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- Task 4, Transforming Talairach image and Talairach VOIs-1 to the original image (2 revisions)
- Transform nonlinear (2 revisions)
- PlugIn Algorithm Median (con't, part 3) (2 revisions)
- Crontab notes (2 revisions)
- Visualizing Images: Displaying images using the cine (movie) view (2 revisions)
- Installing a plug-in (2 revisions)
- Copying images using the Clone command (2 revisions)
- Filters (Spatial): Haralick Texture (2 revisions)
- Making a MIPAV Algorithm Scriptable (2 revisions)
- Viewing the Talairach grid on Talairach images (2 revisions)
- DTI: Create List File (2 revisions)
- Combining scripts and other programs (2 revisions)
- Filters (Spatial): Mode (3 revisions)
- MIPAV Script Running (3 revisions)
- Recording utilities usage with the history feature (3 revisions)
- Task 5, Copying Talairach VOIs to segmented images (3 revisions)
- PlugIn Algorithm Median (con't, part 4) (3 revisions)
- Pad (3 revisions)
- Supported algorithms (3 revisions)
- Skills you need to perform tasks in MIPAV (3 revisions)
- How this guide is organized (3 revisions)
- Inverting the image (3 revisions)
- Filters (Spatial): Kernel Regression (3 revisions)
- Why can't I see the plugins I install in the menu? (3 revisions)
- Load and save profile (3 revisions)
- MIPAV change list pre-1.0 (3 revisions)
- Mapping Brains in Talairach Space (3 revisions)
- How to specify the script name of a plugin (3 revisions)
- DTI Estimate tensor (3 revisions)
- Mask (3 revisions)
- FAQ: How do I setup and use Active stereo display in MIPAV? (4 revisions)
- Editing and deleting scripts (4 revisions)
- Volume 2, Algorithms (4 revisions)
- References (4 revisions)
- Task 6, Calculating statistics on VOIs (4 revisions)
- Setting up scripting (4 revisions)
- Filters (Spatial): Gradient Magnitude (4 revisions)
- Image Math (4 revisions)
- Making a MIPAV Algorithm JISTable (4 revisions)
- Calculating the volume of masks (4 revisions)
- Where to find more information (4 revisions)
- Maximum Intensity Projection (4 revisions)
- MuscleSegmentation plugin (4 revisions)
- Registration: Time Series Optimized Automatic Registration (4 revisions)
- Visualizing Images: Displaying images using the link to another image view (4 revisions)
- Who should use this guide (4 revisions)
- Histogram (4 revisions)
- Segmenting Images Using Contours and Masks:Converting VOI contours to masks (4 revisions)
- Standard Deviation Threshold (4 revisions)
- Reslice-Isotropic Voxels (4 revisions)
- Visualizing Images: Displaying images using the surface renderer view (4 revisions)
- PlugIn Algorithm Median (con't) (4 revisions)
- Subsampling images (4 revisions)
- Task 3, Segmenting the original image (4 revisions)
- Developing and using scripts (5 revisions)
- Histogram summary (5 revisions)
- Sample images (5 revisions)
- Filters (Spatial): Nonmaximum Suppression (5 revisions)
- Generating graphs (5 revisions)
- Using the mipav command (5 revisions)
- Supported file formats (5 revisions)
- Examples of MIPAV plug-ins (5 revisions)
- Plug-in CT MD.java (5 revisions)
- PlugInAlgorithmCT MD.java (5 revisions)
- 2D Histogram (5 revisions)
- TRE Scripts (5 revisions)
- Replacing pixel/voxel value in images (5 revisions)
- Threshold (5 revisions)
- PlugIn Algorithm Median (5 revisions)
- Filters (Spatial): Mean (5 revisions)
- Segmenting Images Using Contours and Masks: Converting masks to VOI contours and paints (5 revisions)
- FAQ: How can I fix a "Cannot load Java Virtual Machine" error (memory limit set too high)? (5 revisions)
- Filters (Spatial): Median (5 revisions)
- FAQ: How can I view the debugging output of MIPAV? (5 revisions)
- Filters (Wavelet): Thresholding (5 revisions)
- Using Scripts (Macros) in MIPAV (5 revisions)
- Rotating images (6 revisions)
- MIPAV feature list (6 revisions)
- Using Shell scripting to lessen typing (6 revisions)
- Select Algorithms and Brain Tools for Talairach Transform (6 revisions)
- Transformation matrix (6 revisions)
- Planning scripts (6 revisions)
- Filters (Spatial): Gaussian Blur (6 revisions)
- Registration: Landmark-TPSpline (6 revisions)
