Category:Help

2

• 2D Histogram

4

• 4 D tools

A

• Adding noise to images
• Allocating Memory in MIPAV
• Autocorrelation Coefficients
• Autocovariance Coefficients
• Automatic de-Skulling

B

• B-Spline Automatic Registration
• B-Spline Automatic Registration Dialog box
• Browsing DICOM images
• BSpline registration: Detecting folding

C

• Calculating statistics on VOI groups
• Calculating VOI statistics
• Changing Image Contrast
• Converting image datasets to different data types
• Converting non-DICOM image files to DICOM format
• Correcting image spacing
• Cost functions used in MIPAV algorithms
• Creating new images
• Cropping images
• Cumulative Histogram
• Customizing MIPAV

D

• Data Repository tools
• Data Validation module
• Degrees of freedom
• Delineating volumes of interest (VOIs)
• Developing new tools using the API
• Displaying and editing DICOM tag information
• Displaying images
• Displaying MIPAV Toolbars
• DTI Color Display
• DTI: Create List File

E

• Edge Detection: Zero X Laplacian
• Edge Detection: Zero X Non-Maximum Suppression
• Examples of BSpline registration
• Extract Brain: Extract Brain Surface (BET)
• Extract Brain: Extract Brain Surface (BSE)
• Extract Surface (Marching Cubes)

F

• Face Anonymizer (BET)
• FAQ: Customizing MIPAV
• FAQ: How can I fix a "Cannot load Java Virtual Machine" error (memory limit set too high)?
• FAQ: How can I view the debugging output of MIPAV?
• FAQ: How do I setup and use Active stereo display in MIPAV?
• FAQ: Trimming VOIs
• FAQ: Understanding Changes in MIPAV
• FAQ: Understanding Image Basics
• FAQ: Understanding Memory
• Fast Fourier Transformation (FFT)
• Filters (Frequency)
• Filters (Spatial) Anisotropic Diffusion
• Filters (Spatial) Laplacian
• Filters (Spatial): Adaptive Noise Reduction

F cont.

• Filters (Spatial): Adaptive Path Smooth
• Filters (Spatial): Coherence-Enhancing Diffusion
• Filters (Spatial): Gaussian Blur
• Filters (Spatial): Gradient Magnitude
• Filters (Spatial): Haralick Texture
• 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
• Flipping images
• Fuzzy C-Means: Multispectral and Single Channel Algorithms

G

• Getting Started Quickly with MIPAV

H

• Histogram Cumulative
• Histogram Equalization: Neighborhood Adaptive
• Histogram Equalization: Regional Adaptive
• Histogram Matching
• Histogram summary
• Hough Transform
• How to specify the location of a plugin in the MIPAV menu

I

• Image Calculator
• Image Calculator: Advanced image calculator options
• Image formats descriptions
• Image Math
• Image submission plug-in
• ImageJ
• Inserting slices into image datasets
• Installing mipav
• Interpolation methods used in MIPAV
• Introducing MIPAV

L

• Load and save profile

M

• Manual 2D Series
• Map IDs
• Mask
• Masking (filling) images
• Matching images
• Microscopy Colocalization Orthogonal Regression
• Microscopy: Blind Deconvolution
• Microscopy: Fluorescence Resonance Energy Transfer (FRET)-Acceptor
• Microscopy: Fluorescent Resonance Energy Transfer (FRET) Bleed Through and Efficiency
• Microscopy: FRAP (Fluorescence Recovery After Photobleaching)
• Midsagittal line alignment
• MIPAV configuration files
• MIPAV mailing list
• MIPAV system requirements
• MIPAV toolbars

M cont.

• Modifying image resolutions
• Morphology
• Muscle Segmentation

N

• NEIRetinalRegistration

O

• Opening and loading image files
• Optimized automatic registration 3D

P

• Posing queries and retrieving images
• Prostate segmentation and surface reconstruction
• Protecting patient privacy using Anonymize

Q

• Quantify Mask
• Quitting MIPAV

R

• Receiving and sending image files
• Registration: Landmark-Least Squares
• Registration: Landmark-TPSpline
• Registration: Manual 2D Series
• Registration: Time Series Optimized Automatic Registration
• Replacing pixel/voxel value in images
• Reslice-Isotropic Voxels
• Reviewing VOI statistics
• Running scripts

S

• Sample images
• Saving and printing images
• Segmenting Images Using Contours and Masks
• Segmenting Images Using Contours and Masks: Advanced paint and Power Paint tools
• Sending and retrieving DICOM images
• Shading Correction: Inhomogeneity N3 Correction
• Slice tools
• Standard Deviation Threshold
• Subsampling images
• Subtract VOI Background
• Supported algorithms
• Supported file formats
• Supported Formats
• Swap slices and swap volumes

T

• Technical Support
• Testing the connection
• Threshold
• Transform
• Transform nonlinear
• Transform to power of 2
• Transform: Conformal Mapping Algorithms
• Transformation matrix

U

• Using MIPAV Algorithms
• Using Scripts (Macros) in MIPAV

V

• Video tutorials
• Viewing MIPAV news and updates
• Volume renderer GPU support listing

W

• Watershed
• Why can't I see the plugins I install in the menu?
• Working with DICOM Images
• Writing MIPAV plugins without MIPAV source code