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 (Spatial): Adaptive Path Smooth]] | **[[Filters (Spatial): Adaptive Path Smooth]] | ||
**[[Filters (Spatial) Anisotropic Diffusion]] | **[[Filters (Spatial) Anisotropic Diffusion]] | ||
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**[[Transform: Conformal Mapping Algorithms]] | **[[Transform: Conformal Mapping Algorithms]] | ||
**[[Transform nonlinear]] | **[[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] | ||
| Line 374: | 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 | + | * [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
