VINCI Version History

Vinci 4.16.0, May 2 2013

• Visual Studio 2012, Update 2 - Vinci now uses the latest MS compiler on the 64-bit WINDOWS platform.
• Qt 4.8.4 - now compiles with the latest Qt 4 libraries on the WINDOWS platform.
• ZLib 1.2.7 - Vinci now uses the newest Zlib library, (C) 1995-2012 Jean-loup Gailly and Mark Adler.

• WINDOWS: File Association - Handling Inappropriate Code Page - Loading an image by double click did not work if the image's file name could not be encoded in the system's code page. - FIXED.
• WINDOWS: Environment Variable - Handling Inappropriate Code Page - Using an environment variable did not work if its name or value could not be encoded in the system's code page. - FIXED.
• WINDOWS: Ogg/Theora Movies - Handling Inappropriate Code Page - Vinci could not create Ogg/Theora movies with a filename that could not be encoded in the system's code page. - FIXED.

• Linux: Debian Package - had wrong paths in the postinst and prerm scripts. - FIXED.

• Zipped Vinci Project - DICOM Subdirectory - saving a zipped Vinci project file again as a zipped Vinci project file renamed any sub-directory of the DICOM-directory to DICOM. - FIXED.

• Report Tool - Memory Leak - in case that the output was not plotted and for Patlak plot output - FIXED.

Vinci 4.15.0, March 28 2013

• Joined Histogram Tool - Create Table - the tool can now output a table of the values of selected images at corresponding voxels that in case of two selected images form the data to produce the joined histograms.
  The generation of the table uses a template file replacing keywords that start with a dollar sign and recognizing special loop keywords defined as HTML escape sequences. Please press the ?-button at the tool's top to get a list of supported keywords.
  So far, only text file templates are supported. We included two templates named A and U, the first for simple, the latter for more elaborate output.
• Joined Histogram Tool - Tab Widget - the tool now creates the joined histograms in the tabbed page Create Image.
• Joined Histogram Tool - VOIs - you can restrict the computation of the joined histogram to the united region of selected VOIs.

• WINDOWS: Load Image - Handling Inappropriate Code Page - Vinci now interprets raw character fields in image files everywhere as being UTF-8 encoded and writes them as such into the files. Especially: The saved HRRT header is now written in UTF-8 encoding and the MicroPET header file is now interpreted as UTF-8 encoded. The Vista image file header part and the Index<TAB>Name type atlas description file are now also read as UTF-8 encoded.
• XML Output - Explicit Encoding - XML header lines now explicitly declare the file to be UTF-8 encoded, e.g. in the Vinci project file.

• Image Group Based Calculations - Function Body Example Script - we added saveallimages.vpy, a script that saves all loaded images up to the first free instance number into a file (named after the original image file appended by _rsl) using current offset and rotation. Python fans may like to look in the file <Vinci install root>/external/python/VinciPy/Vinci_ImageT.py for further options to the function saveYourselfAs, re-write the script to use image groups or arrays, etc.

• WINDOWS: Load Image - Handling Inappropriate Code Page - Vinci could neither read nor write some image types (NIfTI, Analyze, DICOM, etc.) with filenames that the user's code page could not encode appropriately (e.g. an image with japanese file name on a system with latin-1 code page) and where a third party library did the actual reading or writing. - FIXED.
  Vinci could also neither read nor write Zipped Vinci Projects with filename and names of containing files that cannot be encoded in the system's code page. - FIXED.
  BEWARE: The WINDOWS 7 Explorer does not correctly display such file names in zip files, the WINDOWS 8 Explorer does. There may still be some other places where Vinci does not yet correctly handle such file names. This is work in progress.

• VOI Define Tool - Initialization - after project-load, the tool might not have shown the VOI images and their VOIs in the lists if the previously closed project had VOI images as well but at different instance numbers. - FIXED.
• VOI Define, VOI Manipulation and VOI Operations Tool - Memory Leak - while using the context menu of the VOI lists. - FIXED.

• Multi-Frame Movie Tool - Quicktime Stop Recording - stopping the creation of Quicktime movies sometimes failed depending on the timing of some function calls, especially on 64-bit WINDOWS systems. - Hopefully FIXED.
• Multi-Frame Movie Tool - Quicktime Framerate - the frame rate of Quicktime movies was not correctly set. - FIXED.

• Joined Histogram Tool - Showing a Newly Computed Image - sometimes failed - Hopefully FIXED.

• Load Analyze - Default MirrorLR - MirrorLR was not checked by default during drag and drop in Vinci 4.13.0 and 4.14.0. - FIXED.

• Load Project - Undo back to a Zipped Vinci Project - Vinci did not find the images in the zipped project file. - FIXED.
• Change to non-MDI mode - may have asserted depending on the timing of some function calls. - FIXED.
• Closing Workspace in Non-MDI Mode - Memory Leak - FIXED.
• Drag & Drop - Image Files - did not work if the LoadView was closed. Vinci now opens the Loadview if necessary. - FIXED.

• Vinci Lite - Missing Restrictions Implemented - the Vinci Lite version (i.e. Vinci without valid license file) does not support the export of data or files. We restricted the following modules: saving a function body in Image Group Based Calculations, export to file and clipboard in ROI Evaluate and VOI Evaluate, export of data in PlotsView.

Vinci 4.14.0, March 12 2013

• Color Tool - Spin Boxes and Edit Fields - The spinbox has no longer a range fixed to the minimum or maximum of the image and you can now again enter values into the edit fields that are greater than the image maximum or less than its minimum.

• NIfTI Image - Library v 1.43 - Vinci now bases its NIfTI and Analyze image loader on the latest official NIfTI library version.
• Load Analyze - Default Scaling - In order to be consistent with Vinci 2.x and SPM, we load Analyze 7.5 images using their inherent scaling information again. Vinci 3.x-4.13.0 did not do so, so far, as Vinci's NIFTI/Analyze engine is based on the official NIfTI library that also ignores scaling information for Analyze 7.5 images.
  You can still load unscaled Analyze 7.5 images as an option. Project files written by Vinci 3.x-4.13.0 use this option to re-create them as they were saved.
  Of course, we strongly recommend not using Analyze images at all.
• Load NIfTI - Data Type RGB24 - the NIfTI image load plugin can now read images with RGB24 data type. The image's float values are calculated in the simplest way: (red+green+blue)/3.0; i.e. iso-weighted and without prior gray-scale gamma correction.

• DICOM and Paravision Image - Multiple Image Load - the plugins to load DICOM and Paravision images can load multiple images at once. Vinci can now undo / redo all of these load operations, generate OrthoDisplays for the images as necessary and - in case of a test generation - check whether all these images are already in the test environment. Until now, Vinci only handled the first image in this way.

• DICOM Image - 4D-series of Mosaic Images - Vinci can now read DICOM image 4D-series of mosaic images; just choose the frame you'd like to load in the spinbox and press the load button. Selection of and double-click on a list entry of another image resets the spinbox back to the start frame (i.e. one).
  CAVEAT: Frame start time and duration may not be correct, for now. This is work in progress.

• DICOM Image - LoadView As During Load - did not work for frames of a DICOM mosaic image. - FIXED.

• Load DICOM - Crash - the module crashed for images with aquisition times without milliseconds part. - FIXED.

• Load Analyze - Default MirrorLR - MirrorLR was not checked by default in Vinci 4.13.0. - FIXED.

• Loading a Vinci 2.x Project - Wrong Contour Color - FIXED.
• Loading a Vinci 2.x Project - Load Analyze Image - might have been wrongly scaled, see above. - FIXED.

Vinci 4.13.0, March 5 2013

• DICOM Image - Multithreaded and XML-Optimized - the directory scan improved by a factor of 2-10 compared to Vinci 4.04.0 (on a machine with four processors), and by a factor of 4-16 compared to Vinci 4.05.0.
• DICOM Image - Cancel Directory Scan - You can now cancel the directory scan. When you cancel, Vinci fills the image list only with the data of the already completely scanned directories.
• DICOM Image - Double Progressbar - the upper bar shows the progress in the current directory, the lower shows the overall progress. You will only see double progress bars if there is more than one directory to scan.
• DICOM Image - Anonymization - zipping during anonymization now displays a progressbar and can be cancelled.
• DICOM Image - Mosaic Images - Vinci can now read mosaic images with non-numerical characters in the matrix dimension tag (e.g. like 128p*128s instead of the normal 128*128).

• Load DICOM - Unsigned Byte-Data, Tag EVR_OB - Vinci has not been able to read unsigned byte array data since version 4.05.0. - Sorry, FIXED.
• Load DICOM - Mosaic Images - Vinci has not been able to read mosaic images since version 3.73.0. - Sorry, FIXED.
• Load DICOM - Color Settings of Project Ignored - Vinci always used the color settings inherent to the DICOM file and not the settings of the project if the image was reloaded. - FIXED.
• Load DICOM - Massive Memory Leaks - in case of DICOM orphans and loading of mosaic images. - FIXED.
• Load DICOM - Missing Survey Scans - only the first survey scan found in a directory was included into the image list. - FIXED.
• Load DICOM - As Atlas - created an index volume with gray scale palette. - FIXED.

• Aborted Creation of Index Volume - Massive Memory Leak - FIXED.

Vinci 4.12.0, February 15 2013

• Load Analyze - Vinci 2.x Project - a Vinci 2.x project that contained Analyze images with unset MirrorLR and MirrorZ got loaded with the images wrongly mirrored. - Sorry, FIXED.

Vinci 4.11.0, February 8 2013

• Load Analyze and NIfTI Image - Crash - due to Vinci 4.10.0's fix of the memory leak in the Analyze and NIfTI load plugins, Vinci crashed during load of the second image of the same Analyze or NIfTI type. - Sorry, FIXED.
• Update - After Run Tests - due to Vinci 4.10.0's fix of the memory leak in the test environment, the update program could not close the running instance(s) of Vinci after starting and finishing a test once. - FIXED.

• Change Cursor After Creating/Pasting a Graphics Item - you could not change the cursor form (e.g. by changing to cut mouse mode) on a display after you created or pasted a graphics item on that display. - FIXED.
• Change Cursor Automatically Back to Arrow Mode - after you created a graphics item the cursor did not automatically change back to arrow mode on that display. - Hopefully FIXED.
• Change Cursor Within Graphics Item - when you changed the mouse mode (e.g. to cut mode) while the mouse was within a graphics item the cursor did not change on the display under the mouse. - FIXED.

• Annotation Object - Live-Editing on the Display - since Vinci 3.68.0 (Qt 4.7.0), at the start of editing an annotation graphics item on the display, the cursor has not been showing up immediately, nor blinking. After finish it has not disappeared. - FIXED.

• VOI Define Tool - Save Atlas Description - crashed if no VOI image present or chosen. The button is now disabled in this case. - FIXED.

• Default Projects - Missing MD5-Signatures - FIXED.

Vinci 4.10.0, February 05 2013

• Mac-specific problems solved - platform-specific problems related to the DCMTK upgrade (DICOM import) and the recently introduced "Zipped Vinci Project File" prevented Mac releases since Vinci 4.05.0. This release includes a Mac version.

• Save Project As - Change Current Project - Vinci features a new checkbox in the More options part of the Save Project As dialog to determine whether to change the current project to the new project the dialog is about to create, or whether to keep to the current project. Changing to the newly created project is the default as before.

• Memory Leaks - Detection - Vinci now uses Visual Leak Detector (VLD) to detect memory leaks during development on the WINDOWS platform.

• Report Tool - Crash during SaveProject - as the new SaveProject environment of Vinci 4.09.0 did not completely follow the advice to not protocol (i.e. not add to the undo/redo list) the current SaveProject action. - FIXED.
• Report Tool - Crash during Recalculation - Pressing the Report button immediately after the end of the previous calculation might have crashed the tool. - FIXED.

• Reslicing Tool - Image Subscription - possible double image subscription - FIXED.

• WINDOWS 64-bit: Animation Delegate - Crash at the End - the release of the movie writer and the closing of the program were done twice; additionally, the release of the movie writer sent four unexpected characters. - FIXED.

• Pack & Go - Network Images - Pack & Go has not been working with network images (path starting with "\\") since Vinci 4.08.0. - Sorry, FIXED.