- Filters (Spatial): Slice Averaging (6 revisions)
- Filters (Spatial): Unsharp Mask (6 revisions)
- Muscle Segmentation (6 revisions)
- Quantify Mask (6 revisions)
- Task 1, Performing a semimanual transformation on datasets to the Talairach coordinate system (6 revisions)
- Task 2, Applying Talairach VOIs (6 revisions)
- Eclipse installation and configuration documentation (6 revisions)
- Filters (Wavelet): De-noising BLS GSM (6 revisions)
- Receiving and sending image files (6 revisions)
- Adding image margins (6 revisions)
- Adding noise to images (7 revisions)
- Filters (Spatial): Nonlinear Noise Reduction (7 revisions)
- Visualizing Images: Displaying images using the default view (7 revisions)
- Conventions used in this guide (7 revisions)
- Registration: Landmark-Least Squares (7 revisions)
- Technical Information (7 revisions)
- Displaying and editing DICOM tag information (7 revisions)
- Testing the connection (7 revisions)
- Introduction (7 revisions)
- Filters (Spatial): Local Normalization (7 revisions)
- Standard tasks provided through commands on the Utilities menu (7 revisions)
- How to specify the location of a plugin in the MIPAV menu (7 revisions)
- Histogram Equalization: Regional Adaptive (7 revisions)
- Creating a self-contained plug-in frame (7 revisions)
- Background (7 revisions)
- Filters (Frequency) (7 revisions)
- Histogram Matching (7 revisions)
- Flipping images (8 revisions)
- Masking (filling) images (8 revisions)
- Running scripts (8 revisions)
- Matching images (8 revisions)
- Cropping images (8 revisions)
- Modifying image resolutions (8 revisions)
- Filters (Spatial): Regularized Isotropic (Nonlinear) Diffusion (8 revisions)
- FAQ: Understanding Changes in MIPAV (8 revisions)
- Visualizing Images: Displaying images using the default view: Viewing two images together (8 revisions)
- Watershed (8 revisions)
- Getting Started with Eclipse (8 revisions)
- Scope of this guide (8 revisions)
- Customizing the appearance of graphs - Modify graph dialog box (8 revisions)
- Filters (Spatial) Laplacian (8 revisions)
- Degrees of freedom (8 revisions)
- Subtract VOI Background (8 revisions)
- Recording scripts (8 revisions)
- Midsagittal line alignment (9 revisions)
- MIPAV mailing list (9 revisions)
- Transform to power of 2 (9 revisions)
- Filters (Spatial): Adaptive Path Smooth (9 revisions)
- Posing queries and retrieving images (9 revisions)
- Image Calculator: OR (9 revisions)
- Plug-in CT MD, a typical plug-in program (9 revisions)
- Understanding plug-in programs (9 revisions)
- Segmenting Images Using Contours and Masks: Advanced paint and Power Paint tools (9 revisions)
- Microscopy: Fluorescence Resonance Energy Transfer (FRET)-Acceptor (9 revisions)
- Visualizing Images:Displaying images using the default view: Magnifying and minifying images (9 revisions)
- Connecting to SRB BIRN (10 revisions)
- Examples of BSpline registration (10 revisions)
- Volume renderer GPU support listing (10 revisions)
- Protecting patient privacy using Anonymize (10 revisions)
- Filters (Spatial) Anisotropic Diffusion (10 revisions)
- PlugInDialogCT MD.java (10 revisions)
- MIPAV FAQ (10 revisions)
- Installing (10 revisions)
- Barrel Distortion Correction (11 revisions)
- Volume 1, Basics (11 revisions)
- Glossary for MIPAV Help (11 revisions)
- Extract Brain: Extract Brain Surface (BSE) (11 revisions)
- Visualizing Images: Displaying images using the surface plotter view (11 revisions)
- Histogram Equalization: Neighborhood Adaptive (11 revisions)
- Creating a mask using the Paint Grow Segmentation method (11 revisions)
- Microscopy Colocalization Orthogonal Regression (11 revisions)
- Filters (Spatial): Adaptive Noise Reduction (12 revisions)
- Developing new tools using the API (12 revisions)
- Cumulative Histogram (12 revisions)
- Preface (12 revisions)
- Extract Brain: Extract Brain Surface (BET) (12 revisions)
- Changing Image Datasets Using MIPAV Utilities (12 revisions)
- Changing the legends for functions (12 revisions)
- Inserting slices into image datasets (12 revisions)
- Visualizing Images: Displaying images using the triplanar view (12 revisions)
