MIPAV change list 4.x.x

• File handling
  • AFNI: Fixed a bug in the reading of talairach orig origin.
  • BRUKER: Fixed a problem reading files where the FOV order was reversed.
  • DICOM: Added preliminary support for reading Enhanced DICOM files.
  • NRRD: Added support for 'SPACE ORIGIN' and 'SPACE DIRECTIONS' fields for 4D data.
  • RAW: The default units for all raw images is now millimeters.

• Algorithms and utilities
  • Made Despot T1 and T2 tools scriptable.
  • Added 4D support to Despot T1 and T2 tools.
  • Fixed a small bug setting the origin in the Talairach transform algorithm.
  • Increased the maximum number of DICOM files that can be processed by the Anonymize directory tool.
  • The Concatenate utility now sets the resolutions of the new image to that of the first image selected. Also, it now properly sets the axis orientations.

• VOIs and Paint
  • Fixed a VOI listener issue that was the result of one too many being registered unnecessarily.
  • Made a number of improvements and bug fixes to the VOI statistics generator and VOI properties.

• Image views and visualization
  • Added overlay of 3D and 4D images back.

• Miscellaneous
  • Changing the resolution in the Image attributes dialog now properly updates the image.
  • Fixed a problem using the -i and -m command line switches with relative paths in some situations.
  • Fixed a problem running MIPAV on 64-bit systems when the current working directory is not the same as the installation directory.

• File handling
  • DICOM: Fixed a DICOM receiver bug.
  • DICOM: Fixed a problem where some LUT-related tags (0028,1201-1203) were being read when the image type was not PALETTE COLOR.
  • DICOM: Added support for DICOM files that contain no image tag.
  • DICOM: Added support for presentation state DICOM files.
  • DICOM: Fixed a problem reading some tag values with value representation OW (other word).
  • DICOM: Added better error handling when MIPAV cannot decode lossy JPEG image data.
  • DICOM: Fixed a number of minor issues in the DICOM browser.
  • DICOM: Changed check of whether a file was DICOM version 2 to support more file variants. Now accepts files that have 0002 group tags (either implicit or explicit VR) in addition to 0008 tags. Two of a combination of 0002 or 0008 tags is required.
  • ICS: Writes out images as "ch" type instead of "rgb".
  • NIFTI: Fixed issues with reading NIFTI origin information in some datasets.
  • NIFTI: Fixed problem where all NIFTI volumes were forced to have either millimeters or milliseconds as their units of measure.
  • NIFTI: Fixed false detection of second and third header extensions.
  • NIFTI: Improved support for complex and double complex datasets.
  • NIFTI: Saving non-NIFTI 2D images to the NIFTI format now correctly preserves any orientation and origin information.
  • NIFTI: The NIFTI matrices are now properly updated when the user changes the image orientation or resolutions in the Edit attributes dialog.
  • NIFTI: The Qform and Sform matrices are now displayed when viewing the NIFTI header.
  • GE SIGNA 5X: Fixed reading of image header so that it now can be viewed by the user.
  • MIPAV XML: Fixed a misspelling of HARDCOPY (was HARDCODY) and BIOMAGNETIC IMAGING (was BIOMAGENETIC IMAGING) modality types. The image.xsd has been updated to reflect the change.
  • ZVI: Added preliminary support for the Zeiss ZVI format.
  • Fixed error reporting problems when running MIPAV in quiet/hidden mode. If the file type cannot be determined when reading, a message will be printed to stderr and MIPAV will exit. When saving an image as .img in quiet mode, it will first check the MIPAV options to see if the user has specified that the .img extension should always be saved as NIFTI or Analyze. Otherwise it will save in NIFTI format. When saving in .mnc format, it will do the same and save in MINC-1.0 if the user hasn't specified otherwise.

