What's New

Previous changes to MIPAV

4.0.3 (02/29/2008)

• File handling
  • AVI transcoding bug fixed.
  • Added support for many new variations of the TIFF format.
  • Fixed some minor issues with the Interfile reader.
  • Fixed some minor issues in the Afni reader.
  • Fixed some minor issues in the Analyze reader.
  • Solved a problem in MIPAV's support of NIFTI multifile datasets.
  • Added XFM matrix file format support (McGill transforms).
  • Fixed problem storing very large float or double values into a unsigned integer image buffer.
  • Fixed NRRD reader progress bar.
  • The user can now select DICOM tags to save from the Image header dialog (this action is scriptable).
  • Improved dialog for selection of tags to convert from DICOM to XML.
  • Fixed a problem encountered reading DICOM files with malformed slice thickness (0018,0050) or slice spacing (0018,0088) tags.
  • Solved problem reading reading DICOM CT images stored as unsigned short on disk with negative rescaling.
  • Fixed NRRD matrix and origin orientation problem.
  • Added option in the MIPAV options to always open img/hdr files as either Analyze/NIFTI/Interfile or to force MIPAV to always prompt the user. This change may cause some temporary problems when scripting the saving of files to these formats with the -hide option.
  • Modified Par/Rec reader to handle new version of the header file.
• Algorithms
  • Parallelization of Optimized automatic registration, non-linear registration (b-spline and least squares), FFT, and separable convolver-based algorithms to take full advantage of multi-processor and multi-core systems.
  • Fixed a problem with the Transform algorithm.
  • Fixed bug in FFT algorithm.
  • Added beta version of auto-exposure of Insight Toolkit (ITK) filters from within MIPAV.
• Utilities
  • Fixed the Image calculator utility difference and average functions for complex images.
  • Added an Image calculator - bulk images utility to perform calculations on multiple open images.
  • Added a utility to calculate an image's center of mass.
• VOIs
  • Added Coefficient of skewness and Coefficient of kurtosis to VOI statistics/properties.
  • Center of mass has been renamed Geometric center in the VOI statistics/properties.
  • Fixed display of scanner coordinates for VOI points in the VOI statistics/properties output.
  • Fixed problem in Rectangle VOI.
  • Added new button to open VOI properties dialog.
• Image views & visualization
  • GPU renderer (beta) improvements:
    • Added support for GLSL programmable shaders.
    • Ported volume renderer slice view.
    • Fixed miscellaneous bugs.
    • Added volume sculpting support.
    • Added triangular surface mesh support.
    • Improved clipping planes.
    • Added ability to paint on surface meshes.
  • Added new LUT color scheme presets.
• Scripting
  • Added support for graphically selecting transformation matrix files for use when scripting the Transform algorithm (Contributed by Pilou Basin).
• Miscellaneous
  • MIPAV now consistently displays slice positions in a zero-based format.
  • Plugins can now be run without the rest of the MIPAV interface appearing by using the -p PlugInName command line option with the -hide option.
  • Added the following help topics:
    • Morphological filter
    • Skeletonize 3D
    • Surface plotter
    • Barrel/pincushion distortion correction
    • Cumulative histogram
    • Image calculator - bulk images
    • Creating a self-contained plug-in frame
    • Display pixel similarity cost function

4.0.2 (11/15/2007)

• File handling
  • Added support for writing NRRD files.
  • Resolved a problem with some 2D Nifti files.
  • Fixed writing of image matrix to MIPAV XML for 4D+ datasets.
  • Fixed reading of some (uncompressed, ISFT, LIST, IV32, IV41) AVI files.
  • Afni reader now allows the time dim to be set to 1.
• Algorithms
  • Fixed Transform algorithm handling of VOIs when 2.5D processing is performed.
  • Minor bug fixes included for a number of algorithms:
    • Extract brain (BET)
    • Registration mosaic
    • Registration OAR 3D, 3.5D, 4D
• Utilities
  • Merged Pad and Add image margins utilties
  • Minor bug fixes included for a number of utilities:
    • Change type
    • Clone
    • Crop
    • Depth flip
    • Image calculator
    • Image math
    • Maximum intensity projection (MIP)
    • Noise
    • Quantify mask
    • Randomize slice order
    • Remove slices
    • Replace removed slices
• VOIs
  • Fixed a minor bug in VOI histogram when there is no VOI contour present.
  • The Livewire dialog now maps the Enter key to the OK button.
• Image views & visualization
  • More Diffusion tensor tool updates.
  • Continued improvements to the WildMagic GPU-based renderer.
• Scripting
  • Fixed recording and playback of the 'Invert matrix' flag in the Transform dialog.
• Miscellaneous
  • Fixed image min/max calculation for boolean images.
  • Added the following help topics:
    • Background distance map
    • Close
    • Delete objects
    • Dilate
    • Distance map
    • Edge laplacian
    • Edge NM suppression
    • Erode
    • Evaluate mask segmentation
    • Evaluate segmentation
    • Fill objects
    • Find edges
    • Histogram summary
    • ID objects
    • Multi-paint
    • Open
    • Particle analysis
    • Power paint
    • Skeletonize
    • Standard deviation threshold
    • Ultimate erode

4.0.1 (10/12/2007)

• File handling
  • Fixed Image-offset tag value in MIPAV XML files saved from some other formats.
  • Fixed the XML image header file name set for new images created as a result of some algorithms.
  • Fixed an error which would occur when writing Dicom images with some types of sequence tags to the MIPAV XML format.
  • Found and resolved a bug in writing some datasets to the Nifti (.nii) format.
  • Modified the Minc reader to support 4D volumes.
  • An optional tag indicating the dataset slice thickness has been added to the MIPAV XML file format specification.
  • Fixed a problem with handling some version number strings in the NRRD file reader.
  • The NRRD file format has been added to the Medical file type filter used in the Open and Save image dialogs.
• Algorithms
  • Fixed VOI region processing in multiple algorithms:
    • Find edges
    • Particle analysis
    • Thin
    • Prune
    • Ultimate erode
    • Laplacian
  • Removed 2.5D processing option from Particle analysis algorithm dialog.
  • The Extract brain (BET) algorithm now defaults the 'Axial brain orientation' parameter to selected when using an Axial image.
  • Fixed some data value wrap-around issues when running the Laplacian algorithm. New images generated are now always stored in a float datatype. When replacing the source image, the result data values are scaled to fit within the source image datatype (when necessary).
  • When running the Frequency filter algorithm with the replace source image option, the image datatype is now forced to float.
  • Fixed a bug in the Homomorphic frequency filter.
  • When running the Anisotropic diffusion algorithm with the replace source image option, the result data is rescaled if it does not fit within the source image data range.
  • Fixed 2.5D VOI region processing for some combinations of images and parameters in the Laplacian algorithm.
  • Improved the Median filter algorithm dialog and made traditional filtering the default choice.
  • Fixed the AHE local algorithm progress bar for 2D color images.
  • Fixed the display of the wavelet image under certain conditions in the Wavelet threshold algorithm.
  • Removed duplicate data output by the Colocalization regression algorithm.
  • Fixed a small bug in the subsampling routine of the Entropy minimization algorithm.
  • When running the Principal components algorithm, the filtered and average destination image values are rescaled if they exceed the image data type range.
  • Fixed a problem in the Maximum likelihood iterated blind deconvolution algorithm resampling routine.
  • Fixed a bug in the processing of 2D images with the Two MRI images signal-to-noise ratio algorithm.
  • The Subsample algorithm now copies over VOIs from the original image to the result volume.
  • Fixed a few small interface issues in the Transform algorithm dialog.
  • Fixed the behavior of 2D and 3D B-Spline registration progess bars.
  • Constrained optimized automatic registration is now disabled for 2D images.
• Utilities
  • Correct image spacing now operates on all image formats, not just MIPAV XML. It also handles situations where correction is not needed more gracefully.
• VOIs
  • Added a VOI splitter tool, which allows the user to divide one VOI into two.
  • VOI statistic values are now saved in the Parameter set portion of the header of MIPAV XML images.
  • Added sum intensities to the list of available VOI statistics in the VOI properties dialog and VOI statistics generator.
• Paint
  • The buttons to Hide masks and paint in the Multipaint dialog now update the Tri-Planar view as well.
  • Added the ability to Lock/Unlock all masks in the Multipaint dialog.
  • A number of Power paint dialog upgrades have been made:
    • Support for color images has been added.
    • The Threshold GUI has been changed to spinners.
    • Added the ability to use the thresholds during paint growing and dilation.
• Image views & visualization
  • Added support for reading and writing of VTK XML surface files (*.vtp).
  • Added the ability to adjust the raytracing step size in the GPU-based volume renderer.
• Help topic updates and additions
  • Advanced paint
  • Edge dection
  • Histogram tools
  • Morphology
  • Segmentation
  • Utilities
• Miscellaneous
  • Added tools for DTI image segmentation and visualization.
  • Masks created and placed into the ImageB slot are now named according to the current ImageA volume.
  • The Insight Toolkit Kit (ITK) dlls distributed with the 32-bit Windows MIPAV installers have been updated to version 3.2.0.

