Difference between revisions of "Wiki help testing"
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− | =[[Preface]]= | + | == [[Preface]] == |
*[[Scope of this guide]] | *[[Scope of this guide]] | ||
− | = | + | == Recent changes in documentation == |
+ | |||
+ | This section is reflects the recent changes in documentation. It is mostly for Olga to help her tracking changes. Please don't pay any special attention to it. | ||
+ | |||
+ | {{Special:RecentChanges/limit=10, hideminor, hidebots, hideliu}} | ||
+ | |||
+ | == Getting Started Quickly with MIPAV == | ||
<ol type="1"><li value="1">[[Introducing MIPAV]] | <ol type="1"><li value="1">[[Introducing MIPAV]] | ||
− | *[[Introducing MIPAV]] | + | **[[Introducing MIPAV#MipavPlatformIndependence | Platform Independence]] |
− | *[[Understanding MIPAV capabilities]] | + | **[[Introducing MIPAV#MipavCapabilities | Understanding MIPAV capabilities]] |
+ | **[[Introducing MIPAV#JavaPlugIns | Extensibility with Java plug-ins]] | ||
+ | **[[Introducing MIPAV#MipavFeatures | Sampling of MIPAV's features]] | ||
*[[MIPAV mailing list]] | *[[MIPAV mailing list]] | ||
*[[Installing mipav#MipavNews|Viewing MIPAV News and Updates]] | *[[Installing mipav#MipavNews|Viewing MIPAV News and Updates]] | ||
− | + | ||
*[[Supported Formats]] | *[[Supported Formats]] | ||
+ | **[[Supported Formats | Graphical and file formats supported by MIPAV]] | ||
+ | **[[Image formats descriptions | Image formats' descriptions]] | ||
+ | **[[MIPAV configuration files]] | ||
+ | **[[FAQ: Understanding Image Basics#FilesExtensions | Image files supported by MIPAV]] | ||
<li value="2">[[Installing mipav|Installing MIPAV]] | <li value="2">[[Installing mipav|Installing MIPAV]] | ||
Line 16: | Line 28: | ||
*[[Installing mipav#MipavUpgrade|Upgrading MIPAV]] | *[[Installing mipav#MipavUpgrade|Upgrading MIPAV]] | ||
*[[Installing mipav#MipavUninstall|Uninstalling MIPAV]] | *[[Installing mipav#MipavUninstall|Uninstalling MIPAV]] | ||
− | + | *[[Quitting MIPAV]] | |
<li value="3">[[Getting Started Quickly with MIPAV]] | <li value="3">[[Getting Started Quickly with MIPAV]] | ||
+ | *[[Getting Started Quickly with MIPAV#StartingMIPAV | Starting MIPAV]] | ||
+ | *[[Getting Started Quickly with MIPAV#StartingMIPAV | MIPAV main window]] | ||
+ | *[[Getting Started Quickly with MIPAV#ManagingMemoryResources | Managing memory in MIPAV]] | ||
*[[Allocating Memory in MIPAV]] | *[[Allocating Memory in MIPAV]] | ||
*[[Opening and loading image files]] | *[[Opening and loading image files]] | ||
Line 30: | Line 45: | ||
**[[Displaying images#MagnifyingRegions| Magnifying Regions within Images]] | **[[Displaying images#MagnifyingRegions| Magnifying Regions within Images]] | ||
**[[Displaying images#ImprovingContrast| Improving Image Contrast]] | **[[Displaying images#ImprovingContrast| Improving Image Contrast]] | ||
+ | *[[Modifying image resolutions]] | ||
*[[Changing Image Contrast]] | *[[Changing Image Contrast]] | ||
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**[[Changing Image Contrast|Improving contrast by generating and modifying histograms]] | **[[Changing Image Contrast|Improving contrast by generating and modifying histograms]] | ||
**[[Changing Image Contrast|Using Lookup Table dialog box]] | **[[Changing Image Contrast|Using Lookup Table dialog box]] | ||
− | **[[Changing Image Contrast#PredefinedLuts|Applying color to images using predefined LUTs ]] | + | **[[Changing Image Contrast#PredefinedLuts|Applying color to images using predefined LUTs]] |
