Difference between revisions of "MIPAV Help"

From MIPAV
Jump to: navigation, search
m (MIPAV Algorithms)
m (MIPAV Algorithms)
 
(22 intermediate revisions by 2 users not shown)
Line 110: Line 110:
 
*[[Segmenting Images Using Contours and Masks: Using contours to segment a VOI|Using contours to segment a VOI]]
 
*[[Segmenting Images Using Contours and Masks: Using contours to segment a VOI|Using contours to segment a VOI]]
 
**[[Modifying Contours]]
 
**[[Modifying Contours]]
*[[Segmenting Images Using Contours and Masks: Generating Masks|Generating masks]]
+
*[[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]]
 
**[[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 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: 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]]
+
**[[Segmenting Images Using Contours and Masks: Advanced paint and Power Paint tools|Advanced Paint and Power Paint tools]]
  
 
<li  value="8">[[Analyzing Images]]
 
<li  value="8">[[Analyzing Images]]
Line 161: Line 162:
 
**[[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]]
Line 179: Line 181:
 
<li  value="11">[[Developing Plugin Programs]]
 
<li  value="11">[[Developing Plugin Programs]]
 
*[[Understanding plug-in programs]]
 
*[[Understanding plug-in programs]]
 +
*[[Introducing MIPAV#Extensibility with Java plug-ins| Extensibility with Java plug-ins]]
 
*[[Using the API documentation]]
 
*[[Using the API documentation]]
 
*[[Developing plug-in programs]]
 
*[[Developing plug-in programs]]
Line 186: Line 189:
 
***[[PlugInAlgorithmCT_MD.java]]
 
***[[PlugInAlgorithmCT_MD.java]]
 
***[[Plug-in CT_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>
 
<li  value="12">[[Technical Support]]</ol>
Line 202: Line 207:
 
**[[Barrel Distortion Correction]]
 
**[[Barrel Distortion Correction]]
 
<div id="DtiAlgorithms"></div>
 
<div id="DtiAlgorithms"></div>
 +
**[[DTI: Create List File]]
 
**[[DTI Color Display]]
 
**[[DTI Color Display]]
 
**[[DTI Estimate tensor | DTI Estimate tensor - under construction]]
 
**[[DTI Estimate tensor | DTI Estimate tensor - under construction]]
Line 214: Line 220:
 
**[[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]]
Line 237: Line 243:
 
**[[Fuzzy C-Means: Multispectral and Single Channel Algorithms]]
 
**[[Fuzzy C-Means: Multispectral and Single Channel Algorithms]]
 
<div id="HistogramAlgorithms"></div>
 
<div id="HistogramAlgorithms"></div>
 +
**[[Cumulative Histogram|Histogram cumulative]]
 
**[[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]]
 +
**[[Hough Transform]]
 
**[[Image Calculator]]
 
**[[Image Calculator]]
 
**[[Manual 2D Series]]
 
**[[Manual 2D Series]]
Line 269: Line 276:
 
***[[Morphology#Particle Analysis|Particle Analysis]]
 
***[[Morphology#Particle Analysis|Particle Analysis]]
 
***[[Morphology#Skeletonize|Skeletonize]]
 
***[[Morphology#Skeletonize|Skeletonize]]
**[[Morphology#Skeletonize 3D pot field|Skeletonize 3D pot field]]
+
***[[Morphology#Skeletonize 3D pot field|Skeletonize 3D pot field]]
**[[Morphology#Ultimate erode|Ultimate erode]]
+
***[[Morphology#Ultimate erode|Ultimate erode]]
**[[Reslice-Isotropic Voxels]]
+
**[[Muscle Segmentation]]
**[[Watershed|Segmentation: Watershed]]
+
**[[NEIRetinalRegistration | NEI Build macular pigment maps]]
**[[Shading Correction: Inhomogeneity N3 Correction]]
+
**[[Standard Deviation Threshold]]
+
**[[Subsampling images]]
+
**[[Threshold]]
+
**[[Transform to power of 2]]
+
**[[Transform: Conformal Mapping Algorithms]]
+
 
<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]]
+
***[[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]]
Line 290: Line 291:
 
**[[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]]
  
Line 335: Line 346:
 
* [[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?]]
 +
*[[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 ==
 
== Videos ==
Line 356: Line 368:
 
== 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]
Line 362: Line 382:
 
* [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