4.0.0 (09/07/2007)

• File handling
  • Fixed problem reading in multiple matrices in MIPAV's XML image file format.
  • When converting from Minc to DICOM, we now ignore Sequence tags stored within the Minc header since they are generally not stored in a consistent format.
  • Improved the memory management of the Nifti file reader and writer.
  • Fixed the saving of orientation and other header information when converting non-Nifti files to the Nifti file format.
  • Fixed a bug in data type handling for some DICOM files.
  • Fixed a problem in the PAR/REC file reader.
  • Fixed a bug in the Afni file reader.
  • Fixed the image offset value when saving XML files from other image file formats.
  • Fixed a bug reading in encapsulated DICOM files.
• Algorithms
  • Fixed a memory leak in the Colocalization EM algorithm.
  • Added option to insert padding into an image before running the Subsample algorithm to make the image extents divisible by the sub-sampling factor.
  • The Histogram summary now allows the user to specify the summary minimum and maximum.
  • Fixed a bug in the BET algorithm.
  • Fixed the Separable edge laplacian algorithm progess bar for 2D images.
  • Fixed the Auto covariance progress bar.
  • Fixed the Subsample dialog's expected extents labels for 2D images.
  • Fixed a problem in the Subsample algorithm's memory management.
  • Removed the bandpass and bandstop options from the Frequency filter algorithm for Gaussian filters.
  • Solved a progress bar problem for the Adaptive path smooth algorithm.
  • Disabled Boundary attenuation algorithm for 2D images.
  • Fixed a memory management problem in the Coherence enhancing diffusion algorithm.
  • Added a kernel error check for the separable Gradient magnitude algorithm.
  • Fixed a bug in processing a VOI region with the Gradient magnitude algorithm.
  • Fixed a bug in processing a VOI region with the Erode algorithm.
  • Fixed a bug in processing a VOI region with the Distance map and Background distance map algorithms.
• Utilities
  • Fixed Crop utility when Replace image was selected. Also fixed a memory issue when cropping DICOM images. Fixed a problem with a warning dialog which popped up when no VOIs were selected.
  • Fixed a bug in the Pad utility's handling of 3D RGB images when Replace image was selected.
  • Fixed a crash when attempting to run the Rotate utility on 2D, non-DICOM images.
  • Added the option to threshold an image before generating its Maximum intensity projection using the MIP utility.
  • The Flip utility no longer displays the option to flip 2D images along the Z axis.
  • Fixed bounds checking problem in RGB concatenation utility.
  • The Quantify using mask utility can now be run on RGB images. It also outputs the mean and standard deviation for grayscale or RGB images. The mask can be loaded from a file or from an image frame.
• VOIs
  • Improved the progress bar of the Rubberband livewire VOI tool.
  • Fixed a bug in the Smooth VOI with the Replace original contour option selected.
  • When VOI graphs are generated, the mean and standard deviation is now output to the data window.
• Image views & visualization
  • Added a new hardware-shader-based volume rendering system. It is based on a port of the WildMagic libraries to Java. It currently requires a modern Nvidia graphics card and is a beta release.
  • Fixed initial zoom of Tri-planar view on some datasets.
  • Fixed a problem with the magnification when the zoom is set below 1x.
  • Added a new XML surface file format that references a .sur file, which contains the surface mesh data (resulting in faster surface loading).
  • Improved speed of Talairach Tri-planar view.
  • Added support for the .vtk legacy surface file format.
  • Fixed a bug in the saving of VRML and WRL surface file formats.
  • Added the ability to view surfaces within the volume renderer without viewing an image volume.
  • Fixed a number of minor bugs in the Java3D volume renderer.
• Scripting
  • Fixed a problem when executing a script with CloseFrame actions from the Run script dialog.
• Painting
  • The Power paint tools are now disabled for 2D images.
  • Extracting a paint mask to a new image now uses the correct paint intensity.
  • Fixed problem when collapsing paint and mask layers for RGB images in the Multi-paint dialog.
  • Fixed an error in the Multi-paint dialog when a RGB imageB is present.
  • The Paint calculator button now calculates total intensity, mean intensity and standard deviation of the painted region.
• Miscellaneous
  • Added installer support for 64-bit Windows systems.
  • MIPAV installers for Windows and Linux systems now include Java virtual machine 1.6.0_02, JMF 2.1.1e, Java3D 1.5.1, Jogl 1.1.0 and Nvidia Cg Toolkit 1.5.
  • Added BIRN data provenance 2.0 support. This information may be tracked globally and for each image. The provenance data can then be saved to an xml format along side an image file (with an .xmp file extension). It records algorithms and utilities applied to an image volume (i.e., the image's history) and information about the version of MIPAV used.
  • Many improvements and additions have been made to the MIPAV help. A few of the changes include:
    • Added Talairach transform topic.
    • Added MIP utility topic.
    • Updated Quick start chapter.
    • Updated Plugins section.
    • Updated Dicom browser topic.
    • Updated Segmentation topic.
  • Fixed a problem with the image frame resize handling on some systems.
  • Fixed some minor problems in the uniform and gaussian random number generators.
  • Added some SRB security measures:
    • 10 SRB login failure lockout.
    • 30 minute SRB inactivity auto-logout.
    • NDAR privacy notice on successful SRB login.
  • Removed BIRN Xcede-related features.
  • Changed PlugInAlgorithm and PlugInView interfaces to remove the ViewUserInterface parameters from their run() methods.

3.1.6 (06/20/2007)

• File handling
  • PAR/REC save support added.
  • Fixed the DICOM directory anonymizer's handling of directories which contain some non-dicom files.
  • DICOM files are now saved with explicit VRs for the 0002 tag group.
  • The DICOM receiver also attaches 0002 group tags with explicit VRs to the files it receives.
  • The DICOM sender now allows the user to select multiple files to send, skipping any that are not DICOM files.
  • When saving an image as a DICOM file, the Patient age tag (0010,1010) no longer needs to be entered with leading zeros into the Save dicom dialog.
  • Fixed the reading of DICOM images that do not have a DICM preamble.
  • Fixed the saving of individual 2D slices from a 3D XML image.
  • Fixed a problem saving Analyze files with file names longer than 18 characters.
• Algorithms
  • Added Barrel distortion correction algorithm.
  • Fixed a bug in the Fuzzy C means algorithm.
  • Fixed a problem in the Median filter that caused it to ignore its standard deviation parameter.
  • The Transformation dialog now allows for both a transformation and a resampling to be performed at the same time.
• Utilities
  • Added a utility to add padding to an image.
  • Cropping an image without creating a new image now properly updates the image matrices.
  • Help topics have been added for many algorithms.
  • The Quantification utility now uses the individual slice resolutions to make volume calculations.
• VOIs
  • Fixed copy/paste of VOIs.
  • Fixed handling of poly-slice line selection/deselection.
  • Fixed a problem loading some scanner coordinate VOIs.
• Image views & visualization
  • Fixed issues with saving/loading XML surface mesh files in the Volume renderer.
  • The Extract surface algorithm now can produce an XML surface mesh file.
• Scripting
  • Fixed an error in the scripting of the Median filter algorithm.
• Miscellaneous
  • Fixed a problem opening the Multi-paint dialog or creating a new mask with some DICOM images.
  • Fixed a bug where the paint cursor was not getting changed when an image B was open in the Tri-planar view.

3.1.5 (05/31/2007)

• MIPAV 3.1.5 fixes a major file read/write bug in the 3.1.4 release of MIPAV. See the cumulative listing of changes for the many enhancements and changes which were included in MIPAV 3.1.4.
• Fixed a major series of bugs in the handling of dialogs which pop up when the user reads or writes some file types in version 3.1.4. These bugs prevented some file types from being read or saved properly.
• Added a new toolbar icon to link all images with dimensions similar to the current image frame. When the slice of this image is changed, all of the similar images also change their displayed slice.
• When the Multi-paint dialog changes the current paint color, the paint cursor now also changes color to match it.

3.1.4 (05/29/2007)