• Algorithms and utilities
  • Fixed issues copying FileInfo data to result images in some algorithms and utilities.
  • Added concatenation option to Haralick texture algorithm, enabling it to process 3D images in 2.5D.
  • Added option to output Z score to the Haralick texture algorithm.
  • Fixed a bug in the Transformation algorithm where the origin was not being updated properly.
  • Added scripting support to the Quantify masks utility.
  • Fixed a BSpline registration bug that prevented it from running on some multi-core systems.
  • Fixed a minor problem in the convergence test in the BSpline registration algorithm.
  • Thin-plate spline registration now saves the transformation to a .tps file after execution.
  • .tps files can now be used to perform a transformation using the Transformation algorithm.
  • Fixed Thin-plate spline registration result image resolution.
  • The Flip utility now can optionally adjust the image orientation and origin.
  • Changed BSpline registration scripting so that the pass options are now broken out into separate script parameters. Scripts using the old set of parameters should still work.
  • Added port of the ITK Diffeomorphic demons registration algorithm provided by Pilou Bazin.
  • Reduced memory requirements for the Convert 3D to 4D utility.
  • The Flip and Rotate utilities now update the NIFTI matrices as necessary.
  • Fixed a problem in the origin calculation in the Rotate utility.
  • The Insert slice and Add margins utilities no longer tries to update the value of the DICOM tags (0020,0032) and (0020,1041) if they are not present.
  • Fixed a bug where the incorrect value was sometimes being written out to the do_use_avg_volume_as_reference boolean parameter during script recording of the TS OAR algorithm.
  • Removed 3.5D OAR algorithm temporarily. TS OAR should be used instead.
  • Moved DESPOT T1 and T2 plugins into the Systems analysis -> Quantative MRI menu.

• VOIs and Paint
  • VOIs are now saved with the same file name they were read in with (if they were read from disk originally).
  • Fixed a bug in running VOIStatistics scripts.
  • Added an optional script parameter to VOIStatistics (voi_stats_output_file string) to allow users to specify the location of the result table file.
  • When graphing the intensities at a point in a 4D image, the user can now choose to see the frame reference times along the graph's X axis, if they exist.
  • Improved support in the VOI properties dialog for calculations involving multiple VOIs.

• Image views and visualization
  • Fixed a problem in generating surfaces from DICOM images.
  • Improved .ply and .stl surface file format support.
  • Added beta support for stereo display using the NVidia shutter glasses.
  • Added beta support for saving and loading the state of the GPU volume renderer.
  • Fixed a DTI tract loading problem.
  • Added the ability to save and load the Window and Level to absolute values (even if those values are outside of the image range).

• Miscellaneous
  • Improved the Load imageB from frame system to better handle loading images into the same patient-space using their respective origins and orientations.
  • Removed AlgorithmPad and AlgorithmPadWithSlices from MIPAV API. Their functionality has been consolidated into AlgorithmAddMargins.
  • Fixed some issues in the Screen capture utility.
  • Added .tps file extension to the MATRIX file browser filter set.
  • Added message to the MIPAV status bar indicating whether parallel algorithm execution is enabled and the number of cores detected.
  • Implemented support for the PlugInBundle API.
  • Added support for Mils (.001 inch) as a unit of measure.

• File handling
  • LIFF: Can now handle 2 color images with FITC and DAPI dye.
  • PAR/REC: Fixed problem when there was no value for the General Information tag.
  • PAR/REC: Files are now written out in the same version they were read in as.
  • DICOM: Fixed some issues in the DICOM send/recv tool when communicating with dcm4chee.
  • DICOM: Fixed tag length issue in some DICOM files.
  • DICOM: Added option to save DICOM datasets without adding MIPAV secondary capture tags.
  • MINC1/2: If direction_consines is not set in a minc file being read, it is defaulted to the identity matrix.
  • MIPAV XML: Added "NIFTI Scanner Anatomical" as an allowed type for "Transform-ID" elements.

