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MIPAV Changelog

What's new in MIPAV 7.0.1

Oct 24, 2013
  • File handling:
  • DICOM: When trying to open an image with a Transfer Syntax UID that indicates that it is a compressed DICOM, but with an image tag length that implies that it is not compressed, try reading it in without decompression.
  • DICOM: Fixed a problem in the DICOMDIR browser that prevented it from opening.
  • Fixed a problem in the Open sequence tool with the use of progress bars that caused crashes for some file formats (this means that there are no progress bars when opening the sequence).
  • Algorithms and utilities:
  • Added new utility for correction of non-helical CT gantry tilt correction.
  • Fixed some issues running the Prostate segementation algorithm on some systems.
  • The DialogDefaultsInterface has been added back. JDialogBase now implements this interface and provides default versions of the loadDefaults() and saveDefaults() methods.
  • VOIs and paint:
  • The backspace key now behaves the same as delete when working with VOIs to delete points or entire curves (which fixes issues with using an Apple keyboard on Windows).
  • Image views and visualization:
  • Added better handling of when the GPU volume renderer when the videocard doesn't support the required OpenGL or GLSL version.
  • When opening the renderer, apply the LUT that is already set for the image.
  • Miscellaneous:
  • Fixed some issues with scripting plugins that have JDialog in their name.
  • PlugInAlgorithm plugins now are displayed even when no image is open (but are disabled).
  • Fixed some issues in handling command line arguments that start with two dashes instead of one.
  • Added buildSlider() method to GuiBuilder.
  • Auto-restart of MIPAV after a memory change on Windows is no longer supported.
  • MIPAV is now started the same way on 32 and 64 bit systems. Shortcuts to start with or without a debugging window are now installed.

New in MIPAV 5.3.3 (Aug 24, 2011)

  • File handling:
  • Analyze: Fixed a bug in changing the image origins.
  • DICOM: Rewrite of many parts of DICOM reading and writing, improving performance.
  • DICOM: Corrected some invalid Value Representation values in the DICOM dictionary.
  • DICOM: Fixed a JPEG2000-related bug.
  • MATLAB: When writing, boolean images are converted in unsigned byte, since boolean is not a valid MATLAB data type.
  • Algorithms and utilities:
  • Fixed handling of Nifti file info in the Reorientation utility.
  • Fixed a bug in performing the Rotate utility on 4D images.
  • Fixed over-verbose registration algorithm debug printouts.
  • Improved display in Replace slice utility.
  • Added initial version of a new algorithm to convert a 3D mosaic image to a 4D image.
  • Fixed the Reorientation utility.
  • Added Color saturation transformation algorithm.
  • Added a progress bar to the Rotate utility.
  • Fixed a bug in the multi-threaded version of the FFT algorithm for some images.
  • The Frequency filter algorithm is no longer disabled for color images (2D/2.5D processing only).
  • The Gabor filter algorithm is no longer disabled for color images.
  • VOIs and paint:
  • Fixed a bug where the pointer cursor was not getting set properly after using the paintbrush.
  • Fixed some issues with scripting the VOI statistics generator.
  • Image views and visualization:
  • Multiple interface and functional improvements to the multi-histogram GPU volume rendering module.
  • Added tick marks to GPU volume renderer bounding box.
  • Fixed a problem linking Tri-planar views when not using the 2x2 view format.
  • The active image color border size is now configurable in the MIPAV options dialog.
  • The GLSL GPU volume rendering shader system now dynamically generates the shader program based on the options selected by the user in the GUI. This results in a significant performance boost due to reduced shader branching.
  • Miscellaneous:
  • Fixed a number of debugging output issues.

New in MIPAV 5.3.2 (Jun 22, 2011)