• File handling
  • Major refactoring of the DICOM reader and the manner in which DICOM tags are stored. This has resulted in a doubling of the read speed and a halving of the memory required for many DICOM datasets.
  • Added sorting to the file listing in the Open image sequence dialog.
  • Fixed a bug in the PAR/REC reader when the directory containing the files included the strings 'par' or 'rec'.
  • Fixed some issues with NIFTI orientations and the orientation of 2D NIFTI files.
  • Corrected the image file names stored when a GE Genesis 5x, GE Signa 4x and Magnetom Vision dataset is read in.
  • Multi-file datasets with very large numbers (e.g., a dataset UID) in their file names can now be opened. The number is truncated so that it fits within a long and can be compared to the numbers found in other file names.
  • Fixed a problem in reading in multi-file Analyze images.
  • Fixed a bug reading some big endian DICOM files.
• Algorithms
  • Fixed the progress bar in the Unsharp mask algorithm.
  • Updated the 'Registration: Manual 2D Series' help topic.
  • Updated the Brain surface extractor and Brain extraction tool help sections.
  • Maximum likelihood iterated blind deconvolution now resamples the input image to a power of 2 automatically and fixed the algorithm's progress bar.
  • Updated the Maximum likelihood iterated blind deconvolution help section.
  • Added help topics for the 'Talairach transform' and 'FANTASM' dialog boxes.
  • Modified Particle analysis dialog to allow for selection of kernels for the close operation.
  • The Threshold algorithm now defaults the threshold min and max to the min and max of the image.
  • Updated the Threshold algorithm help topic.
• Utilities
  • Mask to paint conversion now operates properly on a RGB image.
  • Added a new help section for the Maximum intensity projection utility.
  • Added the ability to force the result image to contain float values in the Image math dialog.
  • Added a new utility which converts a 4D image with one, two, or three volumes into a RGB image (1st volume -> Red, ...).
  • Quantify mask now checks to see if the input image is a mask image by requiring the difference between its max and min to be less than 100.
  • Added help topic for the Image calculator utility.
• VOIs
  • Added an option in Help -> MIPAV options to save VOIs in either file coordinates (the old method) or in Left-Posterior-Superior coordinates (the new method).
  • An option has been added to the Tri-planar view which forces the Protractor VOI to snap to increments of 90 degree angles when it is released.
• Image views & visualization
  • Resolved an error in the Tri-planar view when the Paint grow dialog was closed and the used clicked in the image.
  • Added the option to extend the Tri-planar view crosshairs so that they intersect.
  • Added the option to link the Tri-planar crosshairs to the original image, so that scrolling through the image slices in the Tri-planar causes the original image frame to do the same.
  • Fixed the performance of the Lightbox view.
• Scripting
  • A script action with no images and no VOIs is now handled correctly.
  • When using raw images in a script from the Run script dialog or from the command line, information about the raw file may be specified before it is opened to prevent the Raw image dialog from opening (select multiple images and right click them in the image listing in the Run script dialog; use the '-r "type;xDim,yDim;xRes,yRes;xUnits,yUnits;endianess;offset"'... option from the command line).
  • Fixed the scripting of the Invert utility.
  • More image attribute changes are now scriptable:
    • Endianess
    • Modality
• Miscellaneous
  • Changed the handling of image matrices within MIPAV. Images may now have multiple matrices, each marked as being of a particular type (e.g., Scanner anatomical (transform to get the dataset coordinates to axial orientation), or Registration (to another dataset). Multiple matrices are now saved in the MIPAV Image XML file.
  • Removed passing of ViewUserInterface from many class constructors and methods. Call ViewUserInterface.getReference() instead. Plug-in methods using ViewUserInterface have been deprecated and will be changed to remove the ViewUserInterface parameter in 3 months.
  • Fixed painting so that it follows the user's cursor as expected when approaching the border of a pixel.
  • The Screen capture utility now adds '_screenCapture' to the name of the original image when naming the generated image and keeps the dialog open after each capture to facilitate capturing multiple windows.
  • Resetting the LUT for RGB images now updates the image immediately.
  • Performing a Quick LUT will now update the Histo/LUT dialog immediately if the dialog is visible.
  • Fixed the Otsu and Maximum entropy thresholds.
  • Added the ability to select the RGB components of the applied paint (and optionally keep the original image date intact for the other channels).
  • Added right click menus to the Quick mask and Paint-to-mask toolbar buttons to allow for either in-place or into-new-image processing.
  • New toolbar icons have been added to indicate buttons which can have their behavior altered by right clicking on them (e.g., the zoom/unzoom buttons and the masking buttons).
  • Added a new help topic titled 'Connecting to SRB BIRN from MIPAV'.

3.1.3 (03/30/2007)

• File handling
  • Added read-only support for Philips PARREC files (.rec/.frec).
• VOIs
  • Fixed the VOI Flip depth operation.
  • The thickness of the lines which make up a VOI can now be adjusted.
  • Fixed VOI contour smoothing.
• Scripting
  • Many image attribute changes are now scriptable:
    • Orientation
    • Origin
    • Resolution
    • Units
    • Talairach
    • Transform
• Miscellaneous
  • Added ability to create and save custom paint brush shapes.
  • Added the option to only include some intensity levels while painting to the Advanced paint dialog.
  • MIPAV is now available for download and use by researchers from any type of organization (non-profit, government, commercial, or an individual).
  • Fixed some bugs in the display of scanner coordinates when dragging through an image with certain orientations.

3.1.2 (03/05/2007)

• File handling
  • Fixed reading of MIPAV image xml files with unknown orientations.
  • Improved the DICOM browser study and series parsing, sorting and image preview.
  • Fixed a problem reading 2D, 3D and 4D TIFF images. Also reduced memory usage of TIFF reader.
• Algorithms
  • Major problems with the Manual 2D registration tool have been resolved.
  • Documentation for 2D histogram, B-spline registration, Face anonymization, and Transform to power of 2 has been added to the MIPAV help system.
• Utilities
  • Fixed the updating of the image origin after the Crop utility is run.
  • The image Flip utility now can also flip VOIs within the image as well.
• VOIs
  • The points that comprise a VOI are now saved in scanner space when written to MIPAV's xml VOI format, instead of voxel or pixel space.
  • The Flip VOI tool now only flips the selected VOI contours.
  • Re-organized the VOI-related items in the MIPAV menu bar and the VOI right-click menu.
  • Added a new xml format used to save VOI Annotations (a text label with optional arrow) (saved with the extension '.lbl').
  • Fixed the adding of points to VOI contours when the 'Draw new contours without holding [SHIFT]' option is enabled.
• Scripting
  • Added scripting documentation to the MIPAV help system.
• Miscellaneous
  • Allow collapsing of masks/paint to a single value in the Multi-paint dialog.
  • Shortcuts have been added to the Multi-paint dialog for faster paint mask editing.
  • Plugins packaged as tar and tar.gz files may now be installed in MIPAV.
  • Plugins may now be assigned keyboard shortcuts using the Shortcut editor.
  • Fixed SRB uploading of xml/raw image datasets.
  • Fixed a bug in downloading and opening .nii files from an SRB repository.

3.1.1 (02/07/2007)

• File handling
  • Fixed a bug where saving an image multiple times to analyze, spm, or nifti format would cause an error.
• Algorithms
  • Fixed a bug that would occur when OAR was run on an image with no VOIs.
  • Updated the help for the FRAP algorithm to better reflect the equation used.
• Image views & visualization
  • Re-enabled the radiological voume view in the Tri-Planar view.
  • The Tri-Planar views can now be zoomed in and out independently using two new buttons. After clicking the one of the independent zoom buttons click within one of the Tri-Planar views to zoom it; hold down the shift button to continue zooming.
• Scripting
  • Re-enabled the ability to delete images and VOIs selected for use in a script from within the Script Run dialog.
  • The Script Toolbar now shows each script's filename, not the whole path.
• Miscellaneous
  • Holding down the shift key while clicking the previous slice/next slice buttons or using the mouse scroll-wheel with an image selected now synchronizes the current slice displayed for all images with the same number of slices as the current active image.
  • Left-clicking within an image now displays the position and intensity of the image location the mouse is placed over next to the mouse cursor. The color of this text can be changed through the MIPAV options dialog.
  • Re-enabled the q -> quickLUT default shortcut that was disabled in version 3.1.0.
  • MIPAV plugins stored as tar and tar.gz files can now be installed into MIPAV.

3.1.0 (01/26/2007)

• File handling
  • Fixed some image position tag precision errors when reading and writing DICOM files.
  • Fixed DICOM communication compatibility problems with the GE and XNAT DICOM servers.
  • Improved handling of saving of files without providing a file extension in the Save image as dialog.
• Algorithms
  • Adaptive median filter added.
  • Added documentation for Maximum likelihood iterative blind deconvolution algorithm.
  • Added support for 2.5D processing in the Fill objects algorithm.
  • Fixed a problem in detection of errors encountered while executing the 2.5D BSpline registration algorithm.
  • Resolved problems which prevented context-sensitive help for some algorithms from appearing correctly.
  • The Threshold algorithm now can produce a masked image (of the same type as the original image), a binary mask, or a short mask.
  • Added 2.5D processing capability to the Level set and Level set diffusion algorithms.
  • Fixed a bug in Histogram generation with the VOI XOR option enabled.
  • Improved face anonymizer algorithm results.
  • Fixed some problems in the 2D Histogram calculation and visualization.
  • Added Cumulative histogram algorithm.
  • The BET Brain extraction algorithm initial center of mass calculation has been improved.
  • Fixed a bug in the Manual 2D serial registration tool on Linux systems.
  • Added Histogram matching documentation.
  • The Optimized automatic registration methods now automatically transform any VOIs in the source image into the space of the result image.
• Utilities
  • Fixed bug in X and Y axis rotations.
  • Fixed bug in progess bar of the Flip utility.
• VOIs and painting
  • Multiple improvements to the multi-paint tool (mask intensity values are now editable, VOI import/export added).
  • VOI interiors can now be shown with a semi-opaque or fully opaque coloring.
  • Added a button to the paint toolbar to toggle display an opaque border around painted regions.
• Image views & visualization
  • Added support for texture mapped or per-vertex intensities from an arbitrary image volume onto surfaces in the Texture-mapped Volume renderer.
  • Added the ability to paint on surfaces with a variety of tools in the Texture-mapped volume renderer.
  • Added Maximum intensity projection view of a 3D volume.
  • Fixed an issue with Talairach visualization in the Tri-planar view.
• Scripting
  • Fixed a minor scripting bug in the Replace value utility.
  • Fixed the saving and loading of the image and VOI file selections from the Script run dialog.
• Miscellaneous
  • Fixed the setting of default keyboard shortcuts in MIPAV.
  • Fixed window resizing and freeze-up problems which occurred on some systems.
  • Image endianess can now be altered in the Image attributes dialog.

