**[[Filters (Spatial): Adaptive Noise Reduction]]
**[[Filters (Frequency)]]
 
 
**[[Filters (Spatial): Adaptive Path Smooth]]
 
**[[Filters (Spatial): Adaptive Path Smooth]]
 
**[[Filters (Spatial) Anisotropic Diffusion]]
 
**[[Filters (Spatial) Anisotropic Diffusion]]
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**[[Muscle Segmentation]]
 
**[[Muscle Segmentation]]
 
**[[NEIRetinalRegistration | NEI Build macular pigment maps]]
 
**[[NEIRetinalRegistration | NEI Build macular pigment maps]]
**[[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]]
 
 
<div id="RegistrationAlgorithms"></div>
 
<div id="RegistrationAlgorithms"></div>
 
**[[B-Spline Automatic Registration | Registration: B-Spline Automatic Registration ]]
 
**[[B-Spline Automatic Registration | Registration: B-Spline Automatic Registration ]]
 
***[[Detect folding]]
 
***[[Detect folding]]
***[[User Dialogs in MIPAV]]
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***[[User Dialogs in MIPAV|B-Spline Automatic Registration Dialog box]]
 
**[[Optimized automatic registration 3D | Registration: Optimized automatic registration 3D and 3.5D]]
 
**[[Optimized automatic registration 3D | Registration: Optimized automatic registration 3D and 3.5D]]
 
**[[Registration: Landmark-Least Squares]]
 
**[[Registration: Landmark-Least Squares]]
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**[[Reslice-Isotropic Voxels | Registration: Reslice-Isotropic Voxels]]
 
**[[Reslice-Isotropic Voxels | Registration: Reslice-Isotropic Voxels]]
 
**[[Registration: Time Series Optimized Automatic Registration]]
 
**[[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]]
 
**[[Volume Renderer]]
  
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== Presentations and Classes ==
 
== Presentations and Classes ==
  
Spring/Summer 2012 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/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/SegAnno.pdf Segmentation and Annotation of Medical Images in MIPAV]
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* [http://mipav.cit.nih.gov/documentation/presentations/algorithms.pdf Medical Image Processing and Registration 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/scripting.pdf The Java Image Science Toolkit and Scripting in MIPAV]
* Developing Java Plugins in MIPAV, I
+
* [http://mipav.cit.nih.gov/documentation/presentations/plugins.pdf Developing Java Plugins in MIPAV]
* Developing Java Plugins in MIPAV, II
+
  
Previous classes:
+
=== Previous classes ===
 
* [http://mipav.cit.nih.gov/documentation/presentations/talairach.pdf Talairach (presented by Pilou Bazin)]
 
* [http://mipav.cit.nih.gov/documentation/presentations/talairach.pdf Talairach (presented by Pilou Bazin)]

Latest 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