• Memory Leaks - VLD detected memory leaks in the following modules: Color Palette Handling, Enter Test Environment, LogView, Load ECAT7 Image, Load NIfTI Image, Load Analyze Image, Splash-Screen, Landmark Co-Registration, TACs of Speckle Series, PlotsView, AMPplus, Standard Movies, Animation - Ogg Theora Movies. - FIXED.

Vinci 4.09.0, January 28 2013

• Paravision Image - Multi-Row Load - You can now load several images of the table at once.
• Paravision Image - Double-Click Load - You can now load an image of the table just by a double-click.

• Multiple Load - ECAT7, HRRT, MicroPET and DICOM - consecutive frames of an image are no longer loaded into the next image buffer if that is already used; they are now loaded into the next free image buffer.

• Zipped Pack & Go - No Copying - Vinci now creates the zipped Vinci project file without copying any image to the target directory.

• Save Project (As) - Clear Protocol - Vinci will now (by default) clear the protocol (undo/redo list) when saving a project. You can de-activate this feature in the Vinci options General tag's new checkbox Clear protocol when loading/saving a project.

• Zipped Vinci Project File - Load - Vinci now shows a progress bar while it unzips the project file to a temporary directory.
• Zipped Vinci Project File - Re-Load Images of the Load-History - Vinci no longer temporarily unzips the whole project but only the files of the image to load; will work for newly loaded images.
• Zipped Vinci Project File - Save Projects with Re-Loaded Images of the Load-History - Vinci no longer temporarily unzips the whole project but only the files of the image to load; will work for newly saved projects.

• Drag - Copy-Action - Vinci now only uses copy-actions while dragging the OrthoTitle buttons.
• Drop - Copy-Action - Vinci now only accepts copy-actions; move- and link-actions are ignored.

• Zipped Vinci Project File - Unzip and Re-zip Externally - Vinci may not have been able to load an externally unzipped and zipped again Zipped Vinci project file. - FIXED.

• DICOM Image - Progress Bar - often jumped back and forth while processing a DICOM directory. - FIXED.
• DICOM Image - Re-Load - re-loading an DICOM image of a zipped project file via the load history after loading an image of a DICOM directory did not work correctly. - FIXED.
• DICOM Image - LoadHistry and Table-Select - selecting an image in the table after choosing an entry in the load history did not work for zipped projects. - FIXED.

• Paravision Image - As During Load - did not re-create the table entry as during the load operation. - FIXED.
• Paravision Image - LoadHistory and Table-Select - selecting an image in the table after choosing an entry in the load history did not work for zipped projects. - FIXED.

• LoadView As During Load - Image of Zipped Project - did not work at all. - FIXED.
• LoadView As During Load - Image with Index Volume - did not check As Atlas. - FIXED.

Vinci 4.08.0, January 21 2013

• Zipped Vinci Project File - Load - Vinci can now load a Vinci project file that you previously saved with Zipped Pack & Go. Use the menu entry Load Project and change the file filter from Vinci Projects (*.vpx) to Zipped Vinci Projects (*.vpx.zip). The images are unzipped into a temporary directory and loaded from there.
• Zipped Vinci Project File - Save (As) - saving a zipped Vinci project file is the same as calling an automated version of Zipped Pack & Go.
• Zipped Vinci Project File - Re-Load Images of the Load-History - Vinci can re-load images that you previously loaded from a zipped Vinci project file. The images are unzipped into a temporary directory and loaded from there.
• Zipped Vinci Project File - Save Projects with Re-Loaded Images of the Load-History - Vinci can save images that you previously loaded from a zipped Vinci project file (see above) in a Vinci project. On Load, the images are unzipped from the zipped Vinci project file into a temporary directory and loaded from there.

• Pack & Go - Zip Default - Vinci now uses Zipped Pack & Go as default if the project file name ends with .zip.
• Pack & Go - Cancel - canceling Pack & Go does no longer threaten to, nor actually leave you with a partially converted project.
• Pack & Go - Abort - aborting Pack & Go during copying does no longer leave you with a partially converted project; all files that have already been copied are removed again.
• Pack & Go - Undo/Redo - redo and one-step undo are implemented now. One-step undo means that Vinci saves a overwritten project file in a backup file and can re-create it from there. But, of course, Vinci can only re-create the last overwritten project file.
• Pack & Go - File in Target Directory Already Exists - Vinci has used an already existing file until version 4.05.0 and aborted Pack & Go in versions 4.06.0 and 4.07.0. Now Vinci uses the already existing file if it is identical to the one to get copied. Otherwise, Vinci now opens a messagebox where it is for the user to decide whether to copy i.e. overwrite the already existing file, continue and use the existing file or stop Pack & Go altogether.

• Save project - Overwrite Protection - Vinci now warns about overwriting an existing (zipped) Vinci project file.

• Exported Vinci Program Files - Relative Paths for Vinci Project and Log File Again - in order to be able to copy a Vinci program files together with its Vinci project without having to edit the program file, Vinci uses relative paths again. Sorry for the trouble.
• Load NIfTI - Image Orientation - Vinci now "complains loadly" when you try to load an image with unknown i.e. not yet implemented volume orientation.

• Repeated Pack & Go - did not work with all image types. - FIXED.
• Zipped Files - Wrong File Dates - the file date month within a file zipped by Vinci was off by one month (e.g. February instead of January). - FIXED.

• Reloading an Index Volume from the Load History - loading an index volume from a project file worked correctly but did not check As Atlas, so a reload from Vinci's Load History did not work. - FIXED.

Vinci 4.07.0, December 20 2012

• Joined Histogram Tool - a new tool that computes the joined histogram of two images, X and Y, for a given number of bins. The images must have identical reslicing parameters, i.e. they should be co-registered in image reset position. They need not have identical dimension or pixel size, the image with less voxels is resampled if necessary.
  The values of corresponding image voxels are binned with their full or their color range of values from minimum to maximum. The dimension of the resulting image is equal to the number of bins in x and y, and one in z-direction. The pixel size will be 1.0 mm in all directions. The image matrix size will be set automatically to the numbers of bins in x and y, and 256 in z. The image type is set to that of image X. If the image type is ECAT7 Image the image values are capped at 32767 so as to not loose precision when saving discrete integer values.
  The tool opens a new OrthoView titled Joined Histogram which shows the result in TruePixel mode and with maximum possible size (divisible by 256) that fits to the screen only limited by the number of bins. So, you will see the image ideally having a one to one joined-bin to pixel ratio.

• Color Tool - Spin Boxes instead of Edit Fields - the input fields for display range, stretch color bar, and gamma are now implemented as spin boxes; undo/redo incl.
• Contour Tool - More Button - changing the OrthoDisplay does no longer uncheck the more button; its settings is saved in the registry now.

• Save Project - Zipped Pack & Go - you can now create a zipped version of the Pack & Go output containing all images and the project file. Just check zipped result right to the Start button in the Pack & Go dialog.

• PlotsView Copy/Export/Print - Scatterplot Selection - when you changed the selection of plots from within the copy/export/print dialog, all but the PDF output might have exported with incorrect height. - FIXED.

• WINDOWS: Pack & Go - Different Drives - on WINDOWS, Pack & Go between directories on different drives did not work correctly. - FIXED.

• Contour Tool - Images with NaN, NaN Outside of Image - images with NaNs or Vinci with activated option to use NaNs outside of the image corrupted the contour values, especially quantiles with display-based histogram. - FIXED.
• ROI Define Tool - ROI Center Spin Boxes - were enabled but did nothing; disabled now. - FIXED.

• Moving Cross - Start-up Position - the moving cross (short-cut X) did not appear at the position of the mouse arrow at startup when the images were cut independently i.e. without link. - FIXED.

• Report Tool - Minimized PlotsView - creating a TAC report with minimized PlotsView tended to crash Vinci. - FIXED.
• Report Tool - Initialization - the tool has not shown existing ROIs and VOIs at start-up since Vinci 3.85.0. - Sorry, FIXED.

• Views Outside of the Screen or MDI Area - were not always shown appropriately on a small screen if saved on a big screen. - FIXED.

• MMM Co-Registration - Registration Result File - registration result filename was not logged with native directory separators. - FIXED.
• WINDOWS: File Associations - Vinci 4.06.0 crashed when you loaded an image by double click. - FIXED.

Vinci 4.06.0, December 7 2012

• Speckle Load-Plugin - I.<date-time>.dat series - the Speckle Load plugin now handles a new type of Speckle series I.<date-time>.dat with UINT8 data.

• Save Project - Pack & Go - we added the missing image formats.
  • Speckle Images - Vinci only copies the currently displayed image, not the whole series.
  • Paravision Images - The images are copied with the structure of the Paravision source images into a sub-directory called Paravision of the target directory.
  • DICOM Images - The images are copied with the structure of the DICOM source images into a sub-directory called DICOM of the target directory.
  • Vista Images - implemented now.
  • 3DT File - implemented now.

• Clear Protocol - Undo/Redo - implemented now.
• Load Project - Undo/Redo - implemented now.
• Load Project - Clear Protocol - Vinci will now (by default) clear the protocol (undo/redo list) when loading a project. You can de-activate this feature in the Vinci options General tag's new checkbox Clear protocol when loading project.

• MDI-Mode - Keep Current Session - changing to and from MDI mode in the Vinci options General tag now reloads the current session from a temporary project created in memory and not just the last loaded project file. The protocol gets cleared only with activated allbeit default option Clear protocol when loading project. Clearing the protocol will be undone/redone now.

• MMM Co-Registration Tool - Multi-Threading - now uses the ideal thread number for UNIX systems as well; was set to two independent of the numbers of processors on the machine.

• 3DT-Plugin - Load History - choosing a 3DT-file from the load history activated the ECAT7- instead of the 3DT-Load plugin. - FIXED.

Vinci 4.05.0, November 22 2012

• DICOM Image - DCMTK v 3.6.0 - Vinci now bases its DICOM image loader on the latest official DCMTK version.
• DICOM Image - Adaption to Minor Changes in Keywords - Vinci now understands the newer DICOM keywords PatientName and PatientBirthDate, which were called PatientsName and PatientsBirthDate in earlier DICOM standards. The old keywords are still processed.
• DICOM Summary Files - VinciDC4.xml - we changed the name and version of Vinci's DICOM summary files to adapt to the DICOM-internal changes. The files allow a quick reload of images in previously scanned directories.

• AMPplus - export result lists - you can now export the result lists to an *.txt file. The first three columns are the indeces of the voxel, the latter columns are added individually by the user via the dialog interface (button <i>).

• Load Vinci Program File - you can now load and run Vinci program files (.vprog) into the Protocol-View (Undo/Redo-View) to append to a given program file. Just use the new menu entry Load Vinci Program File... or press the new Load button in the Protocol-View.
• Run Vinci Program File (GUI) - you can now run Vinci program files (.vprog) step by step forward and backward (see below) using the program runvinci of the Vinci test framework. Please use the new entry Run Vinci Program File (GUI)... in the Edit menu.
• Exported Vinci Program Files - With Undo Commands - Vinci now asks you whether you want to export the Vinci program file with the Redo Commands only, resulting in a smaller file, or complete with the Undo Commands, which is good for debugging when used together with Vinci's test environment, see above.
• Exported Vinci Program Files - Absolute Paths for Vinci Project and Log File - exported Vinci program files now use absolute paths of the Vinci project and log files.

• Annotation - Scale with Temporary Auto-Width - you can now scale an annotation graphics object with temporary auto-width (i.e. pressed-down CTRL-key during the mouse-induced scaling) on the all of its grips. Until now this was implemented only for the side grips.

• WINDOWS 8 - Vinci Installation - When you first install Vinci using a downloaded setup program you will have to explicitly allow starting the installer once as administrator. Updates will then work without additonal interference.
• WINDOWS 8 - Differences to WINDOWS XP - we tested Vinci on the 32-bit version of WINDOWS 8, so far. Our nightly tests only remarked about minor changes in the positioning and/or size of texts in measures and annotation objects.

• WINDOWS: File Extensions declared Searchable - you can now search the contents of Vinci Project (*.vpx), Vinci Program (*.vprog) and *.3dt files using the WINDOWS Explorer. The file associations in the WINDOWS registry now get an additional entry to declare them searchable as text files.