3.0.1 (11/22/2006)

• File handling
  • Fixed 'Save image' for XML images (was saving to imagename.xml.raw).
  • MINC modality attributes are now read by MIPAV, if present.
  • The Save DICOM dialog now sets the modality chooser (for DICOM tag 0008,0060) based on the image's modality.
  • When saving a PET image from another format to DICOM, MIPAV now calculates the intensity rescaling slope and intercept for each slice, allowing for floating point intensities to be stored.
  • MIPAV now sets the image valid-range attribute in MINC headers it writes based on the range of the type of data being written instead of the image intensity ranges (e.g., -32767 to 32767 for a short image). Using the intensity ranges caused problems when the image's minimum and maximum values were too close together and the data was being rescaled to from short to floating point values.
  • Corrected a bug in how MIPAV calculated the x start and y start attributes for MINC images. They are now centered within the first voxel of the image.
• Algorithms
  • Thresholding (Algorithms -> Segmentation -> Threshold) can now produce a short mask image.
  • Optimized the memory management of the Maximum likelihood iterated blind deconvolution algorithm (Algorithms -> Microscopy -> Restoration -> Maximum likelihood iterated blind deconvolution).
• Utilities
  • Fixed the scripting of flipping the Z-axis of an image (Utilities -> Flip -> Depth).
• VOIs
  • A bug in the livewire VOI tool has been fixed.
  • Fixed VOI grid overlay display.
• Image views & visualization
  • Fixed the volume renderer (Image -> Views -> Volume renderers) cube orientation.
  • Fixed a bug in the volume renderer's arbitrary clipping plane.
  • Fixed the linked frame update in the Tri-planar view (Image -> Views -> Triplanar).
• Scripting
  • Improved VOI support in scripting system.
  • Fixed a bug which prevented running a script on multiple images opened from disk.
  • Fixed some drag-and-drop annoyances in the Run script dialog (Scripts -> Run script).
  • Plug-ins may now specify new package locations where MIPAV should look for scriptable actions (see ScriptableActionLoader.addScriptActionLocation(String)).
• Miscellaneous
  • Fixed some minor annoyances in the Multi-paint dialog.

3.0.0-2006-11-14 (11/15/2006)

• A completely re-written scripting/macro system:
  • Improved script readability, robustness, and error reporting.
  • A new, simplified, drag-and-drop interface for executing scripts (Scripts -> Run script).
  • The new system is not backwards compatible. Scripts created with versions of MIPAV before 3.0.0 are no longer supported. Please re-record your scripts using MIPAV 3.0.0 or above..
  • Installers for the last nightly build of MIPAV before our integration of the new scripting system are available upon request.
• The MIPAV coordinate translation system has been consolidated, improved, and simplified.
• A MIPAV installer for 64-bit linux systems is now available from our downloads section.
• An upgrade to the version of InstallAnywhere that we use to create MIPAV's installers should result in the resolution of a number of installer problems on 32- and 64-bit Linux systems.
• A new and improved progress bar system for algorithms and utilities.
• File handling
  • The Z-dimension resolution in MIPAV is now the distance between the centers of two adjacent slices. It is no longer the slice thickness.
  • The default names given to images stored in clinical file formats uses the general format [study-number]_[series-number] (e.g. 1394_2) instead of the patient or file name.
  • MIPAV is now able to open some file formats when the files do not have extensions, without prompting the user.
  • Multiple images may be opened simultaneously from the Open file dialog (File -> Open image (A) from disk).
  • Added user-defined file filters (Help -> MIPAV options).
  • Fixed the optional saving of XML headers with Analyze image files.
  • Improved the MIPAV XML 3D surface format.
  • Color RAW files with 2, 3, or 4 colors can now be read.
  • Added support for complex double RAW files.
  • Many improvements and bug fixes have been made in the following formats:
    • Bruker
    • DICOM
    • GE Sigma 5X
    • Magnetom vision
    • MINC
    • NIfTI
    • XML multi-file datasets
  • The following file formats are now supported:
    • GE Sigma 4X
    • MGH / MGZ
    • NRRD
• Algorithms
  • A bug in the Erosion (Algorithms -> Morphological -> Erode) and Dilation (Algorithms -> Morphological -> Dilate) morphology operations has been fixed.
  • Some improvements have been made to the IHN3 correction algorithm (Algorithms -> Shading correction -> Inhomogeneity N3 correction)
  • Algorithms to calculate Signal-to-noise ratios for MRI images has been added (Algorithms -> SNR)
  • The Fuzzy C-Means algorithm (Algorithms -> Segmentation -> Fuzzy C-means -> Single channel) now produces unscaled probabilities in a float image instead of probabilities scaled by the input image intensities when performing a fuzzy segmentation.
  • The Fuzzy C-Means algorithm now labels the classes it produces 1, 2, 3, ... when performing a hard segmentation.
  • Added non-negative garrote and SCAD thresholding to Wavelet thresholding algorithm (Algorithms -> Filters (wavelet) -> Thresholding).
  • Fixed a matrix bug in the Transform algorithm (Algorithms -> Transformation tools -> Transform).
  • The Extract surface algorithm (Algorithms -> Extract surface (marching cubes)) now allows for blurring before surface extraction.
  • Improved memory management in a few algorithms.
• Utilities
  • The Mask utility has been renamed to Fill image (Utilities -> Fill image).
  • The Pad slices utility has been renamed to Pad slices to power of 2 (Utilities -> Slice tools -> Pad slices to power of 2).
  • Improved memory management in a few utilities.
• VOIs
  • An internationalization error in the VOI statistics generator (VOI -> Statistics generator...) has been fixed.
  • Added a continuous contour VOI drawing option (without holding down the Shift key) (Help -> MIPAV options).
• Image views & visualization
  • Added neurological viewing convention to the Volume Renderer's (Image -> Views -> Volume renderers) Tri-Planar view.
• Miscellaneous
  • The PowerPaint tools have been improved.
  • ImageB can now be separated from the ImageA it is loaded with (File -> Extract image (B))
  • The T key may be used to toggle between viewing ImageA and ImageB intensities when two images are loaded.
  • A number of obsolete plugins distributed with MIPAV have been removed.
  • Running a script with the -hide command line option automatically causes MIPAV to exit once the script has completed.

2.7 (06/23/2006)

• File handling
  • When saving from MINC to DICOM, the minc header is checked for a DICOM-converted intance number tag (0020,0013), and that number is used as the base instance number for each slice of the new DICOM image.
  • Fixed the DICOM browser tag selector dialog column sizing on some Linux systems.
  • All file open/save progress bars now respect the -hide command line option.
• Algorithms
  • Fixed bugs in Subsample, Transform, Direct resample, IHN3 correction, and Transcode algorithms.
  • Allow two types of vector filtering instead of just one for Median and Mean filter algorithms of color images.
  • The interface used to indicate whether an algorithm should be run in a new thread has been changed slightly (this may break some Plugins, requiring them to be changed and recompiled).
• Utilities
  • Paint to Mask conversion fixed for color images.
• VOIs
  • Fixed VOI properties and VOI statistics calculation and tabbing of center of gravity data.
  • Fixed VOI statistics calculation of center of mass for the first rectangle VOI contour in an image.
  • The user can now select the number of digits to calculate to after the decimal point and whether to force the display of trailing zeros in the VOI properties and VOI statistics dialogs.
  • Fixed VOI select-all operation.
  • Fixed a bug in the execution of MaskToVOI script actions with large VOIs.
• Miscellaneous
  • Two bugs in the creation and resizing of image frames on Linux systems have been fixed. These bugs caused MIPAV to intermittently freeze when new images were created by algorithms on some systems.

2.6 (06/09/2006)

• File handling
  • Refactored and improved consistency of image origin determination for all file types.
  • MINC
    • Saving DICOM to MINC now exports all non-array (value multiplicity) DICOM tags to the MINC header.
  • DICOM
    • Saving to DICOM from MINC now exports all DICOM-style tags in the MINC header (a partial set of tags was being exported previously). Tags the user wants to export must be in the MIPAV DICOM dictionary(dicom_dictionary.txt in the MIPAV install directory).
    • Fixed calculation of slope and intercept when saving from MINC to DICOM.
    • When saving to DICOM from another format, the DICOM tag dialog is skipped if a script is being executed.
    • When saving to DICOM from another format, "(0020,0032) Patient position" and "(0020,1041) Slice location (patient)" are now generated for each DICOM slice.
    • DICOM receiver now handles DICOM images with implicit/explicit group two tags.
  • Interfile
    • Support for more image information has been added.
  • NIfTI
    • Fixed sign errors when reading and writing the header.
  • Analyze
    • The user can now decide to always save .img files in Analyze format in the MIPAV options dialog.
• Algorithms
  • Color edge has been added to the list of available spatial filters.
  • Added density-based clustering algorithm.
  • Blind deconvolution
    • Fixed blind deconvolution for 2D grayscale and color images.
    • Added 3D blind deconvolution for grayscale and color images.
    • Added optional microscope-based constraints to blind deconvolution.
  • Option added to do vector median filtering of color images.
  • Option added to do vector mean filtering of color images.
  • Added cell-tracking to the active gradient vector flow boundary algorithm.
  • Fixed a bug in the fill holes 3D morphology operation.
• Utilities
  • Added the ability to rotate an image about the X, Y, and Z axes by 180 degrees.
  • Added the ability to create a 3D or 4D mask for image B of a 4D image (only did so for image A previously).
  • Added utility to find blank slices and replace each with the average of the two adjacent slices.
• VOIs
  • Fixed crash when the VOI statistics dialog is closed.
  • Fixed VOI center of mass calculation in the VOI properties dialog.
  • Much of the VOI interaction code has been refactored to more easily handle contours which span multiple slices.
  • VOI -> Mask operations now produce a new image of the type of mask generated, not the type of the original image (same for Paint -> Short mask).
• Image views & visualization
  • Fixed some problems with the Tri-planar view's crosshairs when using the scroll wheel to move through the image.
• Miscellaneous
  • Image header and attributes buttons have been added to the image toolbar.
  • The File and Help menus have undergone a major reorganization.
  • Scripting menu items have been moved to a new top-level menu.
  • Fixed placement of the output window.
  • Fixed the installation of .jar/.zip plugins (the directory structure of the archives are retained).
• BIRN
  • SRB image open/save and file transfer.
  • DICOM PACS to SRB auto-upload with tag anonymization (after execution of arbitrary pre-upload script -- i.e., Face de-identification).