- Edge Detection: Zero X Non-Maximum Suppression (13 revisions)
- Image Calculator (13 revisions)
- FAQ: Trimming VOIs (13 revisions)
- Converting image datasets to different data types (13 revisions)
- Autocorrelation Coefficients (13 revisions)
- Understanding MIPAV capabilities (13 revisions)
- Segmenting Images Using Contours and Masks (13 revisions)
- Segmenting Images Using Contours and Masks: Generating Masks (13 revisions)
- Developing Plugin Programs (13 revisions)
- Fuzzy C-Means: Multispectral and Single Channel Algorithms (14 revisions)
- Microscopy: Blind Deconvolution (14 revisions)
- B-Spline Automatic Registration Dialog box (14 revisions)
- DTI Pipeline Tutorials (15 revisions)
- Using the API documentation (15 revisions)
- Filters (Spatial): Coherence-Enhancing Diffusion (15 revisions)
- Visualizing Images: Displaying images using the default view:Changing image brightness and contrast using LUTs (15 revisions)
- Converting non-DICOM image files to DICOM format (15 revisions)
- Slice tools (15 revisions)
- Correcting image spacing (15 revisions)
- Extract Surface (Marching Cubes) (15 revisions)
- Visualizing Images: Displaying images using the animate view (16 revisions)
- Image Calculator: Advanced image calculator options (16 revisions)
- ImageJ (17 revisions)
- 4 D tools (17 revisions)
- BSpline registration: Detecting folding (17 revisions)
- Modifying Contours (18 revisions)
- Analyzing Images (18 revisions)
- Autocovariance Coefficients (18 revisions)
- Face Anonymizer (BET) (18 revisions)
- Microscopy: FRAP (Fluorescence Recovery After Photobleaching) (18 revisions)
- Muscle Segmentation problems at UCSD (18 revisions)
- To show the splash screen (18 revisions)
- Quitting MIPAV (18 revisions)
- Examples (19 revisions)
- Data Download module (19 revisions)
- FAQ: Customizing MIPAV (19 revisions)
- Edge Detection: Zero X Laplacian (19 revisions)
- Visualizing Images (20 revisions)
- Visualizing Images: Displaying images using the triplanar-dual view (20 revisions)
- Working with DICOM Images (21 revisions)
- Browsing DICOM images (23 revisions)
- Calculating statistics on VOI groups (23 revisions)
- NEIRetinalRegistration (23 revisions)
- Technical Support (24 revisions)
- Visualizing Images: Displaying images using the lightbox view (24 revisions)
- DICOM Conformance (24 revisions)
- MIPAV configuration files (25 revisions)
- Segmenting Images Using Contours and Masks: Using contours to segment a VOI (28 revisions)
- MIPAV change list (28 revisions)
- Volume Renderer (28 revisions)
- Displaying MIPAV Toolbars (28 revisions)
- Saving and printing images (28 revisions)
- Microscopy: Fluorescent Resonance Energy Transfer (FRET) Bleed Through and Efficiency (28 revisions)
- Developing plug-in programs (31 revisions)
- Data Repository tools (31 revisions)
- Sending and retrieving DICOM images (32 revisions)
- Fast Fourier Transformation (FFT) (32 revisions)
- Hough Transform (33 revisions)
- Matrix, Plot, LUT, VOI and Surface files (34 revisions)
- FAQ: Understanding Image Basics (34 revisions)
- Delineating volumes of interest (VOIs) (34 revisions)
- Manual 2D Series (35 revisions)
- Writing MIPAV plugins without access to MIPAV source code (36 revisions - redirect page)
- Calculating VOI statistics (36 revisions)
- DTI Color Display (36 revisions)
- MIPAV class (37 revisions)
- Shading Correction: Inhomogeneity N3 Correction (38 revisions)
- Opening and loading image files (39 revisions)
- Data Upload module (40 revisions)
- MIPAV Help (42 revisions)
- Installing mipav (43 revisions)
- Data Validation module (44 revisions)
- Optimized automatic registration 3D (47 revisions)
- Morphology (48 revisions)
- Supported Formats (49 revisions)
- MIPAV toolbars (49 revisions)
- DTI pipeline interface (51 revisions)
- FAQ: Understanding Memory (52 revisions)
- Introducing MIPAV (54 revisions)
- Reviewing VOI statistics (54 revisions)
- Displaying images (58 revisions)
- MIPAV system requirements (59 revisions)
- Cost functions used in MIPAV algorithms (60 revisions)
- Understanding Image Basics (64 revisions)
- Transform: Conformal Mapping Algorithms (66 revisions)
- Publications (68 revisions)