**[[Changing Image Contrast|Comparing images using alphablending]] | **[[Changing Image Contrast|Comparing images using alphablending]] | ||
**[[Changing Image Contrast|Restoring images to their original appearance]] | **[[Changing Image Contrast|Restoring images to their original appearance]] | ||
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*[[Creating new images]] | *[[Creating new images]] | ||
**[[Creating new images| Image dialog box]] | **[[Creating new images| Image dialog box]] | ||
− | **[[Creating new images| Annotating images with text]] | + | **[[Creating new images| Annotating images with text]] |
+ | |||
+ | *[[Saving and printing images]] | ||
+ | |||
+ | *[[Delineating volumes of interest (VOIs)| Volumes of Interest]] | ||
+ | **[[Delineating volumes of interest (VOIs)]] | ||
+ | **[[Calculating VOI statistics]] | ||
+ | **[[Calculating VOI statistics#VoiStatistics| VOI statistics dialog box]] | ||
+ | **[[Reviewing VOI statistics]] | ||
+ | **[[Calculating statistics on VOI groups]] | ||
+ | **[[Reviewing VOI statistics|Generating graphs (intensity profiles)]] | ||
− | |||
− | |||
− | |||
− | |||
− | |||
*[[ImageJ | Working with ImageJ]] | *[[ImageJ | Working with ImageJ]] | ||
*[[Customizing MIPAV]] | *[[Customizing MIPAV]] | ||
− | *[[ | + | **[[Customizing MIPAV#MipavOptions | MIPAV Options dialog box]] |
− | *[[ | + | **[[Customizing MIPAV#SplashScreen | Showing and hiding the splash screen on start-up]] |
− | *[[Choosing the default file types to display or save| | + | **[[Customizing MIPAV#DebuggingMipav | Debugging MIPAV]] |
− | *[[ | + | **[[Customizing MIPAV#ActionsHistory | Saving a history of actions on images]] |
− | + | **[[Customizing MIPAV#DefaultFileTypes | Choosing the default file types to display or save]] | |
+ | **[[Customizing MIPAV#AddingShortcuts | Adding Shortcuts]] | ||
+ | **[[MIPAV configuration files]] | ||
+ | |||
+ | *[[Developing new tools using the API]] | ||
+ | |||
+ | *[[Technical Support | Contacting MIPAV support]] | ||
+ | *[[MIPAV mailing list | Joining MIPAV mailing list]] | ||
+ | == MIPAV Basics == | ||
<li value="4">[[Understanding Image Basics]] | <li value="4">[[Understanding Image Basics]] | ||
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*[[Flipping images]] | *[[Flipping images]] | ||
*[[Image Calculator]] | *[[Image Calculator]] | ||
− | **[[Image Calculator: OR ]] | + | **[[Image Calculator: OR]] |
**[[Image Calculator: Advanced image calculator options]] | **[[Image Calculator: Advanced image calculator options]] | ||
*[[Image Math]] | *[[Image Math]] | ||
+ | *[[Inserting slices into image datasets]] | ||
*[[Inverting the image]] | *[[Inverting the image]] | ||
*[[Matching images]] | *[[Matching images]] | ||
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<li value="12">[[Technical Support]]</ol> | <li value="12">[[Technical Support]]</ol> | ||
− | = MIPAV | + | == MIPAV Algorithms == |
*[[Understanding MIPAV capabilities]] | *[[Understanding MIPAV capabilities]] | ||
− | + | *[[Developing new tools using the API]] | |
− | + | *[[Using MIPAV Algorithms | Overview of MIPAV Algorithms]] | |
− | *[[Using MIPAV Algorithms]] | + | **[[Cost functions used in MIPAV algorithms]] |
− | **[[ | + | **[[Interpolation methods used in MIPAV]] |
− | ***[[ | + | **[[Degrees of freedom]] |
− | ***[[ | + | <div id="AutoCorrelation"></div> |
− | + | **[[Autocorrelation Coefficients]] | |
+ | **[[Autocovariance Coefficients]] | ||
+ | **[[Barrel Distortion Correction]] | ||
+ | <div id="DtiAlgorithms"></div> | ||
**[[DTI Color Display]] | **[[DTI Color Display]] | ||
+ | **[[DTI Estimate tensor | DTI Estimate tensor - under construction]] | ||