2.5 (05/02/2006)

• Fixed Minc-to-Minc file saving.
• The Open image sequence dialog (File -> Open image sequence) has been improved. Lexigraphical sorting of files is enforced and the deletion of the previously-used directory is gracefully handled.
• Fixed the drawing of the Triplanar view (Image -> Views -> Triplanar) crosshairs and bounding box display on some image orientations.
• Fixed a bug in the transformation (Algorithms -> Transformation tools -> Transform) of 2D images.
• Added more interpolation methods to the Transformation dialog.
• The MIPAV Secure chat and file transfer utility (File -> Secure file transfer & chat) has been removed.
• (Algorithms -> Brain tools -> Face anonymization) has been renamed to (Algorithms -> Brain tools -> Face de-identification).
• Polyline slice VOI updates -- fixed deletion, and fixed the output of slice distances.
• VOI properties (VOI -> Properties...) now calculates values using time-slice information for 4D images.
• Fixed the behavior of the VOI buttons when changing VOI types.
• Improved the output of the VOI statistics dialog.
• Fixed selection of point VOIs when zoomed in on an image.
• Added logic to allow 4D paint-to-mask functionality.
• An interface for a new type of "Generic" plugin has been added, allowing users to create plugins which do not require the user to open an image before using them. See the PlugInGeneric javadoc for more information.
• Added new Maximum likelihood iterated blind deconvolution (Microscopy -> Restoration -> Maximum likelihood iterated blind deconvolution) method which works better than the old Iterative blind deconvolution (Microscopy -> Restoration -> Iterative blind deconvolution) method.

2.4 (04/17/2006)

• Fixed an error in the image browser (File -> Image browser) when the user treid to open a series of images into separate frames.
• A brute-force registration option has been added to the Mosaic registration tool (Algorithms -> Registration -> Mosaic).
• A handful of bugs in the match images tool (Utilities -> Match images) have been resolved.
• Fixed a problem with the Surface Composite view in the texture volume renderer (Image -> Views -> Volume renderers).
• Improved handling of NIfTI files.
• Improved handling of Bruker image files.
• Floating point MINC files can now be saved as DICOM files.

2.3 (03/31/2006)

• Added a tree view of the VOI structures to the VOI properties dialog (VOI -> Properties...), allowing the user to see and select individual contours on slices.
• Improved Mosaic registration (better blending, and now works with grayscale, color and large images) (Algorithms -> Registration -> Mosaic).
• Changed default directory of the Browse button in the Open Image Sequence dialog (File -> Open -> Open image sequence) to remember the last used directory, or use the user's home directory.
• Fixed Image quick list keyboard shortcuts (Ctrl + num).
• Alt + key shortcuts cannot be used anymore. Alt may be used with Ctrl or Shift.
• Added Multi-paint tools (See the Power paint tools button at the end of the Paint toolbar), developed by Pilou Bazin at Johns Hopkins University.
• MIPAV once again checks that the memory allocations in the LAX/preferences file match by default.
• Slice spacing has been added to the resolutions panel of the Image attribues dialog (Image -> Attributes -> Edit attributes).
• Added a Gabor filter (Algorithms -> Filters (Gabor)).
• Fixed some errors writing NIfTI files.
• When writing .img files, a dialog now pops up to ask the user whether the file should be written as Anaylze or NIfTI.
• The interface for File Plugins has changed. See the MIPAV API documentation for more details.
• Fixed a problem where Algorithm Plugins were sometimes launched twice.
• Added more unique colors to the striped LUT.
• Fixed some problems with the handling of Minc files.
• Fixed a bug where MIPAV would freeze when the Open graph dialog (File -> Open graph) was cancelled.
• Tri-Planar view (Image -> Views -> Triplanar)
  • Fixed an error in Tri-Planar view region grow.
  • Fixed the scale of the crosshairs in the Tri-Planar view when the user zooms in and out.
  • Added thin-plate spline and least squares registration functionality to the Tri-Planar view.
  • Fixed generation of coordinate change events when the mouse wheel is used to change slices.
  • Fixed Tri-Planar frame linking.

2.2 (03/10/2006)

• Some bugs in DM3 file support have been found and fixed.
• Fixed conversion of some DICOM and MINC files to NIfTI format.
• Fixed a bug in the volume calculation of thresholded LUTs.
• Fixed reading of XML files saved with a color LUT.
• Gaussian blur (Algorithms -> Filters (spatial) -> Gaussian blur) in-place processing of 3D images was fixed.
• Added the ability to replace removed slices (Utilities -> Slice tools -> Remove slices).
• Fixed installation of .zip and .jar plugins (Plugins -> Install plugin).
• Added scripting to:
  • VOI -> Mask -> VOI
  • VOI -> Paint -> VOI
  • VOI -> Paint -> Short mask
  • VOI -> Save VOI -> Save all VOIs
  • VOI -> Save VOI -> Save all VOIs to...
• Fixed scripting of:
  • VOI -> VOI -> Mask -> VOI(s) to binary mask
  • VOI -> VOI -> Mask -> VOI(s) to short mask
  • VOI -> VOI -> Mask -> VOI(s) to ubyte mask
• Fixed a bug that prevented disabling irrelevent menu items depending on the current image type.
• A new and experimental GPU-shader-based rendering mode has been added to the Raycast volume renderer (Image -> Views -> Volume renderers).

2.1 (03/03/2006)

• The TriPlanar view (Image -> Views -> Triplanar) has stabilized and is now fully functional.
• A new, interactive method for registration of images into 2D mosaics has been added (Algorithms -> Registration -> Mosaic).
• New tabs can now be created by algorithms to display output data. The contents of these tabs can then be saved to a file. This action is also scriptable.
• Keyboard shortcut customization and handling has been improved.
• The menus in MIPAV have been greatly reorganized and their layout has been changed slightly.
• The font used in menus is now customizable.
• Reading of complex image data has been added.
• Fixed some problems with reading of GE Signa 5X files.
• The Open File dialog now remembers the status of the Multi-file checkbox between MIPAV sessions.
• Minc file attributes can now be anonymized (both dicom-converted attributes and minc-specific attributes).
• When saving a Minc file to Dicom, any dicom-converted attributes in the Minc header are retained in the new Dicom file.
• The Dicom Save dialog now provides a button that fills in required tags with auto-generated data.
• Support for the DM3 file format has been added.
• Fixed a number of problems in the handling of NIfTI files.
• Added option to show the name of VOIs name instead of their label.
• The user's VOI XOR preference is now correctly retained.
• A greatly improved Face Anonymization (Algorithms -> Brain tools -> Anonymize face) algorithm has replaced the old method.
• A label in the LUT window (LUT -> Histogram - LUT...) now shows the thresholded voxel volume.
• Scripting fixes:
  • Algorithms -> Brain tools -> Extract brain surface (BET)
  • Algorithms -> Brain tools -> Extract brain surface (BSE)
  • Algorithms -> Filters (spatial) -> Gaussian blur
  • Algorithms -> Filters (spatial) -> Gradient magnitude
  • VOI -> Statistics generator...
• Volume renderer (Image -> Views -> Volume renderers)
  • Button to enable all clipping planes.
  • The clipping planes can now be used to remove data from the original image volume.
  • 3D stereo view of the volume is now available.
  • Improved ray-cast renderer performance by 20-30 percent.

2.0 (02/01/2006)

• MIPAV is now packaged with Java 1.5 (also known as JRE 5.0), Java3d 1.4beta3, and JMF 2.1.1e. Solaris remains packaged with Java 1.4.2 and an older version of Java3D. In the future Solaris releases of MIPAV may not install a JVM. The Macintosh release of MIPAV remains the same, working with Mac OS X 10.3 or higher (JVM 1.4 or 1.5).
• The user's choice of toolbars is now remembered automatically when selections are made in the Toolbar menu.
• A -m option has been added to open multi-file images from the command line.
• Fixed a problem with the Shortcut editor (Help -> Shortcut options).
• Skeletonize requires 2.5D processing of 3D images.
• Bug in Transform algorithm's (Algorithms -> Transform) matrix inversion has been fixed.
• Watershed algorithm (Algorithms -> Watershed) energy file reuse fixed.
• Fixed scripting of face anonymizer.
• The Image Math dialog (Algorithms -> Image math) now can calculate the absolute value of an image or the average value of all of a volume's slices.
• Improved DICOM file reader and header parser.
• Fixed a bug in the writing of DICOM files from MIPAV.
• NIfTI file handling changed and improved significantly. Please email us with any problems you encounter.
• Handling of MINC files has also been improved.
• The user can now change the resampling method when opening the Volume Renderer view (Image -> Views -> Volume renderers).
• VOI changes:
  • Added the ability to delete the active point from VOI contours by pressing SHIFT + DEL.
  • VOI line info can be printed out through CTRL + left click.
  • Moving VOIs around updates the user interface with the active point's current location.
• The Tri-Planar view (Image -> Views -> Triplanar) continues to improve and is nearing completion:
  • All VOIs and painting should now work in this view.
  • Added option to use old view (which is remembered whenever the Tri-Planar view is opened).
  • Methods ending in _XY, _ZY, and _XZ have been changed to _AXIAL, _SAGITTAL, and _CORONAL (constants with those names changed too).

