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Revision as of 14:37, 7 February 2012
Preface
- Scope of this guide
- Who should use this guide
- Skills you need to perform tasks in MIPAV
- How this guide is organized
- Where to find more information
- Conventions used in this guide
Volume 1: Chapters
- Introducing MIPAV
- Installing MIPAV
- Getting Started Quickly with MIPAV
- Understanding Image Basics
- Working with DICOM Images
- Connecting to SRB BIRN
- Visualizing Images
- Segmenting Images Using Contours and Masks
- Analyzing Images
- Changing Image Datasets Using MIPAV Utilities
- Using Scripts (Macros) in MIPAV
- Developing Plugin Programs
Volume 2: MIPAV Algorithms
- Understanding MIPAV capabilities
- Using MIPAV Algorithms
- B-Spline Automatic Registration
- DTI Color Display
- Edge Detection: Zero X Laplacian
- Edge Detection: Zero X Non-Maximum Suppression
- Extract Brain: Extract Brain Surface (BET)
- Extract Brain: Extract Brain Surface (BSE)
- Face Anonymizer (BET)
- 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) 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): Thresholding
- Fuzzy C-Means: Multispectral and Single Channel Algorithms
- Histogram Equalization: Regional Adaptive
- Histogram Equalization: Neighborhood Adaptive
- Histogram Matching
- 2D Histogram
- Histogram summary
- Manual 2D Series
- Extract Surface (Marching Cubes)
- Mask
- Microscopy Colocalization Orthogonal Regression
- Microscopy: Fluorescence Resonance Energy Transfer (FRET)-Acceptor
- Microscopy: FRAP (Fluorescence Recovery After Photobleaching)
- Microscopy: Blind Deconvolution
- Midsagittal line alignment
- Morphology
- Optimized automatic registration 3D
- Registration: Landmark-Least Squares
- Registration: Landmark-TPSpline
- Registration: Manual 2D Series
- Registration: Time Series Optimized Automatic Registration
- Reslice-Isotropic Voxels
- Shading Correction: Inhomogeneity N3 Correction
- Standard Deviation Threshold
- Subsampling images
- Threshold
- Transform to power of 2