• Algorithms and utilities
  • Fixed an issue processing color images in the Multi-spectral Fuzzy C-Means algorithm.
  • Increased maximum number of Fuzzy C-Means classes from 6 to 12.
  • Added Generate grid utility.
  • Fixed an issue with color tri-linear interpolation in algorithms performing image convolution.

• VOIs and Paint
  • In the Multi-paint dialog, fixed the lock all and unlock all masks works when resizing masks.

• Image views and visualization
  • More improvements to the GPU volume renderer system.
  • Fixed an issue with 'Save LUT as...'.
  • Fixed a problem with saving/loading user-defined LUTs in gray scale and color images.
  • Fixed LUT 0/1 starting value issue.
  • Added bi-linear interpolation to custom zoom.

• Miscellaneous
  • Added Systems analysis menu to better organize DTI (and possibly other) menu items.
  • Continued improvement in DTI-related tools.
  • Improved robustness of MIPAV when an installed plugin does not have all its components available.
  • Uninstalling plugins now attempts to remove orphaned classes.
  • Changed the PlugInBundle class to be abstract with non-static methods that should be implemented by subclasses. The PlugInBundle system has yet to be implemented.

• File handling
  • Made more fixes to the NIFTI orientation and image flipping. An option has been added to Help -> MIPAV options to enable automatic flipping of the image volume (as is done for Analyze datasets).
  • The DICOM reader now accepts tags where the element length is 0.
  • Added better support for DICOM tags that have a blank value.
  • Fixed a DICOM reader bug in the handling of tag (0018,1164) where the second resolution was not set properly.
  • Files with commas in their file names now properly appear in the list of most recently used image files.
  • Fixed the saving of JPEG images to the JPEG2000 format.
  • When saving Minc-HDF5 2.0 files, the direction_cosines written out is taken from the scanner anatomical or DICOM matrix, if available.
  • Fixed a bug in handling 4D Minc-HDF5 2.0 files.
  • Added support for DICOMDIR files.
  • Added support for SiemensText files.
  • Fixed an intermittent problem that could occur when MIPAV was run on many workstations from the same install location (LAX file read problem).
  • Fixed a problem in the XML image header viewer when DICOM tag were present.
  • Fixed some issues reading multifile datasets with strange file numbering.
  • Improved the interoperability of DICOM datasets anonymized by MIPAV.
  • Fixed a problem with the 'Fill from tags' functionality when saving a image volume in DICOM format.
  • Added support for 2 color LIFF datasets with FITC and DAPI dye.
• Algorithms and utilities
  • Added cluster shade and cluster promenance parameters to Haralick texture algorithm.
  • Fixed a bug in algorithms which used the seperable image convolver when multi-threaded operation was disabled (under Help -> MIPAV options)
  • Fixed a small bug in the Regularized isotropic diffusion algorithm.
  • Added Non-local means filter algorithm.
  • Added more options for 4D images in the Swap dims utility.
  • Added registration validation dialog.
  • Added Kernel regression filter algorithm.
  • Improved memory usage in the Transform algorithm for color images.
  • Added setPadValue() method back to AlgorithmTransform and marked it as deprecated. It may be removed in a future release and should not be used by MIPAV plugins.
  • Added support for unsigned short and float ARGB images in the Color concatenation utility.
  • Fixed a scripting problem in the Reorient utility.
  • Fixed 2.5D non-linear transformation operation.
  • Fixed some linear transformation issues with the image origin.
  • Fixed matrix copying problems when running certain utilities on DICOM datasets.
• VOIs and Paint
  • Fixed a multi-threading bug in the VOI properties statistics calculator.
  • The Multi-paint tool now saves the active paint color when the user chooses to save the paint masks to a file.
  • Added additional warning messages to some VOI-related tasks when no VOI is selected.
  • VOI retracing now works in both clockwise and counterclockwise directions.
• Image views and visualization
  • Added the ability to save a range of image slices with a layout similar to the Lightbox view as a compressed JPEG file.
  • Added 4D dataset volume rendering visualization support to the GPU-based renderer.
• Miscellaneous
  • Completely refactored the MIPAV Plugin installation system. Plugin class, jar, zip or tar.gz files are now selected through a more informative process that attempts to automatically check that all of the plugin dependencies are included. We have also added a user interface for the uninstallation of plugins from within MIPAV.
  • Created new Systems analysis menu.
  • Many DTI improvements have been added and the DTI tools have been moved to the Systems analysis menu.
  • Added a checkbox to the MIPAV options dialog which causes the MIPAV DICOM receiver on MIPAV startup. This option used to be located in the File -> DICOM menu. The DICOM send/recv dialog can now be opened without having the receiver startup with MIPAV.
  • If the DICOM receiver cannot start up a warning message is now generated instead of an error (which fixes a problem which could be encountered while running MIPAV with its GUI hidden).