1.60 (01/13/2006)

• The functionality provided by the Dual Tri-Planar view has been collapsed into the Tri-Planar view (Image -> Views -> Triplanar). When a second image is loaded, the Tri-Planar image display changes to show both images, shown as it was in the Dual Tri-Planar view. Region growing and bounding cube operations are still being refactored and do not function correctly in this release. Position information is now shown in a separate window accessible from the menu item (Options -> Show volume coordinates and talariach controls) in the Tri-Planar frame.
• Added the ability to read and save surfaces in a new XML format.
• Scripting support has been added the the Fill Objects algorithm (Algorithms -> Morphological -> Fill holes)
• Scripting and user-defined ranges are now supported by the Replace Value utility (Utilities -> Replace pixel/voxel value).
• Nearest neighbor output interpolation has been added to the various OAR registration methods.
• Image subsampling (Utilities -> Subsample) now supports transforming VOIs within the image.
• Show costs (Algorithms -> Registration -> Display pixel similarity cost functions) now supports 2D images.
• Fixed the VOI perimeter statistic in the VOI property dialog.
• A new image padding utility has been added (Utilities -> Pad with slices)
• A bug in adjusting the paint opacity has been fixed.
• Fixed an issue with 0 to 1 LUT adjustment for image B.
• Point VOIs can now be shown as one of four different images: normal, normal with the center pixel removed, an X, and an X with the center pixel removed. Which one is used can be changed through the MIPAV Options dialog (Help -> Program options).
• Selected VOI points can now be adjusted through use of the arrow keys.
• 2.5D processing is now supported in the Skeletonize algorithm (Algorithms -> Morphological -> Skeletonize).
• Handling of multi-file images when loading a second image into a frame is now consistent with the process for reading in the first image.
• A number of bugs in the Light Box view (Image -> Views -> Light box) have been addressed.
• Miscellaneous bug fixes and improvements have been made in the following areas:
  • Algorithms -> Segmentation -> Graph based
  • Algorithms -> Threshold
  • Algorithms -> Transform
  • Algorithms -> Transform to power of 2
  • Utilities -> Add image margins
  • Utilities -> Insert slice
  • Utilities -> Match images
  • Utilities -> Noise

1.59 (12/12/2005)

• Fixed a problem when running the software when the MIPAV configuration directory does not already exist ($HOME/mipav), which would prevent MIPAV from running unless the directory was manually created. If not found, it is now created automatically.
• The TriPlanar view (Image -> Views -> Triplanar) has been greatly improved and most functions should now function correctly. Coordinate display, mouse wheel navigation, painting, and VOI operations for all image orientations now work.
• When the TriPlanar view is open, clicking with the middle/scroll button in the original image will center the TriPlanar view at the clicked point.
• If MIPAV is run without a GUI (i.e., with the -hide option), encountering an error will cause the software to exit with an abnormal value (1).
• Snap-to-pixel behavior while painting has been finished and is no longer an option that can enabled or disabled.
• Both active and non-active scripts generated by MIPAV can now be used interchangeably.
• The Crop utility (Utilities -> Crop) now always creates a new image.
• Opening the Volume Renderer (Image -> Views -> Volume Renderers) by clicking the padding button when no padding is necessary no longer causes an exception.
• Miscellaneous bug fixes and improvements have been made in the following areas:
  • Algorithms -> Fuzzy C-means -> Multispectral
  • Algorithms -> Histogram equalization -> Neighborhood adaptive
  • Algorithms -> Histogram equalization -> Regional adaptive
  • Algorithms -> Image calculator
  • Algorithms -> Extract brain -> Extract brain surface (BSE)
  • Algorithms -> Morphological -> Particle analysis
  • Algorithms -> Registration -> Constrained optimized automatic registration
  • Algorithms -> Registration -> Optimized automatic registration
  • Algorithms -> Registration -> Optimized automatic registration 2.5D
  • Algorithms -> Registration -> Optimized automatic registration 3.5D
  • Algorithms -> Registration -> Landmark -> Least squares
  • Algorithms -> Transform
  • File -> DICOM browser
  • Writing of some TIFF image files.

1.58 (11/18/2005)

• Multifile and single file images are now opened from the same menu item (File -> Open new image(A)) and how an image is opened is controlled by a checkbox in the File Selection dialog.
• Fixed a number of issues when using MIPAV to receive DICOM images over a network (File -> DICOM receiver on/off).
• The drawing and display of images has been greatly improved. It is now faster, with reduced flicker when moving VOIs and the mouse cursor. The interpolated mode of displaying images has also been updated, allowing for either image A or image B or both to be interpolated independently and making it so that paint on an interpolated image does not appear interpolated (blurry). Work on updating the TriPlanar view (Image -> Views -> Triplanar) to make use of these improvements is continuing and should be available in the next version of MIPAV. Users who need to paint or perform other operations in the TriPlanar view besides simply viewing images should not upgrade at this time.
• An option in the MIPAV Options dialog (Help -> Program options) now allows for the user to choose whether the paint cursor should exhibit snap-to-pixel behavior.
• Added Haralick texture feature measurements algorithm (Algorithms -> Filters (spatial) -> Haralick texture).
• Added a utility which will replace all occurrences of one value in an image with another value (Utilities -> Replace value).
• A number of algorithms have been fixed:
  • Algorithms -> Edge detection -> Zero X laplacian
  • Algorithms -> FFT
  • Algorithms -> Filters (frequency)
  • Algorithms -> Filters (spatial) -> Mode
  • Algorithms -> Filters (spatial) -> Nonmaximum suppression
  • Algorithms -> Filters (spatial) -> Unsharp mask
  • Algorithms -> Fuzzy C-means -> Multispectral
  • Algorithms -> Shading correction -> Inhomogeneity N3 correction
• Running scripts on multiple images from the command line has been fixed.
• Work is continuing on updating and improving Volume Renderer (Image -> Views -> Volume renderers).
• The Volume Renderer now has been tested with the latest versions of Java 1.4 and 5.0 (1.5) on Mac OS X 10.4.

1.57 (10/28/2005)

• The Load Image dialog (File -> Load -> Image(B) from frame) now has the "Match orientations of two images." and "Use image origin information to align images." default to being selected.
• The Save As dialog (File -> Save image as) now defaults to the image's filename.
• Fixed the handling of the image resolution when saving an XML file from a DICOM image.
• Two 2D images can now be matched (Utilities -> Match images).
• Multi-file images can now be opened from either the Open Image dialog (File -> Open new image(A)) or the Open Multi-file dialog (File -> Open multi-file(A)) through the use of a checkbox.
• Reduced the amount of flicker of progress bars and defaulted them to appearing in the center of the screen.
• Added snap-to-pixel logic for the paint brush cursor.
• The Paint Grow dialog has been improved, among the changes are better support for region grows in color images and from the Dual-Triplanar view (Image -> Views -> Triplanar - dual)

1.56 (10/14/2005)

• Many of MIPAV's keyboard shortcuts can now be used when an image frame is selected, not just when the main UI window is selected.
• A Graph-based segmentation algorithm (Algorithms -> Segmentation -> Graph based) has been added.
• The Extract slices (Utilities -> Extract slices / volumes) utility now provides more information to the Output window when run.
• A new set of "power" paint tools have been added to the paint toolbar.
• When the order of slices is randomized (Utilities -> Randomize slice order), the slice mapping is now printed to the data tab of the Output window.
• The paint grow dialog now allows the user to enter in arbitrary upper and lower threshold deltas.

1.55 (09/30/2005)

• Choosing an image out of a multi-file image set through the File -> Open new image(A) menu item now only opens that image, not any of the others in the series. To open the full multi-file image set, use the File -> Open multi-file(A) menu item. Multi-file image sets show up in the recently used images list of the File menu with (M) appended to their file name.
• The DICOM reader has been fixed so that images with singular transformation matrices can still be read.
• The Rotation utility now correctly sets the new image's orientation.

1.54 (09/26/2005)

• Plugins packaged in jar or zip files can now be installed through MIPAV (Plugins -> Install plugin). The class files in these archives are unpackaged into the MIPAV plugin directory in the user's home directory.
• Fixed an error when the user canceled the dialog which allows for the loading of a second image from a file.
• Clicking the New Mask toolbar button with a color image now creates a mask image that is also a color image-type.
• Fixed the display of the count in the logarithmic mode of the Histogram (LUT -> Histogram - LUT).
• Changing the window and level functions by clicking and dragging in the image window now works for color images.
• The user can now open an image's header information (Image -> Attributes -> View header) by pressing CTRL-H while the image's window is selected.
• The user can now open an image's image information editing dialog (Image -> Attributes -> Edit attributes) by pressing CTRL-E while the image's window is selected.
• A problem in the DICOM receiver (File -> DICOM database access) has been resolved and debugging output has been updated to only appear when the "Comms" debugging option is turned on.
• Added support for the reading of the DICOM YBR_FULL_422 JPEG compressed images.
• Reading and writing of DICOM RGB images has been improved.
• Improved the saving of DICOM files, most notably by saving in lexigraphically correct order of image file names (e.g., foo0001.dcm, foo0002.dcm, ..., foo0010.dcm, ...).
• Saving/opening of linked images has been fixed.
• Fixed the reading of MINC label files.
• Fixed an issue reading some LSM image files.
• The MRC image handler now writes image header information correctly when only a subsection of the slices are saved.