• DICOM Image Plugin - Multiple Read - you could select more than one image in the list, howewer, Vinci loaded only one of them. - FIXED.

• Annotations, Rectangular and Elliptical ROIs - CTRL-Scale - Undo/Redo did not work correctly when scaling the mentioned graphics items with the mouse with pressed-down CTRL-key. (During scaling, a pressed-down the CTRL-key transforms an annotation object with freely choosable text width back to auto-width and makes rectangles and ellipses temporarily symmetric.) - FIXED.
• Creation of Annotations with Mouse - when first creating an annotation the Text Define tool opens and the mouse may loose the grip of the text object. In this case the annotation will not get scaled while you drag the mouse.
  The Text Define tool now opens already when you change to text creation mouse mode. So, the mouse will not loose grip and you can always scale the text object. - FIXED.

• WINDOWS: EMF Export - Elliptical ROIs - were not correctly drawn. - Sorry, FIXED.
• WINDOWS: EMF Export - Annotations - were drawn with incorrect font size. - FIXED.

• Closing PlotsView Properties - Vinci crashed when you closed the PlotsView after closing the PlotsView Properties. - FIXED.
• 64-bit WINDOWS: Animation Delegate - the program crashed when you tried to use it without installed WINDOWS Quicktime API. - FIXED.

Vinci 4.04.0, November 7 2012

• 64-bit WINDOWS: Animation Plugin - Quicktime Movies - Vinci can now write Quicktime movies with its 64-bit native WINDOWS version by marshalling the contents images to the temporarily running 32-bit application Animation Delegate that itself uses Apple's 32-bit WINDOWS quicktime dlls.

• Contours-Tool - Percentiles - the contour values are now also shown in percentiles (quantile-percent).

• VinciPy - sys.argv[0] usage reduced to where explicitly needed - the method VinciBin::GetVinciPyDir now really returns the VinciPy directory. You should now be able to move the VinciPy directory without further trouble; of course, you will have to change the path in Vinci_Py.xml accordingly.

• Contours-Tool - To-Values - should be identical to the From-Values as long as there is only one contour level. - FIXED.
• Contours-Tool - Width - showed the wrong values for some PET-images. - FIXED.

• MMM PET Normalization - non-affine schemes failed - error message: in tag <NormSchema>: in attribute <affineRegSchema>: reg. schema 'CC affine 4' not found. - FIXED.

• Image Group Based Calculations - Show Result Image - a single result image has not been correctly displayed since Vinci 3.98.0. - Sorry, FIXED.
• Contours Tool - Change Number of Levels - when you changed the number of contour levels the OrthoDisplay was not redrawn. - FIXED.

• WINDOWS: Copy/Export/Print - Redraw Problem after EMF Export - After using EMF-export in the Copy/Export/Print dialog, any view behind the Ortho-, Planes- or PlotsView (e.g. the LoadView) might no longer have redrawn appropriately. - FIXED.
• LogView - xml-SetMaxBlocks command - really implemented now. Vinci's previous version only set the max-blocks variable and the let actual max block limit unchanged. - FIXED.
• OrthoView - Shortcuts "I" and "W" - were registered twice. - FIXED.

Vinci 4.03.1, October 10 2012

• LogView - xml-Clear command - implemented now to clear the contents of the LogView.
• LogView - xml-SetMaxBlocks command - implemented now to set the maximum number of lines of the LogView. The default was zero up until now, which meant there was no constraint. It is now 100000, as the application crashed on Linux after logging about one million lines (Pipe broken error).

• WINDOWS: EMF Export - WINDOWS run via Remote Desktop (16-bit color depth) - bitmap parts of the image did not draw correctly. - FIXED.

• WINDOWS: EMF Export - Bitmaps with Transparent Background - were not correctly handled. - FIXED.

Vinci 4.02.0, October 5 2012

• WINDOWS: Copy/Export/Print - EMF Export to Clipboard and File - implemented now in Ortho-, Planes- and PlotsView, using WINDOWS system functions.

• Matlab Interface - New Example - added an example which shows how to use the MMMTool and the resampler to create a joint histogram for two images in Matlab. The example is called test_mmm3.m and you can find it in the external/matlab directory.

• Ortho- and PlanesView - New Shortcuts - the new shortcut CTRL-< toggles between button- and pure text-mode of the ortho- and planesdisplay info line. It has the same effect as using the <-button on the outmost right side of the respective info lines.

• Qt 4.8.3 - now compiles with the newest Qt libraries for the WINDOWS versions.

• Matlab Interface - Resampling Bug - The resampling routine +Vinci/resampleImage.m in the Matlab interface (NOT the resampling routine in Vinci) contained a subtle bug which resulted in erroneous results. - FIXED.
• Matlab Interface - Missing File - The file mmm.xml, which is neccessary to run test_mmm2.m was missing - FIXED.

Vinci 4.01.0, September 14 2012

• OrthoDisplay - Find Tool - implemented now; undo/redo incl.
  The Find Tool works on the image shown on the OrthoDisplay the tool is associated with. The tool's Minimum- and Maximum buttons cut the image at its minimum or maximum, resp. There are checkboxes to open the cross marker at the cut position or to determine the minimum ignoring the image's or the background's zero values. If you choose a mask (usually a VOI image) only the voxels within the mask (int(values) ≠ 0) will be taken into account. With Live Update switched on, any move, scaling or rotation of the masking VOI will immediately re-trigger the min-max search. Otherwise you'll have to press the Update button after changing a VOI's position. The bottom three radio buttons switch the 3D-sampling of the tool's target image.

• Threshold Tool - Re-Design - the color and the VOI index shown in the tool do now exclusively represent the color and VOI index of the next VOI that you generate when you press the Create-button. As before, a change of the VOI index changes the color in the tool and any change of the color in the tool changes the color of an activated contour. But the color in the tool does no longer influence the VOI's color after its creation and the VOI index in the tool does no longer influence the VOI's index after its creation.
  Advantage: You can now use almost the complete functionality directly when the tool opens, as long as it works on a display with defined image buffer. You can switch color and VOI index for another VOI that you would like to create without side effects on previously generated VOIs.

• Copy/Export/Print - Adapt Size to Page - the dialogs to copy, export or print OrthoDisplays, Planes- or PlotsViews have a new checkbox Adapt size to page to continuously adapt the size of the resulting image or print-out to the destination page size. Switched-on, the size of the (rest of) the image expands or shrinks when e.g. you hide or show the color legend.
• Vinci Options - Re-Ordered - we renamed the tag Load/Save to Images. We relocated the options Preferred image Units and Image Transparency Default from the General to the this new Images tag. The General tag now features the new option to Adapt size to page in the Copy/Export/Print dialogs.

• Debian Package - copyright - the copyright file is now written in the debian copyright file format specification 1.0.
• Debian Package - vinci.desktop - menu line now contains version number.

• MP4A maskless - result image test - besides the unit tests already created back in 2009, we now have a test that checks the MMM co-registration results and the resulting images k3 and k3dev and thus the whole computation procedure.

• New Licensing - obsolete license files - Vinci now warns the user if it only finds obsolete license files of the Vinci 0.x-2.x series. In either case, please feel free to register again for the new Vinci 4.x series.
• Vinci Web Site - Links to Lists of Previous Versions - the new Vinci 4 web site features links to lists of previous versions of Vinci 3.x-4.x. The 32-bit WINDOWS table entry even a link to old Vinci 1.x-2.x versions. However, the link to the Vinci 2 web site was removed.

• Matlab Interface - MMM Tool Support - Added support for co-registrations using the MMM tool via Matlab. For an example how to use MMM from Matlab, see the examples test_mmm.m and test_mmm2.m in the external/matlab directory.

• Improved Mac installer - the optional installer script has been improved for cases where the destination directory is not writable by the current user and installation requires administrator privileges (thanks, Timm).

• Qt upgrade (Mac only) - the Mac version now ships with Qt 4.8.2.

• PlanesView - Crash while Closing - PlanesView sometimes crashed during closing, especially on Macs with sparce main memory. - FIXED.
• Threshold Tool - Synch with Contour Tool - changing the contour value in the contour tool did not change the threshold in the threshold tool. - FIXED.

• MMM Tool - WINDOWS Handle/Memory Leak - the thread objects used during the co-registration were not released. - FIXED.
• Once-Only Triggered Timers - WINDOWS User Object/Memory Leak - single-shot timer signals with long timeout may have accumulated. - FIXED.
• Ipc - Memory Leak - registration and de-registration at a continuously running IpcManager instance caused memory leaks and blocked ports. - FIXED.

• Matlab Interface - In some situations, Vinci blocked indefinitely after a while because Matlab ignored Vinci's commandline output - FIXED.

Vinci 4.00.0, August 30 2012

• MMM Tool - Co-Registration of Rat Brains - now part of the default distribution. See VINCI - Co-Registration of Rat Brains (PET-MR), TOPIM - 6th Winter Conference, Proceedings, p.35, 2012 for methodical and below (releases 3.90.0 to 3.92.0) for usability details.

• Debian Package - vinci4 - a new Linux installer is available (Debian package) which should work "out-of-the-box" on several Linux distributions. The package has been tested on Ubuntu 12.04 LTS and 10.04 LTS.

• Contours Tool - Improved Integration
  • Complete Undo/Redo
  • Image Value Spin Boxes in Percent and Units
  • Reacts to Contour Changes in Threshold Tool
  • Reacts to Change of Preferred Image Units
  • Reacts to Image Creation, Overload and Deletion
  • Reacts to OrthoDisplay Creation and Deletion
  • Reacts to Change of Color Limits - if the source image's color scale determines the histogram and the user chooses live update.
  • Reacts to Change of Reslicing - if the source image's display determines the histogram and the user chooses live update.
  • Writes Complete Settings into Vinci Project File

• Reslicing Engine - legacy offset removed - an image dependent reslicing offset has been removed in preparation for a new reslicing algorithm (12-parameter affine transformation). Once, the offset was implemented for compatibility with an earlier image processing package developed at our institute. The change was planned for Vinci 4.00.0 but inadvertently took effect in Vinci 3.91.0 already. So, ROI and VOI statistics were different from version 3.91.0 to 3.99.0 compared to version 3.90.0 and earlier, sorry. From Vinci 4.00.0 onwards, the legacy offset will be re-applied automatically when loading projects saved before release 3.91.0 to make the images appear at the same relative position as when saved in these previous versions of Vinci.

• external/python - fmask(a,p,df1,df2) - new function to work on F-images (ANOVA statistics). The result has all voxel values set to zero where the F-image has values below the critical F-value and all values set to one where the F-image has values equal or above the critical F-value. Vinci calculates the critical F-value on-the-fly for a given value of p (e.g. 0.05) and given degrees of freedom df1 and df2. The value is shown in the LogView for comparison with a table.
• external/python - F calculator - the new function vc.rootF(p,df1,df2) allows one to calculate the critical F-values for explicit use in the scripts. So the formula fmask(a,p,df1,df2) is eqivalent to ge(a,vc.rootF(p,df1,df2)).
• external/python - setColorSettings(CTable=CTable,fGamma=fGamma,iStretchBottom=iStretchBottom, iStretchTop=iStretchTop,fDisplayMin=fDisplayMin,fDisplayMax=fDisplayMax) - using this new function, you can change the image's color settings for image objects, and complete groups or arrays of images.

• Image Volume Arithmetics - FMask(p,df1,df2) - you can also calculate FMasks (see above) in the image volume arithmetics tool. Just choose FMask in the combobox.
• Image Volume Arithmetics - F calculator - An additional Compute rootF button appears which logs the critical F value alone without computing the FMask image.

• OrthoDisplay - Drag & Drop - you can now drag and drop image properties like color settings, reslicing and ROIs from one Vinci 4.x session to another (undo redo incl.). If you are interested in a "look behind the scenes", drag the button on the top left corner of an OrthoDisplay (e.g. "<A>") to a text editor of your choice (you should see an XML string).

• Frame Links - All Images - You can now frame-link all frame-linkable images at once and you can now de-frame-link all images in the frame link of the shown image at once.

• LoadView - ECAT7 Image - the plugin can now handle ECAT7 images with up to 200 frames, instead of 100 before.