• The installer for Mac OS X systems now installs native libraries to enable MIPAV's Volume renderers and Minc2 support.
• The Windows-amd64 installer now includes libraries for Minc2 support.
• File handling
  • Fixed orientation inconsistency with some Analyze files.
  • Fixed problem with the orientation of some Nifti datasets.
  • Fixed a bug writing the origin of Nifti images.
  • Fixed a bug writing boolean Tiff files.
  • When a user tries to save an unsigned short image to Analyze, MIPAV now checks to see if the data will fit within the signed short range and prompts the user to see whether the conversion should be done. If the data does not fit, an error message is displayed.
  • Added *.gz and *.bz2 to Medical file filter.
• Algorithms and utilities
  • OAR dialog user interface fix.
  • Gray scale erosion, dilation, open, close.
  • Added gray scale top hat, bottom hat, morphological lapacian.
  • Added Morphological gradient algorithm.
  • Renamed the Crop-related menu entries.
• VOI and paint
  • Mode and median now included in VOI statistics generator and VOI properties.
  • VOI statistic calculations are now done in separate threads to improve performance on multi-core systems.
  • Improved the performance of calcLargestDistance VOI statistic for large VOIs.
  • Fixed a bug when resizing the MultiPaint dialog.
• Image views and visualization
  • Many DTI improvements.
  • Numerous Volume renderer improvements.
  • Mouse wheel can now zoom the Volume renderer view.

• Miscellaneous
  • Plugins can now specify the submenu they appear under (How to specify the location of a plugin in the MIPAV menu).

• File handling
  • Added AVI MJPEG decoder improvements.
  • Greatly improved memory usage in PAR/REC file reader.
  • Fixed a problem setting the image orientation information in the PAR/REC file reader.
  • Improved memory usage in the Tiff file reader.
  • Adjusted the background coloring of tag groups in the DICOM header dialog.
  • Private DICOM sequences and private tags within public sequences are no longer shown in the DICOM header dialog unless the user decides to show all private tags.
  • Added the ability to read DICOM files with an invalid rescaling slope of 0.
  • Removed code which ignored the DICOM tags for rescaling slope and rescaling intercept for MR modality images.
  • Changed DICOM data rescaling to round the resulting values instead of casting them to short.
  • Fixed a number of problems reading DICOM tags stored in Minc2 headers.
  • Fixed reading of Minc2 modality.
  • Improved the Minc2 file header information written out to a new file by MIPAV.
• Algorithms and utilities
  • Added Bilateral and Trilateral filters.
  • Fixed saving of dialog parameters in the Gaussian blur algorithm.
  • Renamed Histogram matching to Histogram image matching.
  • Added Histogram slice matching.
  • Added Histogram slice equalization.
  • Fixed slice indexing problem in Extract slices utility.
  • Fixed a bug in the Powell's optimization used by OAR that caused the Midsagittal alignment algorithm to produce incorrect results.
• VOIs and Paint
  • Conversion of VOIs to binary, short and ubyte now copies the transformation matrices and origin from the source image to the generated mask image.
  • Added the option to use XOR behavior when importing VOIs in the Multi-paint dialog.
  • Improved error handling when trying to load a VOI into an image where it will not fit.
• Image views and visualization
  • Added updated GLSL volume rendering shaders to the GPU-based volume renderer. These are now used instead of the Cg shaders by default, which adds support for many ATI graphics cards. A number of performance improvements in the shader programs have also been implemented.
  • Added the ability to read and write ASCII GIFTI surface files (no compression or encoding).
• Miscellaneous
  • Bundled new versions of the Java Runtime Environment (1.6.0_12), Java3D (1.5.2), Jogl (1.1.1) and Cg Toolkit (2.1) on those systems whose installers include a bundled JVM. This appears to have fixed a problem encountered by a number of users running the 32-bit Linux installer.
  • Fixed handling of OutOfMemoryError when an image is magnified too much.
  • Added buttons to close all image frames or delete all open images to the Image registry dialog.
  • Updated HDF-java libraries used to read and write Minc2 files to version 2.5.
  • Added new MIPAV icon for the Mac OS X release of MIPAV.