+ | **[[DTI Pipeline]] | ||
+ | <div id="EdgeDetection"></div> | ||
**[[Edge Detection: Zero X Laplacian]] | **[[Edge Detection: Zero X Laplacian]] | ||
**[[Edge Detection: Zero X Non-Maximum Suppression]] | **[[Edge Detection: Zero X Non-Maximum Suppression]] | ||
+ | <div id="ExtractSurface"></div> | ||
**[[Extract Brain: Extract Brain Surface (BET)]] | **[[Extract Brain: Extract Brain Surface (BET)]] | ||
**[[Extract Brain: Extract Brain Surface (BSE)]] | **[[Extract Brain: Extract Brain Surface (BSE)]] | ||
+ | **[[Extract Surface (Marching Cubes)]] | ||
**[[Face Anonymizer (BET)]] | **[[Face Anonymizer (BET)]] | ||
+ | <div id="FilterAlgorithms"></div> | ||
**[[Fast Fourier Transformation (FFT)]] | **[[Fast Fourier Transformation (FFT)]] | ||
**[[Filters (Spatial): Adaptive Noise Reduction]] | **[[Filters (Spatial): Adaptive Noise Reduction]] | ||
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**[[Filters (Spatial): Gaussian Blur]] | **[[Filters (Spatial): Gaussian Blur]] | ||
**[[Filters (Spatial): Gradient Magnitude]] | **[[Filters (Spatial): Gradient Magnitude]] | ||
+ | **[[Filters (Spatial): Haralick Texture]] | ||
**[[Filters (Spatial) Laplacian]] | **[[Filters (Spatial) Laplacian]] | ||
− | **[[Filters (Spatial) Local Normalization]] | + | **[[Filters (Spatial): Local Normalization]] |
**[[Filters (Spatial): Mean]] | **[[Filters (Spatial): Mean]] | ||
**[[Filters (Spatial): Median]] | **[[Filters (Spatial): Median]] | ||
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**[[Filters (Spatial): Slice Averaging]] | **[[Filters (Spatial): Slice Averaging]] | ||
**[[Filters (Spatial): Unsharp Mask]] | **[[Filters (Spatial): Unsharp Mask]] | ||
+ | **[[Filters (Wavelet): De-noising BLS GSM]] | ||
**[[Filters (Wavelet): Thresholding]] | **[[Filters (Wavelet): Thresholding]] | ||
**[[Fuzzy C-Means: Multispectral and Single Channel Algorithms]] | **[[Fuzzy C-Means: Multispectral and Single Channel Algorithms]] | ||
+ | <div id="HistogramAlgorithms"></div> | ||
**[[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]] | ||
+ | **[[Image Calculator]] | ||
**[[Manual 2D Series]] | **[[Manual 2D Series]] | ||
− | |||
**[[Mask]] | **[[Mask]] | ||
+ | <div id="MicroscopyAlgorithms"></div> | ||
**[[Microscopy Colocalization Orthogonal Regression]] | **[[Microscopy Colocalization Orthogonal Regression]] | ||
**[[Microscopy: Fluorescence Resonance Energy Transfer (FRET)-Acceptor]] | **[[Microscopy: Fluorescence Resonance Energy Transfer (FRET)-Acceptor]] | ||
**[[Microscopy: FRAP (Fluorescence Recovery After Photobleaching)]] | **[[Microscopy: FRAP (Fluorescence Recovery After Photobleaching)]] | ||
+ | **[[Microscopy: Fluorescent Resonance Energy Transfer (FRET) Bleed Through and Efficiency]] | ||
**[[Microscopy: Blind Deconvolution]] | **[[Microscopy: Blind Deconvolution]] | ||
+ | <div id="TransformationAlgorithms"></div> | ||
**[[Midsagittal line alignment]] | **[[Midsagittal line alignment]] | ||
**[[Morphology]] | **[[Morphology]] | ||
− | |||
− | |||
− | |||
− | |||
− | |||
**[[Reslice-Isotropic Voxels]] | **[[Reslice-Isotropic Voxels]] | ||
**[[Shading Correction: Inhomogeneity N3 Correction]] | **[[Shading Correction: Inhomogeneity N3 Correction]] | ||
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**[[Threshold]] | **[[Threshold]] | ||
**[[Transform to power of 2]] | **[[Transform to power of 2]] | ||
+ | <div id="RegistrationAlgorithms"></div> | ||
+ | **[[B-Spline Automatic Registration | Registration: B-Spline Automatic Registration ]] | ||
+ | ***[[Detect folding]] | ||
+ | ***[[User Dialogs in MIPAV]] | ||