• New Licensing - licenses of Vinci 2.x will no longer activate Vinci from release 4.x onwards. Vinci 3.x licenses will continue to work as normal. If you still use a Vinci 2.x license please feel free to register again for the new Vinci 4.x series.

• Load Plugin - HRRT Images - computing the average during load - implemented now.

• LoadView - HRRT Image and 3DT Image - the plugins did not recognize the *.i files as HRRT image files or the *.3dt as 3DT atlas files, resp. So the corresponding file associations did not work. - FIXED.

• Color Tool - Tab Order - was in dis-order. - FIXED.

Vinci 3.99.0, July 16 2012

• Save Plugin - HRRT Images - implemented now.

• Load Plugin - HRRT Images - the header entries for Patient DOB, study date and study time may not have been correctly interpretable. In this case, Vinci now warns the user and takes the strings as they are. So the new save plugin can write them back verbatim into a new header file.
  Vinci now checks whether the frame number encoded into the file name is identical to that defined in the header file and it warns the user if otherwise. The frame number of the file name has priority.
  All non-integer numbers are now read in as double.

• ECAT7 Image - Fast Load - implemented now (all bed positions only).
• ECAT7 Image - Frame Links - implemented now (all bed positions only).
• Paravision Image - Fast Load - refactured: the plugin- and fast-load now use the same routines.

• Reslicing Tool - Use of MMM Edit Fields - you can now apply transformations from the MMM edit fields even if you have no MMM transformation file.

• Vinci Update - Linux - Vinci's update process is much simpler now. Especially, you can now update Vinci as normal user changing on-the-fly into the super- or sudo-user:
  • on a system where the superuser cannot start X-programs - only the install shell scripts run as privileged user and Vinci will restart as normal user again;
  • on a system where a special sudo enabled user runs the updates - you may edit the Run as user field and use the su -c sudo-option to temporarily change to a user with sudo powers;
  • on a system using Debian installer files (*.deb) - we are ready for the first official Debian installer for Vinci in version 4.00.0.
  CAVEATS: On updates of a version prior to 3.99.0 or on systems without the program awk, Vinci will not re-start after the installation.
• Vinci Download module - Transmitted Data - The Vinci Update and the Demo Data download modules transmit data to the Vinci Update server which we only use internally (e.g. statistics, tracking bugs), see here for details. Vinci asks you to consent "once and for all" or every time anew. Your "once and for all" consent is saved in the registry; you can revoke it in the Vinci options. If you object to the transmission you can, of course, resort to the Vinci web page for a manual download and installation.

• Image Group Based Calculations - Function Body Example Script - in the template/vpy directory, we will once and again provide simple function body sample scripts. We start with convertalltointerfile.vpy, a script that converts all loaded images up to the first free instance number into Interfile format.

• Vinci Update - Messages - Vinci 3.98.0 has delivered an update program that does not show nor re-act to possible server message. - FIXED.

• ECAT7 Image - Multiframe Image Load - did not update the header information before loading and therefore might have complained about inconsistent number of frames - FIXED.

• Color Tool - Using Preferred Image Units - the tool did not correctly interpret directly given display mini- and maxima if Vinci's preferred image differed from the current image's native units. - FIXED.

Vinci 3.98.0, June 21 2012

• Reslicing Tool - general MMM result files - The reslicing tool can now handle general MMM transformations containing zoom and stretch rotations as well as simple translations and rotations.
  You can now choose between working on an image clone (of the reslicing image(s)) or working in-place.
  If you work in-place and the registration result contains only translation and rotation parameters the image data remain unchanged and the tool computes combined transformation parameters, as before. If the MMM result contains additional stretch parameters the reslicing images' data and file names change and the images get marked as existing in-memory only.
  If you work on an image clone the original reslicing images always remain unchanged and the clone's image data display the transformation in reset position.

• external/python - alignToRef - new function to align an image to a reference image, given the scheme name or scheme as data, the filter (Human or Rat brains), pre-rotation, mask images, filename for registration result. For image groups and arrays all contained images are aligned.
• external/python - reapplyMMMTransform - new function to reapply a registration result file in MMM syntax. For image groups and arrays all contained images are handled.
• external/python - gauss3d - new function to gauss-filter an image given the FWHM in mm. For image groups and arrays all contained images are handled.
• external/python - saveYourselfAs - the function features a new tag, which saves the file appending the given value of szNameAppend to the image's file base name. The function returns the new file name now. For image groups and arrays all contained images are handled.
• external/python - Vinci_ImageT.newWrapper, Vinci_ImageGroupT.newTemporary, Vinci_ImageArrayT.newTemporary - the python interface features three new functions to generate image, image group or array objects just from known instance numbers. So your function body scripts no longer have to confine themselves to the pre-defined objects a, ... ,h from the dialog.
• external/python - new bNoLog=True default tag - the functions saveYourself and saveYourselfAs, as well as the new functions alignToRef, reapplyMMMTransform and gauss3d have the new tag bNoLog. If set to False the functions print comments about their parameters.

• Image Group Based Calculations - New Function Body - Vinci features a new button to start editing a new function body.

• Speckle Image - File Size Check - the plugin now rejects images with unexpected file size.

• Vinci Installation for All Users - you usually require administrator priviledges to install Vinci in a globally accessible directory (e.g. as root on UNIX or administrator on WINDOWS). Vinci now features a run-as dialog to copy the licence file, update Vinci and install Vinci's demo data without having to start Vinci itself as privileged user.
  • License - Copy of License File - Vinci now asks if you would like to copy the license file as the user who owns the license file directory. Tested so far using su, sudo, gksu, gksudo, kdesu and kdesudo on LINUX and using the system's runas dialog on WINDOWS 7 and XP.
  • Updater - Run Setup Program - Vinci now asks if you like to run the setup program as the user who owns the installation root directory. Tested so far using su, sudo, gksu, gksudo, kdesu and kdesudo on LINUX and using the system's runas dialog on WINDOWS 7 and XP.
    Please note the subtle difference: Until version 3.97.0 Vinci's Update GUI program started as privileged user. Now only the newly downloaded install-script (UNIX) or installer-program (WINDOWS) run elevated. This is work in progress.
• WINDOWS Installer - Vinci Demo Data - the independent demo data installer now uses NSIS' modern GUI and works in the same way as the Vinci installer, i.e. it asks to install the demo data for everyone and to run as administrator if started by a normal user.

• WINDOWS Uninstaller - When Installed for All Users - if Vinci was installed for all users as administrator the 64-bit Vinci uninstaller did not remove the WINDOWS registry entries, the menu entries, nor the desktop icon. - FIXED.
• WINDOWS Installer - Vinci Demo Data - the menu entry Update/Download Demo Data did not work for the 64-bit version of Vinci for WINDOWS. - FIXED.

• Image Group Based Calculations - Timeout - timeout was logged in milli-seconds instead of seconds as said. - FIXED.
• Image Group Based Calculations - Images with Nan Values - arithmetic operations with images with Nan values were not performed correctly. - Hopefully FIXED everywhere.

• ROI Define Tool - ROI Center Position - did not automatically update while moving the ROI in Vinci 3.97.0. - FIXED.
• SaveView - ECAT7 Image - saved an image with Nan values as if it had only zero values. Now only the Nans themselves are saved as zeros. - FIXED.

Vinci 3.97.0, April 27 2012

• Color Channel Fusion - the Fusion tool provides the new color channel fusion mode. If activated the fused image's color channels are filled by the base image (blue channel), the layer 1 image (green) and the layer 2 image (red); layer 3 is hidden in this mode. The images should be shown with gray scale palette or the new color palettes Blue, Green and Red resp., see below. The fusion sliders are de-activated in this mode. If you want to make one color channel more prominent you can change the palette in the color tool accordingly. Auto-activation in the Zoomed OrthoView and PlanesView and undo/redo are implemented.

• Color Palettes - Red, Green and Blue - Vinci features three new color palettes Red, Green and Blue which range from black at index 0 to the full colors red, green and blue resp. at index 255.

• Image Group Based Calculations - Exclude Images/Groups - the settings get saved in the registry now.
• Image Group Based Calculations - clone() and clone(value=<number>) - you can now easily create image clones, and clones with constant value. For image groups and arrays the command handles clones every image separately.

• LoadView - [RGB] Speckle series - the Speckle Load plugin now handles the three types of Speckle series [RGB].<date-time>.dat separately, so that the images can be in one directory.

• Qt 4.8.1 - now compiles with the newest Qt libraries for the WINDOWS and 64-bit-Linux and Solaris versions.

• Image Group Based Calculations - rowsum, rowsd and rowvariance - did not get created with column table type. - FIXED.
• Image Group Based Calculations - on WINDOWS: bad file descriptor - on WINDOWS, the computation may stop in complex function bodies in some print command with the error message bad file descriptor. Probably the program pythonw.exe closes its stdin, stdout and sterr channels after some time. We changed back to the console program python.exe again. - Hopefully FIXED.
• Image Group Based Calculations - complex function bodies - VHist generation may have crashed. - FIXED.
• Image Group Based Calculations - complex function bodies - undo and redo may have crashed. - FIXED.
• Image Group Based Calculations - complex function bodies - redo did not work if the function body contained the string %1. - FIXED.
• Image Group Based Calculations - Undo/Redo Title - removal of comment and empty lines did not always work. - FIXED.
• Image Group Based Calculations - unused image buffers - if you computed an expression or function body in a project where some image buffers "in-between" where left unused, the tool did not start to use them during the computation. - FIXED.
• Image Group Based Calculations - function body with Python list of variables - the initial variables a, b, ..., h were not recognized if used in a Python list. - FIXED.
• Image Group Based Calculations - variables within comments - were found and accepted as really used variables and e.g. written into the VHist file. - FIXED.

• ECAT7 Image - Load - the image data units were logged before they were set, so the LogView always showed [undefined]. - FIXED.
• OrthoDisplay Context Menu - As During Load - did only work if the LoadView was already open. - FIXED.

• MMM Co-Registration - Crashes
  • Switching OrthoDisplay during Run - resulted in a crash. You can no longer switch OrthoDisplays during the co-registration run. - FIXED.
  • Closing the Tool during Run - resulted in a crash. You can no longer close the tool during the co-registration run. - FIXED.
  • Opening a new Instance during Run - resulted in a crash. You can no longer open new instances of the tool. - FIXED.

Vinci 3.96.0, April 17 2012

• Image Group Based Calculations - Socket Mode - on WINDOWS, this mode proved to be 5-10 times faster than the pipe mode exclusively used until now; though on Linux it is the slower variant. So the socket mode is the default on WINDOWS and the pipe mode is the default on Unix. Vinci will save the latest used mode, anyway.
• Image Group Based Calculations - Line Numbering - so that you can more easily find problems in the code, the lines of the function body are now numbered in the LogView.
• Image Group Based Calculations - Undo/Redo Title - does no longer contain initial comment lines.
• Image Group Based Calculations - Full VHist Support - as for a single returned image before, the view now supports VHist for all kept images, as well as for all kept image groups and arrays.
• Image Group Based Calculations - rowmean, colmean - the calls to rowmean and colmean in the python interface, as did the calls to mean before, now support the arguments iStartIndex and iEndIndex, which reduce the indices of averaging but not the indices of the resulting group.
• Image Group Based Calculations - rowsum, colsum, rowsd, colsd, rowvariance, colvariance - the image group arithmetics tool supports these new functions now. They create column and row groups that contain the sums, standard deviations and variances over the rows and columns.
• Image Group Based Calculations - rowsum, colsum, rowsd, colsd, rowvariance, colvariance - the python interface also supports these new functions, including index restriction.
• Image Group Based Calculations - In-Place Operations with Different Operand Types - if the higher-dimensional operand group is in the second place (e.g. image + group), in-place computation is done for the second operand, if activated. The image array (two-dimensional) is considered higher-dimensional than the image group (one-dimensional) which itself is higher that an individual image (zero-dimensional).
• Image Group Based Calculations - Exclude Contained Images - in order to get shorter menus, you can now exclude images from the menu if they are contained in other groups or arrays.
• Image Group Based Calculations - Exclude Row and Column Groups - in order to get shorter menus, you can now exclude auto-created row and column groups of an image array.