• Added Java Web Start Nightly and Release versions of MIPAV to our download page. Java 1.5 or higher must be installed on your system. Minc2 support and the Volume renderer tool are not supported at this time. Using JWS will keep you up to date with the latest version of MIPAV automatically.
• File handling
  • Fixed some minor Analyze format issues (one of which was related to handling the image origin).
  • Fixed a bug automatically determining the format of .img/.hdr files (Analyze, Nifti, SPM).
  • Some minor FITS format writing fixes.
  • Multiple improvements to AVI support.
  • Fixed an AFNI memory usage issue.
  • Added JPEG2000 (JP2) support.
  • Added encapsulated JPEG2000 support to DICOM.
  • Fixed issue saving from Minc to DICOM (rescaling).
  • Nifti scanner anatomical transforms are now shown as 'NIFTI Scanner Anatomical' in the Image attributes dialog instead of 'Scanner Anatomical'.
  • Updated the DICOM dictionary used by MIPAV (1234 new entries, 44 corrected).
  • Dicom browser automatically parses the selected directory when it is opened.
  • When viewing the header of a DICOM image, tag groupings are now displayed with alternating blue and green backgrounds. Private tags are shown with a red background.
  • Some DICOM image header display bugs related to unknown VRs and private tag sequences have been fixed.
  • Added support for autoconversion of Cheshire float images to short when saving as DICOM.
  • Fixed an issue in the tag autogeneration in the dialog that appears when saving images as DICOM which caused problems in the MIPAV nightly build.
  • Added support for data rescaling (from short to float) when reading PARREC images.
  • Switched a number of file formats to use store separate file information objects for each image slice (behavior was inconsistent previously). AFNI, BFLOAT, BioRad, BRUKER, Cheshire, DM3, FITS, ICS, Interfile, MRC, OSM.
  • The 3 flipped and unflipped orientations are now supported for SPM (instead of just the 3 unflipped orientations).
  • Corrected the writing origins of non-SPM files to SPM format.
  • Fixed a few other orientation-related bugs in the Analyze and SPM format handlers.
  • SPM files can now be opened from either the .hdr or .img files.
  • When writing a SPM file, if the origin is within a half pixel of the image center for every dimension, the origin is set to (0,0,0) to designate that the image center is intended to be used.
  • Removed extra 'All files' file filter from the Save dialog.
  • When reading an Interfile dataset, MIPAV now tries the default name for the data file if the name indicated in the header's data file line is not present.
  • MIPAV will now automatically open single-file image datasets ending in .bz2 and .gz by uncompressing them to a customizable temporary directory before reading the image files. Since this only works with single-file formats, only MINC1, MINC2 and .nii NIFTI files are currently supported.
  • Single-file formats (NIFTI .nii, MINC1 and MINC2) can be written out with gzip or bzip2 compression by adding .gz or .bz2 to the file name in the Save as dialog (e.g., example_image.mnc.gz).
  • The MIPAV XML file format now supports gzip and bzip2 compression of the raw image data. The image.xsd file has been updated accordingly.