  • File handling:
  • DICOM: Added support for encapsulated lossy JPEG2000 files.
  • DICOM: Added new "AT" dicom tag element to correctly read pointer information.
  • DICOM: Added new save option to gui for saving DICOM and non-DICOM files in enhanced DICOM format (3D and 4D).
  • DICOM: Fixed some sequence length bugs.
  • MATLAB: Fixed a bug in the allocation of the buffer used to decompress MATLAB files.
  • TIFF: Changed the MAX_IFD_LENGTH to 100000.
  • XML: When opening an image with a linked image, fixed a bug where the LUT of the linked image would not get loaded.
  • Algorithms and utilities:
  • Added scripting support to Tranform non-linear.
  • Corrected Transform non-linear naming for JIST.
  • In the Transform dialog, when opening a matrix from file, both center and origin rotation are enabled.
  • The ACPC dialog has been improved, addressing a number of bugs.
  • Improved layout of Haralick texture algorithm dialog.
  • Added a tool to concatenate multiple 3D volumes into a new 3D volume.
  • Fixed a bug in the 3D Ultimate erode morphology algorithm.
  • The OAR, Least squares, and Thin-plate spline registration algorithm dialogs now allow the user to specify a directory where the matrix or deformation files should be saved.
  • Fixed a bug in the Change type utility which caused problems correctly choosing values for some data types (mostly binary).
  • The BSE Brain segmentation algorithm now uses the morphological fill holes operation to more correctly address interior holes in the generated mask.
  • VOIs and paint:
  • Fixed error in max statistics calculation, if first element was not in range and all values were < 0, MIPAV would incorrectly report max as 0.
  • VOI statistics calculations now ignore NaN values.
  • Image views and visualization:
  • Improved multi-histogram shader in the GPU volume renderer.
  • Added NVidia-based stereo mode back into the GPU volume renderer.
  • Fixed GPU renderer on Java Web Start release of MIPAV.
  • Further bug fixes to the GPU volume renderer.
  • Added ability to animate checkerboard view.
  • Fixed bugs in surface mask creation, which improves performance when the surface changes.
  • Fixed errors initializing the DTI visualization framework.
  • Miscellaneous:
  • Added the ability to start up ImageJ from MIPAV and exchange images between the two programs.
  • Added the ability to open ImageJ plugins from MIPAV.
  • Added the ability to compile and run plugins for MIPAV and ImageJ from within MIPAV.
  • Added "GPU enabled" status button next to the Multi-core button on the MIPAV status bar to indicate OpenCL support.

New in MIPAV 5.3.1 (Jun 10, 2011)

  • VOIs and paint:
  • Improved the memory usage of VOIs.
  • Image views and visualization:
  • Modified multi-histogram blending in the GPU volume renderer.
  • Added keyboard shortcut ('s') to save the GPU volume renderer view to a .jpg file.
  • Miscellaneous:
  • Fixed a an issue with the Image overlay preferences.
  • Fixed a case-sensitivity issue when (re-)installing plugins on some OSes.
  • Improved error handling during plugin installation.

New in MIPAV 5.2.0 (Jan 25, 2011)

  • File handling:
  • DICOM: Added support for Siemens mosaic image private tags.
  • DICOM: Fixed a bug in the reading of some 4D enhanced DICOM files.
  • JPEG/GIF/other: Added support for writing out a number of non-medical image formats when the image is not contained within an image frame.
  • MATLAB: Added support for Matlab .mat files.
  • Analyze: Fixed image file checking routine issue.
  • Minc: 64-bit Mac versions of the jHDF libraries are not currently available. Fixed the handling of not finding the libraries when trying to determine the type of a given file.
  • Bruker: Fixed some problems in the selection of data files and added support for more fields.
  • LIFF: Removed support for LZO compressed LIFF files.
  • Removed DCCIE conversion code.
  • Algorithms and utilities:
  • Fixed memory leak in Insert slice utility.
  • Restructured a number of base mathematical classes to use different b-spline, optimization and integration routines.
  • Added extended precision versions of a number of mathematical classes.
  • Improved performance of VOI landmark registration with new VOI system.
  • The RGB to gray utility now properly updates the (0028,0002) and (0028,0004) DICOM tags to match the image data, if run on a DICOM image.
  • Added Complex concatenation utility.
  • Added Complex to real conversion utility.
  • Added more options to Maximum intensity projection algorithm.
  • The Flip and Reorient utilities now correctly update the matrix and origin of DICOM and NIFTI files.
  • Fixed two errors in level eight of OAR 3.5D registration. OAR 3.5D should be used instead of the now-removed TSOAR.
  • Linked in a working version of the Diffusion levelset ITK method. Also, added geodesic active contour and threshold level set filters.
  • Made ITK levelset filter algorithms scriptable and compatible with JIST.
  • Fixed a bug in handling some Afni files using the ACPC dialog.
  • Fixed a problem handling VOIs confined to one slice in the Watershed algorithm.
  • VOIs and paint:
  • Fixed some issues with choosing custom VOI colors.
  • Fixed VOI colors when using the Preset hue and New VOI buttons.
  • Fixed VOI colors when using Load all VOIs from...
  • Fixed a problem when generating VOI stats with no VOI selected.
  • Fixed an issue handling unaffected curves during VOI splitting.
  • Improved the bounding-box scaling of VOI contours.
  • Added optional field to text annotation files (.lbl).
  • Added a tool to "manually" evolve 2D VOI boundaries. The user can specify the amount to shrink/grow a contour in image units (i.e., mm).
  • Added the ability to convert point VOIs to mask images, in addition to the other VOI types.
  • The VOI statistics generator has been modified to make it extensible by plugins.
  • Fixed issues with the VOI statistics generator in some situations.
  • Added the ability to exclude some intensity ranges from VOI statistics calculation.
  • Added VOI logical operations utility (replaces 'Allow VOI holes' option).
  • Fixed a problem with the VOI livewire's determining when to finish VOI construction.
  • Fixed VOI contour point deletion while holding down the shift key.
  • Added ability to create circles using the VOI ellipse tool while holding down the CTRL key. The circle diameter can also be directly edited by the user by right clicking.
  • Added ability to create squares using the VOI rectangle tool while holding down the CTRL key. The square length can also be directly edited by the user by right clicking.
  • Image views and visualization:
  • The GPU volume renderer no longer requires images to be resized to a power to two in each dimension.
  • The GPU volume renderer now calculates the gradient magnitude and laplace images on-demand (on checking the grad mag check box or the multi-histogram check box).
  • Added the ability to link scrolling of images of unequal dimensions.
  • Added a + bi and re^itheta displays for complex data when dragging in the image.
  • The surface colors in the volume renderers should now exactly match the colors used for VOIs (based on the striped LUT).
  • Fixed bugs in DTI visualization framework. Systems analysis - DTI now works as expected.