• VHist Workflow-Step - MMM Co-Registration - is now handled as VHist workflow step, i.e. (a) the reslicing image is accompanied by a image VHist file and (b) the co-registration step is appended to project VHist file if the general VHist settings in Vinci's options dialog approve resp.
  The workflow step of the image VHist file describes the chosen scheme, the initial resling of all participating images, the co-registration result vector. It contains file-information of the reslicing, reference and mask images in detail (embedding the VHist files of the latter three if they happen to exist) and last not least embeds a project file of Vinci's state at the time of the co-registration.
  Furthermore, Vinci will generate or add to a project's VHist file. The workflow step contains the same information as described above but also embeds the VHist file of the reslicing image and does not contain a snapshot of the project file.

• WINDOWS Uninstaller - improved the uninstall entry in the WINDOWS registry: added icon, publisher-, version- and estimated size information, urls for product- and help-site, install location, entries for NoRepair and NoModify to inform WINDOWS that our un-installer does not modify, nor repair, but only un-install the program.

• Image Group Based Calculations - Image op Group|Array, Group op Array - numeric operations op in (+, -, *, /) with the higher-dimensional operand in the second place did not work. - FIXED.
• Image Group Based Calculations - Group mult Array, Array mult Group - array multiplication of group with array and array with group crashed. - FIXED.
• Image Group Based Calculations - Button Alignment - the evaluate buttons were not aligned on all platforms as expected. - FIXED.
• Image Group Based Calculations - Program Editing - editing the program did not always update the checkbox use in-place computation. - FIXED.
• Image Group Based Calculations - Program Editor - could not shrink. - FIXED.
• Image Group Based Calculations - Python 2.5.2 crash - the Vinci - Python combination crashed (at least on LINUX) because the XML string was cut off when the temporary image filenames got extraordinary long. - FIXED.

• MMM Co-Registration - createOutputFile - if the flag was set to "1" the output image got created but was filled with the untransformed image data only. - FIXED.

• PlotsView - Shortcuts of Copy Plot - were equal to the shortcuts to load old Vinci projects. Changed from ALT+<number> to CTRL+<number>. - FIXED.
• LoadView - ReplacePath - sometimes complained without good reason. - Hopefully FIXED.

Vinci 3.95.0, March 27 2012

• Image Group Based Calculations - a new project tool that replaces the Image Based Calculations dialog. It can compute expressions and functions of images, as its predecessor before. It can further compute with image groups and image arrays and any combination of them.
  • Additionally, you can now define a function body that may contain any code allowed in a python function definition and make use of the predefined variables a, ..., h that may represent images already loaded in Vinci and any image group or array already defined. Please be aware that in Python a function itself may contain import statements and even local function and even class definitions.
  • Vinci now saves the last 20 expressions in the registry; you can choose them from a list to re-use them in a computation. You can save and load function bodies as *.vpy text-files. Again, Vinci saves the last 20 files used in the registry and you can choose them from a list to re-use them in a computation.
  • You can use in-place computation mode in the function body part of the dialog. Simply press the check box use image in-place computation to start the function body with the string #use attach() to prevent in-place computation which itself signals the mode to our framework. This mode saves considerable time and image buffers as any image, image group or array generated during the computation will change in memory (in-place) in all the following computations. But, if you assign any such object to a python variable you must be very careful not to use this variable later in the code at multiple places, see example below, unless infact the object represented by the variable gets so-called attached. Attached images, image groups or arrays will always get cloned before further use. The predefined variables a,...,h are attached by default.
  • Example attach(): the code p=a+b; x=p+c; y=p+d yields x=a+b+c and y=a+b+d without in-place computation but x=a+b+c and y=a+b+c+d in this mode, as the system computes p in-place meaning x=p+c is done as p+=c; x=p and then y=p+d as p+=d; y=p. Remedy: the code p=(a+b).attach(); x=p+c; y=p+d yields x=a+b+c and y=a+b+d in both cases as the attached image, image group or array p always gets cloned before further use.
  • You can keep an image, image group or array which means the object is (a) attached (i.e. gets cloned before further use) and (b) is not deleted together with other temporary images, image groups or arrays at the end of the computation. So you can use a kept object for further analysis within Vinci. Of course, the image, image group or array returned at the end of the function body is kept in this sense. You need not keep it explicitly.
  • You can name a kept image, image group or array simply by giving a name in the keep-Function p.keep(name="<newname>")
  • Example keep(): the code p=(a+b).keep(name="p"); x=p+c; y=p+d; return y keeps the images p and y for further use in Vinci, where y=a+b+d, as any kept object p is also attached. p changes its name from a_plus_b to p.
  • Deletion of Temporaries - in order to retrieve memory, in the function body code, you can delete any temporarily created image, image group or array p simply by writing p.killYourself().
  • Save Image Files - in the function body code, you can save any temporarily created image, the images of any temporarily created image group or array p simply by writing p.saveYourself(). You can further determine to rename the image, image group or array including their images before saving by writing p.saveYourself(name="<newname>")

• Image Group Arithmetics - Array Operations - the tool can now add, subtract, multiply and divide complete image arrays of the same structure (equal number of rows and columns). The result is a new image array of the common structure that contains the resulting images of the required operation invoked on the corresponding image buffers of the two arrays. The tool can also multiply and add a floating point number to the image buffers of an image array, or exponentiate the whole array.
  You can compute the image of the voxel-based sum or average and variance or sample standard deviation of all the image buffers in an array.
  You can further compute the so-called Row-Mean and Column-Mean image groups that contain the means of all rows (subjects) and all columns (e.g times) resp.
  Last but not least, the tool can Array Multiply two image arrays, or an image group with an image array. Of course, the number of columns of the first operand must equal the number of rows of the second.
  
• Image Group Arithmetics - Array Operations with Groups and Images - the tool can also handle arithmetic operations of image arrays with groups of both row and column type and with image buffers.
  You can choose the group as operand in the comboboxes A and B. Arrays have a light blue background in the combobox, while image groups, as before, have a light red background and image buffers a light yellow one.
  An image array and an image group of row or column type operate the group with every (row) column of the image array. So the number of columns or rows must be equal in the image array and group. An image array and an image buffer operate the image with every image buffer of the image array.

• Image Array Define - Delete Associated Image Groups - deleting an image array now also deletes all of its associated row and column image groups; undo/redo incl.
• Image Array Define - Delete Image Buffers - when you delete an image array you are now asked whether you would also like to delete all of its image buffers; undo/redo incl.

• Image Group Define - Associated Groups Disabled - image groups associated with an image array are now disabled in the Image Group Define tool.
• Image Group Define - Delete Image Buffers - when you delete an image group you are now asked whether you would also like to delete all of its image buffers; undo/redo incl.

• external/python - case-sensitive - the expressions and function bodies defined in the Image Based Calculations dialog are now case-sensitive, as any python programmer would expect.
• external/python - number results allowed - the expressions may now result in a simple number. Up until now, expressions like 2+3 were not executed.
• external/python - Vinci_IO.SaveYourself - commands the image to save itself using its filename and type.
• external/python - Vinci_IO.KillYourself - commands the image to delete itself.
• external/python - Vinci_MMM - you can now re-use a previuously created MMM tool.

• LoadView - Flat Image - the maximal number of image values was 200 million. We encreased it to the maximum of about 512 million on a 32-bit platform and to roughly 1024 million on 64-bit platforms. Individual dimension limits for x, y and z are now 2048, which - in view of the limits above - you cannot make complete use of in all three dimensions.

• SaveView - Interfile Image - the image units are now saved with tag image data unit as is usual for HRRT images.

• Image Arithmetics - Min > 1.0e9 - the image minimum was corrected wrong if the minimum was greater than the allowed limits of 1.0e9. - FIXED.

• LoadView - Hrrt Image - possible out-of-memory error FIXED.

• Image Array Define - Operation "a * A / B + c" - the given "value if NaN" was ignored. - FIXED.

• MMM Co-Registration - crashed sometimes while trying to reslice the result-image. - FIXED.

Vinci 3.93.0, February 21 2012

• Image Array Define - a new tool to define an ordered and unique set of image buffers in the form of an array which is displayed in a table showing the image instance numbers. The image filenames are visible as tool tips.
  You can add or remove rows or columns using the appropriate spin boxes. Rows should contain subjects, they are named S<number>. Columns should contain groups (e.g. images taken at the corresponding times), they are named G<number>. When you create or delete rows or columns, the tool automatically creates and deletes so-called associated images groups of the same name (combined with the name of the image array): S<number>(image array name) and G<number>(image array name) resp. You can use the add and del buttons to do the same thing.
  Newly added rows or columns are empty, they do not contain images by default. You can edit the table items by double click. There appears a combobox to choose images from a list. This list only contains so-called compatible images, i.e. images that have the same dimension and pixel size as the images already chosen before. You can move the image items of the table using drag and drop.
  All images added, moved or deleted get also added, moved or deleted in the associated image groups S<number>(array name) and G<number>(array name) resp. Renaming the image array automatically renames the associated image groups.

• Image Group Arithmetics - Operation with Images - the tool can now handle arithmetic operations of image groups with images and images with images as well.
  You can choose the image as operand in the comboboxes A and B. Images have a light yellow background, while image group now have a light red background in the combobox.
  An operation between an image group and an image uses the singular image with every image of the image group.
• Image Group Arithmetics - Sum and Variance - you can now compute the image of the voxel-based sum and variance of all the image buffers in a group.
• Image Group Arithmetics - a * operation(A) + c - for the operations average, standard deviation, sum and variance you can now compute the image "a * operation(A) + c" in one step, where a and c are floating point constants and A is an image group.

• Scripts or Vinci Program Files - no longer clear the undo/redo list after their run, so that you can now undo their commands at their end.

• external/python - Image Group Calculations - Vinci now features two new scripts for image group calculations RunImageIGroupCalc.py and runimagegroupcalc_ia.py. As they can compute images as well, they now replace the old scripts RunImageIGroup.py and runimagecalc_ia.py that only conducted image calculations.
• external/python - Calculations More Precise - the computation factors and constants are now transported to Vinci with double precision.
• external/python - Classes Refactured - we slightly changed the structure of the Python classes Vinci_Image and Vinci_ImageT. So now Vinci_ImageT inherits from Vinci_Image. The examples were changed accordingly.
• external/python - New Classes - we introduced new classes Vinci_ImageGroup and Vinci_ImageGroupT to handle and compute with Vinci's ImageGroup objects.
• external/python - index and length operators defined - the classes Vinci_ImageT and Vinci_ImageGroupT now define the index and length operators. So for images you can now simply address individual image frames by index (e.g. a[2] will provide frame two of image a) and the number of all frames by len(a). For an image groups a you can address the i-th image simply by writing a[i], and number of all images by len(a).
• external/python - sum function - with the index and length operators defined, the built-in Python function sum will automatically work now; so the simple expression sum(a) will sum up all frames of an image, or all images of an image group a, resp.

• LoadView - ECAT 7 Image - for a multi-frame file with incorrect number of frames in the main header, Vinci now checks for and uses the correct number internally.
• LoadView - Speckle series - the Speckle Load plugin can now handle [RGB].<date-time>.dat series. They may have a separate default color table in normal display type (no difference and no quotient).

• Image Group Arithmetics - Undo/Redo - when you compute an average and use undo/redo everything is fine. But when you called undo/redo a second time, the average result image was created three times. - FIXED.
• Image Group Arithmetics - RemoveImage undefined - when you undid the creation of a image group in the image group arithmetrics tool the image group object complained about RemoveImage not being a defined tag in Vinci 3.92.0. - FIXED.
• Image Arithmetics - Power Operation - the power operation was logged false. - FIXED.

• Vinci Project File - XML compliance - µ, ² and ³ were not correctly escaped in the Vinci project file. - FIXED.

• Image VHist Files - Vinci's Image Based Calculations called "vhistadd" with pathless header-file for Anylyze images, with wrong header file name for Interfile images and with un-set header file name for MicroPET images. - FIXED.

• Load Speckle - Speckle Color Defaults - changing a parameter (e.g. the color table) in the Speckle Color Defaults dialog did not immediately update the speckle image. - FIXED.
• Load Speckle - *.<date-time>.dat - the images were read in with an offset of one float number (4 bytes). - Sorry, FIXED.

• LoadView - Interfile Image - there might have been problems loading a .hv, .v interfile image if it was not in the directory of the project file. - FIXED.