• Algorithms and utilities
  • Fixed issue in Gradient magnitude filter.
  • Fixed some problems with the Constrained OAR 3D algorithm.
  • Fixed an issue in the OAR 3D algorithm.
  • Fixed some issues with the cost functions and optimization algorithms used by the different registration algorithms.
  • Fixed a bug in the regisration algorithms where the origin and matrices of the registered image where not being set to match those of the reference image.
  • The Histogram summary algorithm now outputs the mean, standard deviation, median and mode to the Output window's Data tab. Also changed the Data tab output to be more like tab delimited text with column headers at the top.
  • Fixed a bug in the Haralick texture algorithm with some parameters.
  • The Haralick texture algorithm no longer requires an unsigned byte image to run.
  • In the Haralick texture algorithm, data is rescaled if necessary to allow any float and double data and to keep grey level co-occurrence matrix size to between 8 x 8 and 64 x 64.
  • Added support for color images to the Haralick texture algorithm.
  • Changed the padding value in the Transform algorithm to a float value to better support its use with floating point datasets (also affects the registration and Match images algorithms).
  • Added a field to the Transform algorithm that allows the user to specify what value should be used to fill areas in the result image that were out of the bounds of the original image (also used in registration algorithm results).
  • Added dialog to create morphological foreground and background maps.
  • Fixed the copying of the source image matrix to the result image in the Insert slice utility.
• VOIs and Paint
  • Fixed an issue with notifying windows listening for paint changes when the Paint grow dialog is being used.
  • Added some measurements to the VOI properties and VOI statistics generator dialogs:
    • - largest line segment completely contained within a VOI slice
    • - largest line segment completely contained within a VOI
  • In the VOI properties and VOI statistics generator dialogs, the center of mass and geometric center are now displayed with the resolutions applied (dim * res) and in scanner coordinates.
  • Added Shape-based VOI interpolation algorithm.
  • Added the ability to Save intensities in VOI to..., which produces a comma delimited file.
  • Added the ability to Merge VOIs.
• Image views and visualization
  • More improvements to the GPU Volume renderer
  • Added the ability to change the slice interval in the Lightbox view.
  • Fixed a layout issue that prevented the currently displayed slice number from being shown in the Surface plotter view.
• Scripting
  • In ChangeName script action, added a 'image_name_action' parameter that can be either 'replace' (the default), 'append' or 'prepend'.
  • Fixed scripting of Histogram summary algorithm.
• Help updates and additions
  • Updated the 'Retracing a VOI' and 'Annotating with Text' sections.
  • Updated the 'Supported Formats', 'Image Basics' and 'Quick Start' sections.
  • Added a 'Haralick Texture' section.
• Miscellaneous
  • Fixed some issues with image and global provenance recording and display.

