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 == | == Getting Started Quickly with MIPAV == | ||
Line 136: | Line 142: | ||
*[[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]] | ||
Line 178: | Line 185: | ||
== MIPAV Algorithms == | == MIPAV Algorithms == | ||
*[[Understanding MIPAV capabilities]] | *[[Understanding MIPAV capabilities]] | ||
− | + | *[[Developing new tools using the API]] | |
− | + | ||
*[[Using MIPAV Algorithms | Overview of MIPAV Algorithms]] | *[[Using MIPAV Algorithms | Overview of MIPAV Algorithms]] | ||
**[[Cost functions used in MIPAV algorithms]] | **[[Cost functions used in MIPAV algorithms]] | ||
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**[[DTI Color Display]] | **[[DTI Color Display]] | ||
**[[DTI Estimate tensor | DTI Estimate tensor - under construction]] | **[[DTI Estimate tensor | DTI Estimate tensor - under construction]] | ||
− | **[[DTI Pipeline | + | **[[DTI Pipeline]] |
<div id="EdgeDetection"></div> | <div id="EdgeDetection"></div> | ||
**[[Edge Detection: Zero X Laplacian]] | **[[Edge Detection: Zero X Laplacian]] | ||
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**[[Cumulative Histogram]] | **[[Cumulative Histogram]] | ||
**[[Histogram summary]] | **[[Histogram summary]] | ||
+ | **[[Image Calculator]] | ||
**[[Manual 2D Series]] | **[[Manual 2D Series]] | ||
**[[Mask]] | **[[Mask]] | ||
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**[[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> | <div id="TransformationAlgorithms"></div> | ||
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**[[Transform to power of 2]] | **[[Transform to power of 2]] | ||
<div id="RegistrationAlgorithms"></div> | <div id="RegistrationAlgorithms"></div> | ||
− | **[[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]] | ||
− | **[[Optimized automatic registration 3D]] | + | **[[Optimized automatic registration 3D | Registration: Optimized automatic registration 3D and 3.5D]] |
**[[Registration: Landmark-Least Squares]] | **[[Registration: Landmark-Least Squares]] | ||
**[[Registration: Landmark-TPSpline]] | **[[Registration: Landmark-TPSpline]] | ||
**[[Registration: Manual 2D Series]] | **[[Registration: Manual 2D Series]] | ||
+ | **[[Midsagittal line alignment | Registration: Midsagittal line alignment]] | ||
+ | **[[Reslice-Isotropic Voxels | Registration: Reslice-Isotropic Voxels]] | ||
**[[Registration: Time Series Optimized Automatic Registration]] | **[[Registration: Time Series Optimized Automatic Registration]] | ||
+ | **[[Volume Renderer]] | ||
== Glossary == | == Glossary == | ||
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*[[FAQ: Understanding Changes in MIPAV]] | *[[FAQ: Understanding Changes in MIPAV]] | ||
*[[FAQ: Trimming VOIs]] | *[[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 == | ||
* [[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.