+ | **[[Optimized automatic registration 3D | Registration: Optimized automatic registration 3D and 3.5D]] | ||
+ | **[[Registration: Landmark-Least Squares]] | ||
+ | **[[Registration: Landmark-TPSpline]] | ||
+ | **[[Registration: Manual 2D Series]] | ||
+ | **[[Midsagittal line alignment | Registration: Midsagittal line alignment]] | ||
+ | **[[Reslice-Isotropic Voxels | Registration: Reslice-Isotropic Voxels]] | ||
+ | **[[Registration: Time Series Optimized Automatic Registration]] | ||
+ | **[[Volume Renderer]] | ||
− | =Glossary= | + | == Glossary == |
[[Glossary for MIPAV Help]] | [[Glossary for MIPAV Help]] | ||
− | =Appendices= | + | == Appendices == |
<ol type="A"><li value="1">[[References]] | <ol type="A"><li value="1">[[References]] | ||
<li value="B">[[DICOM Conformance]] | <li value="B">[[DICOM Conformance]] | ||
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</ol> | </ol> | ||
− | =Talairach= | + | == Talairach == |
*[[Introduction]] | *[[Introduction]] | ||
*[[Installing]] | *[[Installing]] | ||
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**[[Viewing the Talairach grid on Talairach images]] | **[[Viewing the Talairach grid on Talairach images]] | ||
− | =Frequently Asked Questions ( | + | == Frequently Asked Questions (FAQs) == |
*[[FAQ: Understanding Memory]] | *[[FAQ: Understanding Memory]] | ||
*[[FAQ: Customizing MIPAV]] | *[[FAQ: Customizing MIPAV]] | ||
*[[FAQ: Understanding Image Basics]] | *[[FAQ: Understanding Image Basics]] | ||
*[[FAQ: Understanding Changes in MIPAV]] | *[[FAQ: Understanding Changes in MIPAV]] | ||
+ | *[[FAQ: Trimming VOIs]] | ||
+ | |||
+ | == Videos == | ||
+ | |||
+ | *A video tutorial that explains how to load images into MIPAV and change the memory allocation - [http://www.youtube.com/embed/npSYWYJa530 play]. | ||
+ | |||
+ | *A video tutorial that explains how to do basic image display options - [http://www.youtube.com/watch?v=02vUrfSaGWE&feature=relmfu 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 - [http://www.youtube.com/watch?v=uCr-Zlxu454&feature=relmfu play]. | ||
+ | |||
+ | * A video tutorial that explains how to save and capture PDFs of images - [http://www.youtube.com/watch?v=Zfh5nKITbkA&feature=relmfu play]. | ||
+ | |||
+ | * A video tutorial that explains how to do basic image manipulations - [http://www.youtube.com/watch?v=uCr-Zlxu454&feature=relmfu play]. | ||
+ | |||
+ | All tutorials are courtesy of [http://www.youtube.com/user/MIPAVvideos MIPAVvideos]. | ||
+ | |||
+ | == Publications == | ||
+ | * [[Publications]] |
Latest revision as of 15:42, 12 June 2012
Contents
Preface
Recent changes in documentation
This section is reflects the recent changes in documentation. It is mostly for Olga to help her tracking changes. Please don't pay any special attention to it.
No changes during the given period matching these criteria.
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
- Inserting slices into image datasets
- Subtract VOI Background
- Standard tasks provided through commands on the Utilities menu
- Using Scripts (Macros) in MIPAV
- Developing Plugin Programs
- Technical Support
MIPAV Algorithms
- Fast Fourier Transformation (FFT)
- Filters (Spatial): Adaptive Noise Reduction
- Filters (Frequency)
- 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
- 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
Frequently Asked Questions (FAQs)
- FAQ: Understanding Memory
- FAQ: Customizing MIPAV
- FAQ: Understanding Image Basics
- FAQ: Understanding Changes in MIPAV
- FAQ: Trimming VOIs
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.