Vinci 3.92.0, January 24 2012

• MMM Co-Registration - Masks - similar to the Vinci 2.x implementation, you can now again mask out parts of the reference or reslicing image during the co-registration process, e.g. to keep the voxels of a rat head and exclude all voxels of surrounding gadgets.

• INTERNAL: MMM Co-Registration - Pre Rotate Angle - you can now freely set the pre-rotation angle, i.e. the rotation given to the reslicing image at the start of the co-registration.
• INTERNAL: MMM Co-Registration - Improved "X to Y" Scheme - converges faster now.
• INTERNAL: MMM Co-Registration - Changed "MR to Reference Brain" Scheme - now works successfully with one more of our low contrast test images.

• Shortcuts of Previously Loaded Projects - changed from N to ALT+N, for N in 0 to 9, as otherwise you could load a project accidentally on some read-only edit fields just by pressing a number.

• Visual Studio 2010, SP1 - Vinci now uses the newest MS compiler version for the WINDOWS platform.

• Load MicroPET - Multiframe-Images - in single frame mode Vinci always loaded the first frame; in range mode Vinci always started with the first frame. - Sorry, FIXED.

• Load ECAT7 - MD5 checksums - the additional computation of the whole file md5 checksum considerably slowed down loading of multi-frame files since Vinci 3.90.0. - FIXED.

• Matlab Interface - Internal XML Parsing - Characters such as the micro-, squared- or cubed-sign in messages passed from Vinci to Matlab caused problems. - FIXED.

Vinci 3.91.0, January 10 2012

• INTERNAL: MMM Co-Registration - Rat Schemes
  • Improved Schemes - compared to the gold standard (manually co-registered).
  • Low-Quality MR Schemes - we now discriminate between schemes for good- and low-quality MR images, defined by the number of z-planes of the images.
  • Low-Quality PET Schemes - we now also discriminate between schemes for good- and low-quality PET images, though it is not always obvious when exactly which setting should be used. The low-quality scheme co-registers two water PET images and all our test DOPA images, however, two thirds of the DOPA images show better results with the good-quality schemes. F18 PET data is still work in progress.
  • Reference Brain - the reference brain is now part of the release.

• INTERNAL: MMM Co-Registration - Convenience
  • Helper Images Invisible - the co-registration helper images do no longer appear in the reslicing image list.
  • Keep Reslicing Image Selected - during undo/redo of a change of the reference image, scheme or brain filter.

• Running a Vinci Program File (.vprog) - Vinci program files (.vprog) include the Vinci options that were current when they were saved. The options are re-created during the run of the Vinci program file. If run from within Vinci (Menu entry: Edit/Run Vinci Program File...) the options set by the program file are now reset at the program end.

• Online Update - Unix - the Vinci Update program has to wait for tar to extract the program files. Until now Vinci Update waited 20 seconds which may not be enough on some machines as the setup has again and again got bigger. We increased the timeout to 60 seconds now.
  If the update does not work because of this problem, you will have to get the new version from the vinci web site once. - Sorry, FIXED.

• Image Reset Position - Cut Position in Z - for images with z-dimension less or equal to 10 the reset cut position may have had an offset. - FIXED.
• Opening Context Menu with open Rubberband - did not hide the rubberband during a zoom on the Ortho- or PlotsView and during graphics item selection. - FIXED.

Vinci 3.90.0, December 8 2011

• INTERNAL: MMM Tool - Co-Registration of Rat Brains - Vinci now features a new set of schemes to co-register rat MRI images to a reference brain in a normalized position, also to co-register rat PET images to corresponding MRI data (provided these are in a normalized position). We have had very promising results with anatomical MRI data and FDG-PET images. On the other hand, one third of the DOPA-PETs and the one F18-image, we tested, did not work well. This is work in progress.
  If you do not have MR images of your rats, you may try to co-register the PET images directly to the reference brain, which, alas, may not work as precisely in the angles as desirable (up to +/- 5 degrees difference to what you expect). However, even so the result may help you to start the manual registration from a more convenient position.
  Please be aware that most of the new features are experimental and internal, i.e. they are only available at the institute or with an appropriate license file, for now. The reference brain is not part of this release.
  • Requirements for MRI data - the MRI image should contain the rat's complete brain. It should be positioned in the opposite octant of the reference brain (rotation around the z-axis).
  • Requirements for PET data - the PET image should contain the rat's complete brain in addition to its nose. It should be positioned in the same octant as the reference brain.

• INTERNAL: MMM Co-Registeration - Special GUI Features
  • Filter - the tool now differentiates between the handling of "Human brains" and "Rat brains"; here you can choose between the two sets of schemes. Without appropriate license file, you will only see the "Human brains" part, as before.
  • Reference Image Type - the edit field shows the reference image type of a given reference image (if available).
    Two types are currently defined: "head mask" and "ref brain". If a scheme pre-scribes a specific type of reference image the tool pre-selects the image for the given scaling, see below; if the file is already loaded into the project, the pre-loaded image is used, if not, the reference image will load during the start of the co-registration. If you change the scaling the reference image will change accordingly.
  • Scaling - MMM supports the automatic use of the correct reference image for a chosen scaling. For now, you can choose only between the fixed scaling factors of 90%, 95% and 100%.
  • Pre-Rotation - a scheme can determine that an reslicing image in reset position is rotated before the actual co-registration starts. You can switch off the pre-rotation defined in the scheme temporarily with the pre-rotation checkbox, the edit field shows the pre-rotation angle, and the "as scheme" checkbox indicates whether the current setting is the same as in the scheme.

• INTERNAL: MMM Co-Registeration - Rat Schemes - Vinci also features some new tweaks of image preprocessing in MMM's registration schemes. Please be aware that these new possibilities are also experimental and internal, i.e. they are only available at the institute or with an appropriate license file, for now.
  
  • threshold type="border" - uses a heuristic method to determine the "border" of a PET image and threshold it.
  • averageScale="..." - in threshold of type value, scale it by the given value times the image average; in threshold of type border, scale it by the given value divided by the image average.
  • preRotate="..." - rotate an reslicing image in reset position by a given angle before the co-registration starts, e.g. "0 0 3.14159..." i.e. 180° around the z-axis.
  • recursive schemes - it is now possible to use one MMM co-registration as pre-processing of another one.
  • reference image types - schemes can now pre-scribe a given type of reference images; the actual reference image used depends on the chosen scaling.

• MMM Co-Registeration - Multiple Targets - you can now start the co-registration of a set of images at once; undo/redo included. The Cancel button next to the progress bar cancels the whole operation. The Finish button in the status dialog cancels the co-registration of the image in progress, as usual.
• MMM Co-Registeration - RunMMMJob.py - adapted to multi target requirements. As a result, the reference and reslicing images are now set explicitly after sending the InitJob-command; also, the MMM task now waits for its own thread to finish, so there is no more need to wait within the python code.
• MMM Co-Registeration - Undo - implemented now.

• MMM Co-Registeration - New Vinci Options -
  • Scroll to Image - MMM - in multi target mode - scrolls the currently handled image into view if you switch on the new option Scroll to OrthoDisplay that shows the currently co-registering image, which is the default.
  • Live Reslicing - the image will reslice "online" on every iteration step if you switch on the new option Live reslicing on each iteration step, which is not the default. We recommended to only use this feature on fairly fast computers.
  • File Dialog - MMM opens a file dialog - without any questions asked - to load a reference image into the current project if you switch on the new option Show file dialog to search for and load a reference image the system cannot locate by itself, which is the default.
  • Hide Sub-Schemes - MMM hides all schemes only used as helpers within other schemes if you switch on the new option Hide sub-schemes called recursively by other schemes, which is the default.
  • Scheme Filter Setting - the scheme filter is saved in the registry. So when you close Vinci and start it again, MMM opens up with the filter of your last usage.

• Matlab Interface - Resampling - added a resampling function (Vinci.resampleImage) to bring two images into the same coordinate system. You can use this function to co-register two images in Vinci and then resample them, so that they are co-registered in reset position. You can then easily compare both images in Matlab. See test_resample.m for an example. Warning: this function is in beta state, undocumented and might be changed in future releases.
• Matlab Interface - Typechecks - started to add type checks to the Matlab interface.
• Matlab Interface - Updated Tutorial - the tutorial about the Vinci Matlab interface now contains more material. You can find the online version of the tutorial here.
• Matlab Interface - HTML API Reference - An HTML version of the new Matlab interface reference is available here.

• MMM Co-Registration - Wrong Initial Reslicing - using initial reslicing of the images did sometimes not work correctly if they were rotated around more than one axis or were both resliced before registration, resulting in a jump of the reslicing image during pre-processing, see also below. - FIXED.
• MMM Co-Registration - Reversible Reslicing Jump - during pre-processing the reslicing image's position did sometimes jump reversibly if their was another run of MMM beforehand. - FIXED.
• MMM Co-Registration - Version Independent Personal Schemes - due to a typo, you could not use the version independent MMM co-registration schemes in Vinci_Common/MMM; Vinci always used the schemes of the current Vinci version instead. - FIXED.
• MMM Co-Registeration - Auto Zoom - MMM did not delegate the computed reslicing parameters correctly if image auto zoom mode was activated. - FIXED.
• MMM Co-Registration - Reslicer - may have crashed under special circumstances due to an unset variable. - FIXED.
• MMM Co-Registration - Redo - FIXED.

• Matlab Interface - Rectangle Roi Coordinates - setting and then getting geometry yielded slightly different coordinates - FIXED.
• Matlab Interface - Ellipse Roi Coordinates - setting and then getting geometry yielded slightly different coordinates - FIXED.
• Matlab Interface - Polygon Roi Coordinates - setting and then getting geometry yielded slightly different coordinates - FIXED.
• Matlab Interface - Profile Coordinates - setting and then getting geometry yielded slightly different coordinates - FIXED.
• Matlab Interface - Annotation Properties - Getter function for bold, italic, strikeThrough and underscore did not function - FIXED.
• Matlab Interface - Exception Identifiers - Exception identifiers used varying formats - FIXED.
• Matlab Interface - Timeouts - Matlab sometimes blocked indefinitely if Vinci crashed or did not resond to a request - FIXED.
• Matlab Interface - Ortho View - Vinci.OrthoView.getFirstOrthoView() did not work - FIXED.

Vinci 3.85.0, November 4 2011

• Speckle Image - Now with VOIs - due to the twenty-plus bug fixes in this and the last release, VOI creation, editing and operations on images in TruePixel mode with non standard image matrix size (i.e. the default for Speckle images) should work now.
  Please keep in mind that, for now, the image and its VOI image should stay in the same 3D-interpolation mode (e.g. both in TruePixel mode) and should be displayed with the same sampling dimension and image matrix size.

• OrthoView and PlanesView - Image Rotation - you can no longer rotate images displayed in TruePixel mode. Until now, when you tried, it had no visible effect but infact rotated the image invisibly.
  You can still set the rotation center but afterwards the mouse now switches back to arrow instead of rotation mode.

• PlanesView - Linear Double Click Zoom - the zoom factor now increases with each double click and decreases with each double click with pressed ALT key.
• PlanesView - Graphics Item Creation - you can now activate the mouse modes for interactive graphics item creation in every menu or context menu of the PlanesView.

• RunTests - Test Result Files - the test result html page does no longer contain absolute paths. So, you can open the links directly on any network drive now.

• Search Dialogs - You can now click into the log view or the text panel of the info view and press Ctrl+F to open a search bar at the bottom of the widget.
• Project View - Menu Update/Show Project File - The project view now closes automatically when Vinci closes. It is now a real MDI-window in MDI-mode (the default on WINDOWS).

• Vinci Matlab Interface - small improvements
• Updated Documentation - added documentation for most display objects.
• Version Check - When Matlab connects to Vinci, it will compare the version of Vinci with the version of the Matlab bindings and warn if they are not compatible

• OrthoDisplay and PlanesView - Copy/Export/Print did not show the images in Vinci 3.84.0. - Sorry, FIXED.
• Contours Tool - Histogram - the histogram has been too small since Vinci 3.73.0. - FIXED.