New in MIPAV 5.1.0 (Sep 16, 2010)

  • File handling
  • PARREC: Improved reader support of some axis orientations.
  • DICOM: Fixed DICOMDIR preview and opening of images.
  • DICOM: Fixed a problem writing the q and s matrices of NIFTI images out to DICOM format.
  • DICOM: Added a better error message when trying to open an unsupported DICOM spectroscopy file.
  • NIFTI: Fixed reading of some files with Nifti extensions stored with gz/zip/bz2 compression.
  • NIFTI: Corrected some Y-axis origin and matrix issues when reading NIFTI images that need to be flipped.
  • NIFTI: Improved orientation support when writing to NIFTI from DICOM.
  • NIFTI: Added improved NIFTI header extension support. There is now no limit on the number of extensions. Added ecodes for MIND, AFNI, ascii, and Caret extensions. Improved display of extensions in header dialog.
  • ANALYZE: Improved memory usage when reading and writing binary files.
  • Added a better error message when trying to load an XML Image header as a VOI and vice versa.
  • Fixed an error when creating a blank image.
  • Algorithms and utilities
  • OAR algorithms now can be performed with a non-orthogonal Powell's method (by default orthogonal line minimization is used).
  • The Fuzzy C-Means algorithm now produces a NIFTI result image when run on a NIFTI source image.
  • Fixed the updating of NIFTI matrices in the Flip utility.
  • Fixed the updating of NIFTI matrices in the Reorient utility.
  • Fixed progress bar for Anisotropic diffusion algorithm.
  • Added Mosaic to 3D volume utility.
  • Fixed a bug in the Crop using VOI utility.
  • VOIs and paint
  • Added many more VOI bug fixes and improvements related to the new VOI subsystem.
  • Added a preferences file settings for changing the paint opacity.
  • Added 2x2 brush to the set of default paint brushes.
  • Image views and visualization
  • Fixed image overlay display bug.
  • Added abilility to jump to specific coordinates in the Tri-planar view.
  • Added tab to the Tri-planar view for Scanner RAS coordinates.
  • Added the ability to pan around the image when the scrollbars are visible via dragging the image while holding the Shift key.
  • Miscellaneous
  • Removed missing preferences file warning dialog when running MIPAV from JWS.
  • Added "Close all images" item to the File menu.
  • Added -pluginDir command line argument to allow the user to specify a place in addition to $HOME/mipav/plugins/ that should be searched for plugins to be included in the Plugin menu (this location should also be included in the Java Classpath).
  • Added a better error message when trying to run non-generic plugins from the command line.