MIPAV change list 3.x.x

• 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.

• 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.

• 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'.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.