• File handling
  • Added automatic detection of DICOM ver. 2 files without the .dcm extension.
  • Eliminated some memory leaks in the DICOM reader and writer.
• Algorithms and utilities
  • Added Morphological algorithm support for processing Byte and Short images that have no negative values.
  • Fixed an error that sometimes occurred while running the BET algorithm.
• VOIs and Paint
  • When commiting masks for a 4D image, the multipaint dialog has radio options for commiting masks as 3D or 4D; for regular painting in the 2D view and in Tri-planar image, a dialog pops up asking if masks are to be commited in 3D or 4D when trying to commit paint to mask.
  • Fixed a problem with the Protractor tool in the Tri-planar view.
• Help updates and additions
  • Added help topics on the Hough circle, ellipse, line and parabola algorithms.
• Miscellaneous
  • Fixed a problem setting the output directory of the generated file when performing a screen capture.
  • Fixed support for printing the contents of the Output window.

• Fixed a problem with the MIPAV installer which caused the 4.1.1 release for Windows-amd64 systems to fail to start up.
• File handling
  • Fixed an issue with decoding 24-bit CVID AVI files.
  • Added support for black and white CVID AVI files.
• Algorithms and utilities
  • Fixed a matrix-copying issue when running algorithms and utilities on DICOM images.
• VOIs and Paint
  • More improvements to VOI text annotation.
• Image views and visualization
  • Fixed a problem with the GPU renderer on Macintosh systems.
• Help updates and additions
  • The MIPAV Help system has been changed significantly. Each help topic now contains information on using the component it is associated with and a link to a page on the MIPAV website which has background information for that algorithm or utility. This has significantly reduced the amount of disk space taken up by the MIPAV Help system.
• Miscellaneous
  • Fixed a problem which prevented the command line argument usage window from appearing when the -hide command was not used.

• File handling
  • Cleaned up memory usage of a number of file handlers.
  • Added 8-bit grayscale support to JIMI reader (JPEG, etc).
  • Added support for saving Analyze float images to DICOM.
  • Fixed an issue with capital letters in file extensions.
  • PAR/REC files may now be opened by selecting either the .par or .rec file.
  • Improved SPM file format detection.
  • Fixed a problem with reading COR files.
  • Fixed an issue with the VOI file filter.
  • Changed the saving of 3D DICOM datasets to be done on a slice-by-slice basis to reduce memory usage and prevent problems with large datasets.
  • Fixed some issues with MINC2-HDF orientations.
  • Added AVI decoder support for 24-bits-per-pixel CVID files.
• Algorithms and utilities
  • Fixed a number of minor bugs:
    • Regularized isotropic diffusion
    • Gradient magnitude
    • Gaussian blur
    • Center of mass
    • Watershed
    • Edge lapacian
    • Image calculator
    • Registration patient position
    • Registration B-spline
    • Registration mosaic
    • Registration OAR 2.5D
    • Registration TSOAR
    • Transform
    • Subsample
    • Pad
  • Added the display of the standard deviation when the Image calculator and Bulk image calculator are run.
  • Added Poisson noise to the Noise generation utility.
  • Added a utility to swap the 1st and 4th dimensions of a 4D image.
  • Added a new utility to reorient (and optionally resample) an image (contributed by Pilou Bazin).
• VOIs and Paint
  • Corrected some minor issues with the Multi-paint tools.
  • Improved memory management while painting, reducing memory creep and removing a garbage collection call performed on 64-bit JVMs.
  • Livewire VOI now works with color images.
  • Fixed a Power paint dialog bug.
  • Fixed a problem with creating custom brushes.
  • Changed paint behavior so that when the user paints in the main image frame, the paint in the Tri-planar frame is only updated on mouse release.
  • Fixed a race condition when switching paint colors in the Multi-paint dialog.
  • Fixed some issues with VOI annotations.
  • Improved how backing up and reverting to the paint bitmask backup is performed. This significantly improved paint performance with large images on initial mouse press and when undo-ing an action.
  • Converting a VOI in a 4D dataset to a mask image now produces a 4D volume with the VOI converted on all time slices.
• Image views and visualization
  • Improved the surface decimation algorithm.
  • Added PLY surface format support.
  • Added the ability to save the current camera and object parameters in the GPU Volume renderer and restore them again later.
  • Improved surface extraction algorithms to automactially reduce surface complexity.
• Scripting
  • Fixed Transform scripting bug when resampling.
  • Fixed a scripting issue with the Optimized automatic registration algorithms.
  • A number of algorithms were being run in a separate thread during script execution (FFT, std dev thresholding, registration OAR 2.5D and 3.5D, background distance map, evaluate mask segmentation, evaluate segmentation, remove t-slices).
• Help updates and additions
  • Muscle segmentation plug-in.
  • Conformal mapping algorithms.
  • DICOM query dialog.
  • DICOM images section.
  • Wavelet thresholding.
  • LUT for two images (A and B).
  • Filters (frequency).
  • Wavelet BLS GSM.
  • Talairach transform
  • Modify graph
  • Paint grow
  • 2D B-spline registration
  • Mosaic registration
  • Scripting
• Miscellaneous
  • Added menu items Open graph to same frame
  • MIPAV classes no longer use Java3D vecmath classes. Instead WildMagic vector and matrix classes are now used. Usage of Jama classes has been refactored and the location of the code within the MIPAV classpath has been changed. MIPAV Vector*, Color* and Point* classes have all been removed.
  • Added -outputDir command line option for selection of the directory where files written out to disk by MIPAV should be located (to be used with scripting).
  • Changed -dir command line option to -inputDir.
  • Fixed a problem where an error dialog would sometimes pop-up when running MIPAV with the -hide command line option.

