Difference between revisions of "MIPAV Help"
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*[[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]] | ||
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*[[Converting image datasets to different data types]] | *[[Converting image datasets to different data types]] | ||
*[[Correcting image spacing]] | *[[Correcting image spacing]] | ||
− | **[[Correcting image spacing#UnderstandingContiguousPlanes | + | **[[Correcting image spacing#UnderstandingContiguousPlanes|Understanding contiguous planes]] |
− | **[[Correcting image spacing#UnderstandingImageSpacing | + | **[[Correcting image spacing#UnderstandingImageSpacing|Understanding how MIPAV solves the image spacing problem]] |
− | **[[Correcting image spacing#ViewImageAttributes | + | **[[Correcting image spacing#ViewImageAttributes|Image attributes]] |
− | **[[Correcting image spacing#SaveDicomXml | + | **[[Correcting image spacing#SaveDicomXml|Saving DICOM images as XML files]] |
− | **[[Correcting image spacing#SaveOtherXml | + | **[[Correcting image spacing#SaveOtherXml|Saving other (than DICOM) images as XML files]] |
− | **[[Correcting image spacing#CorrectImageSpacing | + | **[[Correcting image spacing#CorrectImageSpacing|Correcting image spacing]] |
*[[Cropping images]] | *[[Cropping images]] | ||
*[[Masking (filling) images]] | *[[Masking (filling) images]] | ||
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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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<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]] | ||
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***[[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> | ||
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**[[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]] | ||
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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 (Spatial): Adaptive Path Smooth]] | **[[Filters (Spatial): Adaptive Path Smooth]] | ||
**[[Filters (Spatial) Anisotropic Diffusion]] | **[[Filters (Spatial) Anisotropic Diffusion]] | ||
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**[[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]] | ||
− | |||
**[[Histogram summary]] | **[[Histogram summary]] | ||
+ | **[[Hough Transform]] | ||
**[[Image Calculator]] | **[[Image Calculator]] | ||
**[[Manual 2D Series]] | **[[Manual 2D Series]] | ||
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**[[Midsagittal line alignment]] | **[[Midsagittal line alignment]] | ||
**[[Morphology]] | **[[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> | <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]] | ||
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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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* [[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 == | ||
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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 | + | * [http://mipav.cit.nih.gov/documentation/presentations/plugins.pdf Developing Java Plugins in MIPAV] |
− | + | ||
− | 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
Contents
Preface
Getting Started Quickly with MIPAV
- Introducing MIPAV
- Installing MIPAV
- Getting Started Quickly with MIPAV
- Starting MIPAV
- MIPAV main window
- Managing memory in MIPAV
- Allocating Memory in MIPAV
- Opening and loading image files
- MIPAV toolbars
- Displaying MIPAV Toolbars
- Displaying images
- Modifying image resolutions
MIPAV Basics
- Understanding Image Basics
- Working with DICOM Images
- Visualizing Images
- Displaying images using the default view
- Displaying images using the animate view
- Displaying images using the cine (movie) view
- Displaying images using the lightbox view
- Displaying images using the link to another image view
- Displaying images using the triplanar view
- Displaying images using the triplanar-dual view
- Displaying images using the surface plotter view
- Displaying images using the surface renderer view
- Displaying images using the volume shear view
- Displaying images using the volume renderer view
- Segmenting Images Using Contours and Masks
- Analyzing Images
- 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
- Adding image margins
- Copying images using the Clone command
- Converting image datasets to different data types
- Correcting image spacing
- Cropping images
- Masking (filling) images
- Flipping images
- Image Calculator
- 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
- Subtract VOI Background
- Standard tasks provided through commands on the Utilities menu
- Using Scripts (Macros) in MIPAV
- Developing Plugin Programs
- Technical Support
MIPAV Algorithms
- 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
- Registration: B-Spline Automatic Registration
- Registration: Optimized automatic registration 3D and 3.5D
- Registration: Landmark-Least Squares
- Registration: Landmark-TPSpline
- Registration: Manual 2D Series
- Registration: Midsagittal line alignment
- Registration: Reslice-Isotropic Voxels
- Registration: Time Series Optimized Automatic Registration
- Reslice-Isotropic Voxels
- 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
Appendices
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
Frequently Asked Questions (FAQs)
- FAQ: Understanding Memory
- FAQ: Customizing MIPAV
- FAQ: Understanding Image Basics
- FAQ: Understanding Changes in MIPAV
- FAQ: Trimming VOIs
- FAQ: How can I view the debugging output of MIPAV?
- 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: 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 - 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
- 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:
- Introduction to Medical Image Processing in MIPAV
- Segmentation and Annotation of Medical Images in MIPAV
- Medical Image Visualization in MIPAV
- Medical Image Processing and Registration in MIPAV
- The Java Image Science Toolkit and Scripting in MIPAV
- Developing Java Plugins in MIPAV