• Deletion of the last View - in MDI mode, deleting the last view left over the specific menu entry of the view in the main menu bar. Vinci used to crash when you clicked on this remnant menu entry. - FIXED.
• Red Tool Tip Warnings - Vinci's red tool tip warnings no longer block the execution of the program, which has led to a crash in very special circumstances. - FIXED.

• OrthoDisplay - Fusion of Image with cubic and non-cubic Image Matrix Size - when you fused an image with cubic (e.g. 256x256x256) with an image with non-cubic (e.g. 768x512x256) matrix size:
  • One image was squeezed or blown up depending on which of the images serves as fusion background image. - FIXED.
  • The image coordinates shown in the OrthoDisplay info line might have been wrong. - FIXED.
  • Moving cross, cross marker and rotation center might have been drawn at the wrong position. - FIXED.
  • Contours might have been drawn squeezed or blown up. - FIXED.

• PlanesView - Changing the Image Matrix Size - when you changed the image matrix of an image in fusion on PlanesView from a cubic (e.g. 256x256x256) to a non-cubic (e.g. 768x512x256) value, one image was squeezed or blown up depending on which of the images serves as fusion background image. - FIXED.
• PlanesView - Fusion of TruePixel and non-TruePixel Image - when you generated PlanesView via the info line of an OrthoDisplay that showed the fusion of an image in TruePixel mode and an image in non-TruePixel mode the PlanesView display size might have been wrong. - FIXED.

Vinci 3.84.0, October 21 2011

• Vinci Matlab Interface - Several new features:
• Reslice Parameters - New properties RotAngles, RotCenter, CutPosition, Offset, SmplDimension and Zoom in Vinci.Image.
• Roi Evaluation - Rois can now return the original values used to calculate statistics. You can use these values to calculate statistics other then the ones provided by Vinci.
• Creation of New Images - You can now create new images from a three-dimensional floating point array. Various properties, such as the filename or the pixel size of the image can be set during the creation of the image.
• Cloning Images - You can clone an existing image and reset the pixel size and image volume of the cloned image. Cloning copies metadata, reslicing parameters, ROIs and color settings of the original image.
• Measure - It is now possible to create and manipulate measures from within Matlab. The length of a measure (in mm) is available through the length property of the measure.
• Close and Kill Vinci - We have added methods to close and kill a running Vinci instance. Vinci.Connect.closeVinci() can be used as long as the connection to Vinci did not break before (which usually does not happen). Vinci.Connect.killVinci is only for emergency situations, in which closeVinci() cannot be used.
• New Tutorial - We started to write a tutorial, which explains how to use the Vinci Matlab interface. To find it, open up the Vinci documentation, click on the Docu Home Button in the top left corner and then select the "Matlab Interface" link in the introductory text. Alternatively, go to the online tutorial. The tutorial is not complete, yet, but it already contains some information on how to get started when using the Matlab interface.

• Geometrical VOIs - Convenience
  • Small Geometrical VOIs on Small Images - on images with pixel size below the auto zoom threshold (usually 0.5 mm) the default size of geometrical VOIs is scaled down by the auto zoom factor (usually 10.0).
  • Position Limits - geometrical VOIs can now move outside of the image by a small margin.

• Geometrical VOIs - Load Vinci Project File - loaded from a Vinci project file, geometrical VOIs on images with non-standard image matrix size (unequal 256) changed positions and widths. - FIXED.
• Geometrical VOIs - Change of Image Matrix Size - changing the image matrix size of a VOI image changed positions and widths of geometrical VOIs. - FIXED.
• Geometrical VOIs - In TruePixel Mode - did not always show the correct widths. - FIXED.
• Geometrical VOIs - In TruePixel Mode - did not always rotate by mouse. - FIXED.
• Geometrical VOIs - Changing 3D-Sampling Method from and to TruePixel mode did not reflect correctly in the positions and widths of geometrical VOIs. - FIXED.

• OrthoDisplay Props - Image Matrix Size - if you had a fused display (on an Ortho- or PlanesDisplay) showing the base image and the graphics items of the fused image and you changed the matrix size of the fused image the graphics items would paint with wrong size and the cross marker would change its position. - FIXED.
• OrthoDisplay Props - Image Sampling Dimension - reducing the image sampling dimension may have crashed Vinci since 3.82.0. - FIXED.
• OrthoDisplay - Changing 3D-Sampling Method from and to TruePixel mode changed the cut position of linked images. - FIXED.
• OrthoDisplay - CrossMarker and Rotation Center was drawn in the coordinate system of the graphics item base image instead of the fusion base image. - FIXED.
• OrthoDisplay - Moving Cross was almost invisibly thin if the image was drawn with a matrix size > 256. - FIXED.
• OrthoDisplay - Moving Geometrical VOIs on a Zoomed OrthoView brought the main OrthoView into the front if it had an open VOI tool and thus obscured the movement of the VOI. - FIXED.

• PlanesView - Creation via OrthoDisplay Info Line - Vinci crashed when you created a PlanesView via the OrthoDisplay info line on a display that showed a fusion of two images with different matrix size in TruePixel mode. - FIXED.
• PlanesView - Moving Cross - may have had a vertical offset for the coronal or sagittal slices of an image in TruePixel mode. - FIXED.
• PlanesView - Frame Repaint - when the user changed the OrthoPart the info line did not repaint; when the user increased the number of displays and scrollbars appeared the scroll bars and their corner widget did not repaint, neither. - FIXED.
• PlanesView - Moving Geometrical VOIs on OrthoView or PlanesView did not update the VOI image on the PlanesView. - FIXED.

• VOI Image - NaN Option - if you chose in the Vinci options dialog's Load/Save tag to display the area outside of an image as having NaN values, then the area outside of a VOI image was shown with the color of the highest VOI entry instead of the color black of the background. - FIXED.

• Vinci Matlab Interface - programming interface changes since the last release:
• Image.get/setResliceParameters - RotAngles are now stored in radians instead of degrees.
• Image.getDObjects - Now returns objects of type Vinci.DisplayObject, instead of structs with internal data.

Vinci 3.83.0, October 7 2011

• Image Group Define - a new tool to define an ordered and unique set of image buffers. You can use image groups to operate on all the image buffers of the group at once, or compute one new image from all the image buffers of the group.
• Image Group Arithmetics - a new tool to add, subtract, multiply and divide image groups. The result is a new image group that contains the resulting images of the required operation invoked on the corresponding image buffers of the two groups.
  The tool can also multiply and add a floating point number to the image buffers of an image group, or exponentiate the whole group.
  Last but bot least you can compute the image of the voxel-based average and sample standard deviation of all the image buffers in a group.

• Vinci Option - Keep ROI Position Relative to 2D-Images - Vinci now features a new option in the Graphics Items tag which allows to keep the ROI position fixed relative to the image background for all image reslicing operations if the image's z-dimension is less or equal to a given dimension (10 by default).
  The operations include mouse induced reslicing of the image incl. link channels, Reset Image Buffer and Reset Link Channel, Reset to Saved Reslicing State and Reset to Saved Link State, Drag and Drop Sync Resl and Sync Zoom, Magic tool general reslicing, Sync Resl and Sync Zoom, enter link channel Initial Reslicing, OrthoDisplay Props tool Change of Sampling Dimension (TruePixel Zooming).
• Drag and Drop - Reslice - synchronizes reslicing and zoom parameters at once, as before, and consistent with the Magic tool again.

• Major Update of the Vinci-Matlab-Interface
  • Matlab 2009a Support - The interface should now function with Matlab 2009a and newer. We tested the examples using Matlab 2009a, 2009b and 2011a.
  • Shortened Package and Class Names - We renamed the package from VinciMatlab to Vinci and removed the Vinci-prefix in most classes. For example, VinciMatlab.VinciImage is now called Vinci.Image.
  • Added Classes for Most Display Objects - You can now create and manipulate profiles, annotations and groups from within Matlab.
  • Added Classes for Many Views - You can now create and use OrthoViews, OrthoDisplays and PlanesViews from within Matlab.
  • New Examples - Added new examples, which show the new features.
  • More Documentation - Added more inline documentation, which can be accessed from within Matlab using the help or doc commands. One of the next releases will contain an HTML version of the API reference.
  • The Matlab API is subject to change without notice in all its aspects. However, we try to keep it compatible with older and with future versions from now on.

• TruePixel Mode - Linked Zoom - implemented now; undo/redo incl.
• TruePixel Mode - Reset Link Channel - implemented now; undo/redo incl.
• TruePixel Mode - Save Link State - implemented now; undo/redo incl.
• TruePixel Mode - Reset to Saved Link State - implemented now; undo/redo incl.

• Qt 4.7.4 - now uses newest version of Nokia's Qt libraries.

• Magic Tool - Reset Cut Position - did not work correctly in TruePixel mode - FIXED.
• OrthoTool - Change OrthoDisplay - wrote tool deletion into the undo/redo-list - FIXED.
• Profiles Tool - Position Spinboxes - changing the position of a vertical or horizontal profile with the spinboxes changed the move restriction back to free. But this change was not immediately reflected in the tool - FIXED.
• Text Define Tool - Generic Text - some automatic text substitutions did not work - FIXED.
• Reslicing Tool - Undo Select None - may not have worked correctly after Insert All - FIXED.

• Object Representation in Matlab - in some situations, saving and loading Vinci projects while using them with Matlab caused problems with objects having different names after loading the project file. - FIXED.
• Roi Names - Vinci crashed when creating two ROIs with the same name - FIXED.

• Renaming Views - Renaming OrthoViews and PlanesViews will cause Matlab proxy objects to break, so far.

Vinci 3.82.0, August 19 2011

• Interface for Controlling Vinci from within Matlab (First Preview) - you can now remotely control Vinci from within Matlab. This code is a first preview. All features are supposed to work but the interface is not stable yet and will change in the future. A set of examples can be found in the external/ directory in your Vinci directory/.app bundle. The Matlab interface should work with Matlab2009b and later, but not with earlier versions of Matlab. Features supported so far are:
  • Starting and Connecting to Vinci - Matlab can start a new instance of Vinci or connect to an already running instance of Vinci. One Matlab script can start several Vinci instances if neccessary.
  • Loading Images - Matlab can load both, flat images as well as images stored in one of the formats supported by Vinci.
  • Getting and Setting Meta-Information - Matlab can inspect Vinci images and query meta-information about an image. Setting properties of an image to new values is also supported for some properties, such as PatientName or Comment.
  • Manipulating Image Volumes - Matlab can read and change Vinci image volumes. Image volumes are represented as three-dimensional arrays of floats in Matlab. Manipulating images makes it possible to write complex image filters in Matlab while still using Vinci to load, save and display images.
  • Creating and Evaluating ROIs - Matlab scripts can create and evaluate ROIs. Rectangular, elliptic as well as polygonal ROIs are supported.
  • Executing Program Files - Matlab scripts can execute Vinci program files exported from Vinci.
  • Miscellaneous Functions - Fusing views, opening ortho views and planes views, loading projects and making screen shots is supported.
  • Examples - You can find a set of examples in the external/matlab directory. Note that these examples may only work correctly when the default project is set to an empty project.

• VOI Manipulation - Mouse Edit - you cannot edit geometrical VOIs. So, when you only have geometrical VOIs you may come to think that the tool does not work at all. In this case, when you activate mouse edit mode, you now get the warning: "You can edit boids only !".
• Drag and Drop - Reslice and Zoom - you can now synchronize reslicing and zoom parameters at once.
• Magic Tool - Sync Resl and Zoom - the tool now works only on TruePixel images if the reference image is shown in TruePixel mode and it works only on non-TruePixel images if the reference image is shown in next neighbour or triliniear mode.
• Meta Link - Always Accessible - the popup menu entry "Meta Link" is now always accessible displaying an appropriate error message if it does not work in a given situation.
  Beware: You can only create a meta link between two link channels on an OrthoDisplay that fuses images from these two channels.

• Non-Cubic Matrix Size - in non-TruePixel mode - non-cubic matrix size values are now fully supported also for tri-linear and next neighbour interpolation; in TruePixel mode everything is supported, as before.

• XMLTarget FrameWork - Binary Data - you can now use the XML target framework to send binary data from another application to Vinci or read binary data from Vinci into another program. We have implemented SetImageVolume and GetImageVolume to set and get the float matrix of an existing Vinci image buffer.