1.53 (09/12/2005)

• The Mask utility (Utilities -> Mask) now works with color images.
• Fixed the copying of image headers after slices are removed (Utilities -> Remove slices).
• Fixed an issue in the numbering of anonymized images (File -> Anonymize DICOM directory).
• Fixed a minor issue in the ordering of VOIs in the VOI Extraction algorithm (VOI -> Mask -> VOI).

1.52 (09/02/2005)

• The reading and writing of a number of different image types has been greatly sped up. The speed of some algorithms which do many image buffer imports and exports has also been improved.
• Improved the adding of linked images in MIPAV XML image files.
• A new system for specifying the amount of debugging output to display has been added to the options dialog (Help -> Program Options). Current options include minor, algorithm, file and communication messages.
• We are continuing to refactor and improve the volume renderer (Image -> Views -> Volume renderers) and its opacity controls.

1.51 (08/26/2005)

• Fixed bug in handling of some LSM files.
• Fixed a bug in the reading of some TIFF files.
• Fixed a problem where MINC images were being written out upside down.
• Improved the memory management of VOIs.
• Resolved problem with the alpha blending of fused images within the volume renderer.

1.50 (08/19/2005)

• The appearance of a number of windows on Mac OS X has been fixed, including the Tri-Planar view and the Volume Renderer.
• Image frames, the Output window, and the Animation window now have new icons which differentiate them from the main user interface window in the taskbar.
• Image Math (Algorithms -> Image math) now handles complex images.
• The Image Calculator (Algorithms -> Image calculator) no longer destroys phase information when clipping complex image values.
• Flipping (Utilities -> Flip) now works with complex images.
• Handling of LSM files has improved slightly.
• Fixed bugs when opening or closing masks generated from the Paint Toolbar.
• The flexibility of the Image Sequence Loader (File -> Open image sequence) continues to improve.
• Fixed a bug in the zero-padding of filenames in the DICOM receiver (File -> DICOM database access).
• Fixed an error in the labeling of VOI contours created by the Rubberband Livewire method.
• Fixed the loading of the linked image when an image is opened using the Recently Used Image list.

1.49 (08/12/2005)

• MIPAV has a new splash screen.
• The UI no longer is displayed when the -hide option is used from the command line.
• Improved memory management in the Image Sequence Loader (File -> Open image sequence).
• Added an option to load any grayscale image scaled to the range 0-255 from the Image Sequence Loader (File -> Open image sequence).
• The LightBox, Tri-Planar, and Volume Renderer views now each have special icons which are displayed in the corners of their windows and on the taskbar.

1.48 (08/05/2005)

• Holding down the 'Q' key now enters Quick LUT mode.
• Images can now be subsampled as they are being loaded from the Image Sequence Loader (File -> Open image sequence).
• Window and Level adjustment sliders have been added to the Image Sequence Loader.
• Added the option to add blank padding slices to an image volume to have the dimensions be powers of two when loading it into the Volume Renderer (Image -> Views -> Volume renderers).
• Added a surface area calculation to surfaces within the Volume Renderer.
• When switching between surfaces in the Surface tab in the Volume Renderer, the opacity and shininess sliders now update correctly.
• The behavior of the Particle Analysis algorithm (Algorithms -> Morphological -> Particle analysis) has been fixed.
• The menu items for RGB -> Gray, RGB -> Grays, RGB -> HSB, and Grays -> RGB in the Utilities menu work correctly once more.
• Fixed an error where the image produced from an AND mask operation did not have the original image's attributes.
• Enhanced the LSM file reader to handle Ziess format 3.5.
• Fixed a bug related to an assumed directory structure in the XCOSM algorithm (Algorithms -> Microscopy -> Restoration -> XCOSM_EM).
• Improved the BET Brain Extractor (Algorithms -> Extract brain -> Extract brain surface (BET)) segmentation slightly.
• Constructors for FileIO and ViewJFrameImage which take ViewUserInterface objects have been deprecated. All other constructors which take ViewUserInterface will be deprecated over the course of the next month or so. Eventually, these constructors will be removed completely. ViewUserInterface has been changed to be a singleton class, meaning that there is only one occurance of it anywhere within MIPAV. The practical upshot of this is that plugin writers will have to adjust to use the new constructors as they are added, and use the function ViewUserInterface.getReference() if they need to use the user interface for something.

1.47 (07/29/2005)

• Ctrl-C/X/V now copy/cut/paste selected VOI contours within an image.
• The DICOM/image overlays have been improved, allowing for prefix strings to be added to tags displayed in the image.
• Running the Median filter (Algorithms -> Filters (spatial) -> Median) on VOI regions has been sped up significantly.
• Fixed resetting of the LUT when painting into a image, when the paint intensity is between the image's min and max values.
• The dialog used to open multi-channel Image Sequences (File -> Open image sequence) (formerly the TIFF Image Sequence dialog) now handles all image types and has had a number of other improvments.
• An option has been added to the FRET efficiency algorithm (Algorithms -> Microscopy -> FRET efficiency) to show the efficiency image.

1.46 (07/22/2005)

• A method for opening multi-channel TIFF image sequence has been added (File -> Open TIFF sequence).
• Added an algorithm to attenuate an image along the boundaries of VOIs placed within it (Algorithms -> Filters (spatial) -> Boundary attenuation).
• Whether the DICOM and/or image overlays should be shown is now saved in the MIPAV preferences file and remembered at each startup (Image -> Show image/DICOM overlay).
• Buttons to open and save a user-defined LUT have been added to the main MIPAV toolbar.
• The Transformation dialog (Algorithms -> Transform) now allows for the matrix which will be used to be automatically inverted before the transformation is applied.
• Some of the menu items have been altered slightly, so that their names make some more sense and the capitalization scheme is followed consistently.
• Resolved some issues reading in LSM files.
• Improved memory usage of Coherence Enhancing Diffusion (Algorithms -> Coherence-enhancing diffusion).
• Fixed auto-rotation image capture of the Raycast Renderer (Image -> Views -> Volume renderers).
• Fixed sizing of the Tri-Images in the Volume Renderer (Image -> Views -> Volume renderers) when the window is maximized.

1.45 (07/15/2005)

• The MIPAV API documentation has been updated and is available online.
• The DICOM Receiver now pads the instance number of received images.
• A new Paint toolbar button has been added to allow for the paint on the current slice to be erased. Another button erases all of the paint in the image volume.
• The undo button on the Paint toolbar now reverses one level of any paint change (including region growing).
• The FFT (Algorithms -> FFT), Autocovariance (Algorithms -> Autocovariance coefficients) and Autocorrelation (Algorithms -> Autocorrelation coefficients) algorithms no longer crash when run.
• Fixed a bug in the viewport clipping plane, in the Volume Renderer (Image -> Views -> VolumeRenderers).
• Histogram Summary (Utilities -> Histogram summary) can now be run on the entire image or just VOIs.
• Improved handling of nested objects and holes in VOI to mask conversion.
• Dragging of non-contour VOIs has been fixed.
• The MIPAV splash screen now displays the version of MIPAV in the title bar.
• In the SUV PET Plugin, more parameters are available for user review and modification.

1.44 (07/08/2005)

• The Image browser now properly cleans up the preview images it uses and removes them from the image registry.
• An option has been added to the 3D OAR Registration (Algorithms -> Registration -> Optimized automatic registration) method to perform a Least Squares registration (Algorithms -> Registration -> Landmark - Least Squares) and then a OAR registration on the resulting volume.
• When running a script in MIPAV from the command line, relative paths to images specified with -i will be searched for in the current working directory of the user's terminal when he or she runs MIPAV. This directory will be set to be the new default directory for MIPAV to look for images in, the default directory will also be changed to the path to an image the user specifies with -i if the path is absolute.
• When the -hide option is specified, the text which would appear in a dialog if MIPAV was running normally is now printed to the terminal's standard error.

1.43 (07/01/2005)

• A crop function has been added to the VOI pop-up which appears when a VOI is right clicked.
• When raycast rendering in the MIP and DDR modes in the Volume Renderer, fixed an issue which caused the LUT to not update when changed.
• Simplified method calls needed to change the image displayed by the TriImage and DualTriImage views. Only calls to the methods setImageA() and setImageB() should necessary.
• An error in the Inhomogeneity N3 Correction (Algorithms -> Shading correction -> Inhomogeneity N3 correction) algorithm has been corrected.
• DCCIE convertsion (File -> DCCIE Image Conversion) now copies TIFF files from the old directory to the new directory automatically.
• The DICOM parser now properly handles tag 0018,1164 Imager Pixel Spacing.
• Fixed exception which happened when transforming (Algorithms -> Transform) an image and its VOIs.
• Mask images are now created with the correct file information from the original image.
• Dialogs with Gaussian fields, now accept values in the range (0.0 - 10.0) instead of (0.5 - 5.0).
• When dialog parameter saving is enabled in the Program Options (Help -> Program Options), dialogs which normalize the Z scale of gaussians no longer save the normalized value.
• The Nonmaximum Supression algorithm (Algorithms -> Filters (spatial) -> Nonmaximum suppression) now saves its parameters when the feature is enabled in Program Options.

