Difference between revisions of "MIPAV Help"

From MIPAV
Jump to: navigation, search
m (Frequently Asked Questions (FAQs))
m (MIPAV Algorithms)
 
(15 intermediate revisions by 2 users not shown)
Line 162: 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 180: 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 187: 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 203: 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 215: 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 274: Line 279:
 
***[[Morphology#Ultimate erode|Ultimate erode]]
 
***[[Morphology#Ultimate erode|Ultimate erode]]
 
**[[Muscle Segmentation]]
 
**[[Muscle Segmentation]]
**[[Reslice-Isotropic Voxels]]
+
**[[NEIRetinalRegistration | NEI Build macular pigment maps]]
**[[Watershed|Segmentation: Watershed]]
+
**[[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 293: 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 360: 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 366: 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