• File handling
  • Gzipped archives (containing a single file in a format supported by MIPAV) can now be automatically un-archived and opened in MIPAV.
  • Improved the processing of determining the file format of files with an unknown or non-existent extension.
  • Fixed a problem where .tiff files would not show up in the Image browser when the TIFF file filter was selected.
  • New file formats supported:
    • BFLOAT
    • LIFF
    • Minc2
    • STL surface format (.stla and .stlb)
    • VTK surface format
  • File formats with bug fixes or improvements:
    • Analyze
    • Biorad
    • DICOM (UT supported as explicit VR with 32-bit length; reading of critical tags that were incorrectly written)
    • DM3
    • ICS
    • Minc (slice thickness now saved to the acquisition -- slice_thickness attribute)
    • OSM
    • PARREC
    • TIFF
• Algorithms
  • Added automatic parsing of ITK filter interfaces for access from the Algorithms menu (available only on 32-bit Windows systems, by default).
  • Image calculator (added color support)
  • Image math (added color support)
  • Match for reference
  • Match images
  • Maximum intensity projection (added color support)
  • Transform (adjusts units of measure of input image to match reference image)
  • The Threshold and dual threshold tools now output unsigned byte instead of short masks.
  • Improved the multi-threaded image convolution support.
  • Parallelized the Optimized automatic registration algorithm.
  • Integrated the Talairach transform plugin from JHU Medic into MIPAV.
• Utilities
  • Moved Center of mass from the Algorithms menu to the Utilities menu.
  • Improved the Center of mass output sent to the Output window's data tab.
  • Fixed the way that the Rotate utilities handled setting the VR of DICOM image tags.
• VOIs and Paint
  • Fixed a problem with cloning some VOIs.
  • Fixed some issues with the Livewire VOI tool.
• Image views & visualization
  • Parallelized the Raycast volume renderer.
  • Many improvements have been made to the GPU-based volume renderer.
  • Multipaint dialog improvements -- auto-save for multiple masks and keyboard shortcuts that work with the triplanar view.
  • Changed the paint brush sizing in the triplanar view to be consistent regardless of the image resolution.
  • Added Paint -> Unsigned byte mask conversion tool.
• Scripting
  • The Transform algorithm now saves the relative path to the transformation matrix file in its script action line, if a file is selected in the dialog.
  • Added -dir option for setting the default image directory when running scripts from the command line.
• Miscellaneous
  • The MIPAV installer now tries to correct the permissions of file containing memory limit.
  • Added a checkbox in the MIPAV options dialog for the enabling/disabling of the parallelization of algorithms.
  • A Capture screen memory leak was fixed.
  • Many DTI algorithm and visualization improvements have been added.
  • Moved the keyboard shortcut file (accessory.dirs) from the user.home directory to user.home/mipav.

• 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

• 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

• 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.

• 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.