1.42 (06/28/2005)

• Scrolling the mousewheel in the Tri-Planar view now changes the displayed slice.
• The user can now change the image slice displayed from within the Surface Plotter view.
• Right clicking on the zoom buttons on the toolbar allows the user to change between exponential (1x, 2x, 4x, 8x, ...) and linear zoom (1x, 2x, 3x, 4x, ...) increments.
• Fixed a bug which caused the Tri-Planar view to initially display a different slice of an image than shown in the position labels.

1.41 (06/27/2005)

• The plane displayed by the arbitrary clipping pane in the Volume Renderer (Image -> Views -> Volume Renderers) can now be extracted to a new image.
• Fixed a bug where image origin information was not being copied when a mask was extracted from a VOI (VOI -> VOI->Mask).
• Fixed bug which prevented opening of DICOM files once a DICOM image was cloned.
• Added paint propagation buttons to the paint toolbar (Toolbars -> Paint toolbar).
• Added a new color LUT optimized for display of bones in the Volume Renderer.

1.40 (06/20/2005)

• A memory usage monitor and garbage collection button have been added to the main MIPAV window.
• The Zoom controls now only perform one magnification / de-magnification when the user clicks in the image. Holding down Shift allows for multiple Zoom actions. Right clicking in the image does the opposite of the selected Zoom action. (i.e., If Un-Zoom mode has been selected, right clicking would cause the image to zoom in, while a left click would un-zoom the image.)
• Fixed issue reading in some TIFF files.
• Added support for an additional method of identifying data type for BRUKER files (e.g., ip_short).
• The algorithm history log now includes a timestamp.
• Cropping (Utilities -> Crop) can now be performed by using a VOI or entering parameters into a dialog.

1.39 (06/09/2005)

• Fixed handling of saving unsigned short DICOM files to Analyze format. These files are now saved as signed short Analyze files since unsigned short DICOM images typically range between 0 and ~1000. MIPAV will now also read in the non-standard-compliant unsigned short Analyze images which some previous versions of MIPAV would save.
• More improvements have been made to the DICOM browser (File -> DICOM browser).
• If an image's units or Z dimension resolutions differ by more than a factor of 20, a warning dialog is brought up.
• Fixed loading of multi-image sets when the numbers in the file names are not padded with zeros.
• Added scripting support to Least Squares Registration (Algorithms -> Registration -> Landmark - Least Squares).
• Added scripting support to Thin Plate Spline Registration (Algorithms -> Registration -> Landmark - TPSpline).

1.38 (06/02/2005)

• The DICOM browser's (File -> DICOM browser) table display of DICOM tags has been improved. It can now be configured to show custom tags, the columns can be rearranged by the user and the tag columns are sortable.
• Replace Slice (Utilities -> Replace slice) allows the user to replace a slice with another open image.
• Saving of point VOIs fixed.
• Histogram calculation for images with a large range of values has been sped up.
• Talairach VOI extraction bug fixed.
• Button added to toolbar for inverted masking of the currently selected VOI contours.
• BET (Algorithms -> Extract brain -> Extract Brain Surface (BET)) initial sphere size tweaked slightly.
• Utilities -> Invert now displays a dialog which gives the user the option of placing the inverted image in a new frame or the source image frame.

1.37 (05/24/2005)

• New PDFs of recent MIPAV course presentations have been placed in the documentation section of our website.
• Mac users no longer need to install Java WebServices.
• The Image Calculator (Algorithms -> Image Calculator) now works with complex images.
• The default directory for saving files is now the directory of the currently open image.
• Fixed user defined lut and transfer function save/load.
• Scripting support added for extract slices volume.
• Added ability to put a prefix on images saved within a script.
• The splash screen no longer shows up when MIPAV is run with the -hide option.
• Fixed bug closing image frames in a script.
• Fixes made in AFNI file support.
• VOI -> Paint Mask now only operates on selected voi contours.
• Polyline VOIs can now be closed into polygons.
• Arbitrary clipping plane behavior in the Volume Renderer has been fixed.
• Texture aligned rendering mode available again in 3D texture rendering.
• Fixed talairach position information display in tri-planar view.

1.36 (05/13/2005)

• The Algorithms -> Extract brain -> Extract Brain Surface (BET) and Algorithms -> Extract brain -> Extract Brain Surface (BSE) algorithms can now optionally extract the brain as paint instead of masking off the brain from the original image.
• On Windows systems, the MIPAV installer now places msvcp71.dll and msvcr71.dll, which are required by the ITK libraries, into %SystemRoot%\System32 if they are not already located there.
• More improvements to Dicom file handling.
• VOI -> Paint -> Mask now works for 2D and 3D images.
• The VOI statistics file is now saved in the current image's directory.
• VOI Statistics (VOI -> Statistics Generator...) and Properties (VOI -> Properties...) now handle XOR VOIs correctly.
• A number of fixes to the Histogram (LUT -> Histogram - LUT) dialog when imageB is loaded.
• The masking intensity button on the paint toolbar has been replaced by a spinner.
• Opening an image from the recently opened image list now sets the current default directory to that image's directory.
• More improvements to Talairach support.

1.35 (05/10/2005)

• Fixed handling of encapsulated JPEG Dicom files.
• "QuickMask" Utilities -> Mask shortcut button added, which runs the mask algorithm with the default parameters.
• Holding down Crtl while in paint mode erases paint.
• Added Mask -> Paint conversion menu item.
• LUTs are now 1-based by default.
• An image of the LUT with transfer function points indicated on it can be saved to disk (LUT -> Histogram - LUT).
• Points on the transfer function can now be redistributed at even intervals.
• Fixed reading of VOI files for which the user does not have write permission.
• The VOI statistic dialog (VOI -> Statistics Generator...) is now scriptable.
• VOI statistic information can now be saved to a location the user specifies as a text file.
• Fixed error when opening the lightbox view (Image -> Views -> Light Box).
• More talairach fixes have been made.
• Algorithms -> Extract Surface -> Cube has been renamed to Algorithms -> Extract Surface (marching cubes).
• The extract surface dialog now allows the user to select the format that the surface mesh is saved as (either text (.txt), surface (.sur), or VRML (.wrml)).
• In the extract surface dialog, the surface file directory is now shown in the tooltip of the surface file name.
• Improvements have been made to the surface boundary view in the volume renderer's plane renderer.
• Added $home/mipav/plugins and $home/mipav/plugins/plugins.jar back into MIPAV's classpath.
• Fixed error when starting mipav when $home/mipav/mipav.preferences doesn't exist.

1.34 (05/06/2005)

• Talairach support improvements:
  • MIPAV's XML image header now includes a section containing Talairach information.
  • Talairach tab added to the image attributes dialog (Image -> Attributes -> Edit attributes).
  • Tri-planar view (Image -> Views -> Triplanar) now loads the image into Talairach space when the information is present in the image's XML header.
  • Talairach information can be read from Medic's file format into the Talairach section of MIPAV's XML header.
  • The transformation dialog (Algorithms -> Transform) can now transform an image with Talairach information into Talairach space.
• The layout of the Image Browser (File -> Image browser) has been improved.
• The Image Browser now shows .tiff files.
• When saving (File -> Save image) an image to a file name which already exists, the user is now prompted before the file is overwritten.
• The Zoom In and Zoom Out toolbar buttons now stay activated after the user's first click in the image (holding down Shift is no longer necessary).
• The sharpness of the paint border has been improved when an image is being shown in interpolated mode.
• The user can now switch to a 1-based LUT (LUT -> Histogram - LUT).
• Fixed a number of NullPointerExceptions in the image and tri-planar image frames.
• Preliminary support for invocation of ITK methods from within MIPAV. See Algorithms -> Insight Toolkit -> Gaussian blur for an example. ITK dll files are included with the Windows release of MIPAV. Users on other platforms must compile the ITK libraries and Java bindings and place them in /path/to/mipav/InsightToolkit/bin/.

1.33 (04/21/2005)

• A new option has been added to the command line. -o (or -O) allows the user to specify the name of an output file for the scripting command SaveImageAs.
  Usage example:
  
  save.sct:
  SaveImageAs $active .xml
Exit

C:\>"C:\Program Files\mipav\mipav.exe" -i c:\images\oldimg.xml -s c:\images\save.sct -o newimg -hide
  This would read in oldimg.xml and save it as newimg.xml.
• The CT Presets dialog has been altered to allow the user to specify a custom set of thresholds for CT images.
• A number of useful image masking tools have been added to the paint toolbar.
• The behavior of the Zoom In and Zoom Out toolbar buttons has been changed. The user must now click within the image, causing it to change the image's magnification while centering the image on the clicked point. Holding the Shift key while clicking allows the user to Zoom In or Out multiple times.
• The user can now center the image window on a specific point by holding down Control when clicking within the image.
• Holding down the shift button while in paint mode allows the user to move the mouse to paint without holding down the left mouse button.
• The Program Options dialog (Help -> Program Options) has been reorganized and the color of the VOI rubberband can now be altered.
• Histogram Summary (Utilities -> Histogram summary) now allows the user to specify a number of b