• Group Object - Member Selection - sometimes in a group object with switched off bounding rectangle, when selecting the group not all members showed their grips. - FIXED.
• Measure Object - Selection - you could sometimes not select Measure Objects correctly. When you tried only the profile would move but did not show its grips - FIXED.
• Measure Object - Length - the length was computed wrongly on images shown with non-cubic matrix size in tri-linear or next neighbour interpolation - FIXED.
• Measure - Rotation - when you rotated a measure with the mouse undo did not set back the measure's rotation angle and complained about the undefined XML tag handler for SetProfileGeometry. - FIXED.
• Measure Object - Zoom - zooming a measure object also changed the text size - FIXED.

• Drag and Drop - Sync Zoom - did not work for images with non-cubic matrix sizes e.g. Speckle images - FIXED.
• Set to Saved Resl State - TruePixel Mode - the image was not correctly set back to the saved reslicing parameters; there was a small change in the cut position, offset and center of rotation - FIXED.
• Vinci Start-Up - Delayed - with an open OrthoDisplay Properties tool in the Vinci project file, Vinci sometimes started rather slowly due to a rather big clipboard contents - Hopefully FIXED.

• Meta Link - Cut Sync Only - if you had, say, the red link channel in cut-sync-only mode and, say, the green link channel in normal mode and these two link channels in a meta link, then moves, zoom and rotations were not propagated by the meta link. - FIXED.
• Meta Link - Sync Rotation - undo/redo did not propagate to the other link channel. - FIXED.
• Meta Link - Reset Link Channel, Save Link State and Reset to Saved Link State - these commands were propagated to the meta-linked channel. - FIXED.

• Zoomed OrthoView - Thresholded ROIs - the ROI area within the threshold values did not show at the correct position on a Zoomed OrthoView since Vinci 3.47.0. - Sorry, FIXED.
• Change Matrix Size - Thresholded ROIs - Vinci crashed when you changed the image's matrix size while using a thresholded ROI. - FIXED.

• Speckle Frame - Template - was corrupt - FIXED.

Vinci 3.81.0, July 28 2011

• Undo/Redo for Deletion of Views and OrthoTools

• InfoView - Navigation - Vinci now protocols TreeView navigation.
• InfoView - Save Project - Vinci can now re-create the InfoView on the correct page.

• Load Speckle - Find Combobox - when you choose an entry from the find combobox Vinci now searches for strings that match exactly. When you press the find button, though, Vinci searches for strings that start with the given substring, as before.
• Report Tool - Test Templates - we added a new Speckle template to generate tables that do not contain the image path. The common image path is now given in the table header.
• VOI Define Tool - Save Atlas Description - saves a table of index <TAB> name rows for all VOI entries ready to be loaded again with the button Load Atlas Description.

• Report Tool - Lots of Frames - the creation of a report for very many frames (e.g. 10000) was very slow and consumed too much memory. - Hopefully IMPROVED.
• ROI Report / VOI Report - Column Separator - each row contained an extra column separator at the lines' ends. - FIXED.
• ROI Groups - Statistics - may not have correctly worked on images with NaN values. - FIXED.
• Measure Object - Middle Grip - displayed the profile's middle grip to change its width if created by mouse. - FIXED.
• Profiles - Image with NaNs - when you created a profile with open PlotsView on an image with NaNs Vinci may have entered an infinite loop. - FIXED.
• Profiles - NaNs outside of the Image - when you moved a profile with open PlotsView out of the display Vinci may have entered an infinite loop. - FIXED.

• Frame Link - Remove a Single Last Image - Vinci crashed if you removed the single last image from a frame link. - FIXED.
• LoadView Speckle - Speckle Slider - the slider did not work when the image path contained a "..\" directory. - FIXED.

Vinci 3.80.0, March 29 2011

• Geometric VOIs - Cuboids, Ellipsoids and Cylinders - Vinci now features geometric VOIs, i.e. VOIs that are only defined by their shape, position, width and orientation. They can be manipulated with the mouse using rectangular and/or elliptical graphics items that represent the positions, widths and angular orientations of the VOI face visible on the three OrthoParts. CAVEAT: geometric VOIs are never saved in the VOI image but in the Vinci project file alone.
• Differences to the Vinci 2.x versions
  • Cylindrical Entries - Vinci 3.x features cylindrical VOIs; they are represented by one elliptical and two rectangular graphics items.
  • Symmetrical Entries - you can use symmetrical VOIs i.e. VOIs that have identical widths in all three dimensions.
  • Copy / Paste - you can copy and paste all sorts of VOIs from one index volume to another, even to one with different zoom level, see below.
  • Point VOIs - do no longer exist; use symmetric ellipsoids instead.

• 64-bit WINDOWS Version - Vinci now also features a native 64-bit WINDOWS flavour of its programs (amd64 compatible build); tested on WINDOWS 7, so far. This version will, of course, not run on a 32-bit WINDOWS system, and the setup program will refuse its installation. Please consider the image formats to be restricted to 4 GB length as before.
• Differences to the 32-bit WINDOWS versions
  • Noticably Faster - about 15 % on our test machine.
  • No Quicktime Movies - as there is no 64-bit Quicktime SDK for WINDOWS.
  • 64-bit Icons - i.e. icons that carry the number 64 in their lower right corner.
  • ROI Statistics - our tests found lots of insignificant differences in the ROI statistics.
  • MMM Registration - our tests also found differences in the registration parameters which were, as usual, within the range of parameter limits MMM was configured to observe.

• VOI Evaluation - Zoomed Index Volumes - Vinci can now evaluate VOIs on linked images with different zoom level. In particular, you can now evaluate a VOI on an image that has another zoom level as the image the VOI is defined on. As usual, in the VOI Define tool you only have to change from the VOI defining image's OrthoDisplay to the other image's OrthoDisplay.

• Load NIfTI - now also loads data in (L2R, A2P, I2S) orientation.

• Load Flat Image - now also supports UINT16 (unsigned short) data type.

• Image VHist Files - Vinci called "vhistadd" with wrong command-line arguments for MicroPet and Interfile images. - FIXED.

• VOI / ROI Report - a redo of the table creation might not have worked - FIXED.

Vinci 3.76.0, March 11 2011

• Load NIfTI - now also loads data in (A2P, I2S, L2R) orientation.

• Qt 4.7.2 - now uses newest version of Nokia's Qt libraries.

• Reset Link Channel - did neglect a small offset which is important for images with different sampling pixel size i.e. different zoom level. - FIXED.

• ROI Define Tool - Statistics Update - the ROI statistics did not change immediately when you chose another graphics item base image in the OrthoDisplay info line. - FIXED.
• Report Tool - 2D-Template "Speckle Frame" - Zoom Method place holder was corrupted. - FIXED.
• Load Test Project/Load Test - Vinci did no longer ask what to do after loading the test project or the test, it simply used the default answer "Append". - FIXED.

Vinci 3.75.0, January 28 2011

• LoadView - 2D-Image - the plugin can now read indexed 8-bit image types i.e. images with included palette; the image values are set to the index in the palette.

• SaveView - Interpolation: Next Neighbour - the option to save the image using next neighbour interpolation is now switched on by default for any index volume.

• Graphics Items - Multi-OrthoPart Click Selection - on an OrthoDisplay, you can now add a graphics item of one OrthoPart to the selection on another OrthoPart simply by pressing the CTRL-key while clicking on the item.

• OrthoDisplay - Reset Link Channel - resetting the link channel on images with different zoom level (e.g. to provide for size differences between young and adult rats) led to an offset in the rotation center and cut position. - FIXED.
• LoadView - Speckle Image - when you loaded a Speckle image into an empty project, undid the load and redid it again, Vinci might have crashed. - FIXED.

• VOI Manipulation - Erase Connected Voxels - if the voxels of a given index were separated by a gap that itself was bridged by a voxel group of an higher index and you clicked on one part of the separated voxels, all of these voxels were erased. - FIXED.
• VOI Define - VOI Index - when you changed the VOI index you sometimes got warned multiple times that the index was in use. - FIXED.
• VOI Define - Find VOI - when you pressed the Find button to cut the image at the center of the currently selected VOI, the undo/redo list sometimes showed multiple entries. - FIXED.

• Rectangle and Ellipse Items - Symmetric - when you made a rectangle or ellipse item symmetric it sometimes jumped and changed its size unpredictably. - FIXED.
• Graphics Group - Change Member Object Type - changing the object type (e.g. from rectangle to ellipse) of a member of a graphics item group did not work properly. - FIXED.
• Graphics Items - Undo Deletion - when you deleted graphics items of different OrthoParts on an OrthoDisplay or on different image buffers in a PlanesView and afterwards undid the deletion, not all of the re-created items were properly selected. - FIXED.
• Graphics Items - Multiple Selection - click-selection did not always work correctly on an OrthoDisplay showing an image buffer that was also visible twice on a PlanesView. - FIXED.
• Temporary Graphics Items - their creation and/or deletion may unnecessarily have appeared in the undo/redo list in some cases:
  • Speckle Calibration - Measure - the measure you draw to calibrate the Speckle series. - FIXED.
  • VOI Manipulation - Encircle a Voxel Group - the polygon you draw to encircle the voxels if it gets deleted immediately. - FIXED.

Vinci 3.74.0, December 23 2010

• Speckle LoadView - Synched Set of Range - with activated checkbox Frame Link, the buttons Set First Frame, Set Last Frame and Reset to Full Range now work for all Speckle series in the frame link. The type of frame link is observed, which means e.g. for a frame link by absolute time that the first frames of the other series will have their absolute times near the given value of the absolute time of the first frame of the series the LoadView is currently working on.

• Load Image - Auto-Zoom - by default, images of all image types are now auto-zoomed (i.e. loaded with zoom factor 10, by default) if their minimum transaxial pixel size is less than the auto zoom threshold, 0.5 mm by default.
  Images loaded using auto-zoom now stay auto-zoomed during calls to Reset Image Buffer and Reset Link Channel. You can save auto-zoomed images using offset and rotation in the same way as un-zoomed images.

• Link - Cut+Zoom Synch Only - Cut Synch Only image link mode, designed for manual co-registration, now includes zoom operations, by default, and changes its name accordingly to Cut+Zoom Synch Only.

• Vinci Options - Vinci supports the following new options:
  • Auto Zoom - Load/Save Tag - you can switch off auto-zoom now, determine the auto zoom factor and threshold pixel size.
  • Cut+Zoom Synch Only - OrthoView Tag - here you can switch back to the traditional Cut Synch Only image link mode.
  • MMM Schemes File - MMM Tag - on this new tag you can choose which MMM schemes file to use. Default is the schemes file of the current Vinci version. The button Copy Used to Common copies the currently used MMM schemes file into the "Vinci_Common/MMM" directory in Vinci's install root directory and afterwards uses this copy. With the Browse button you can choose an arbitrary schemes file on your machine. The button Use Default switches back to using the default schemes file of the current Vinci version.
  • Transparency on Fused Displays - Load/Save Tag - here you can define what is transparent on fused displays: color 0 (black) if used in the color table or color index 0 of the color table as always stated.

• VHist Workflow-Step - OrthoDisplay Copy/Export/Print - copy to clipboard and the export of an OrthoDisplay as BMP-, PNG- SVG- and PDF-files is now handled as VHist workflow step, i.e. (a) the exported files are accompanied by flat image VHist files and (b) the export step is appended to project VHist file if the general VHist settings in Vinci's options dialog approve.
  The flat image VHist files are based on the possibly existing VHist file of a source image if the OrthoDisplay shows only one image. If the OrthoDisplay shows more than one image (e.g. in fusion) existing source image VHist files are embedded. The workflow step describes the chosen options of the Copy/Export/Print dialog and the source images in detail and contains a project file of Vinci's state at the time of the export.
  Furthermore, Vinci will generate or add to a project's VHist file. The workflow step describes the options of the Copy/Export/Print dialog and the source images in detail (embedding the VHist files of the latter if they happen to exist).

• VHist - Undo Add Workflow Step - in any operation protocolled by VHist, the program adds a workflow step to a VHist file. An undo of the operation now removes this added workflow step from the VHist file.

• Vinci_Python - RunStudy.py - example script for Vinci automation, like file conversion, data analysis, etc. Aim: You do it once, for one data set, then run a script that does it for all other data sets.
  In-between you'd have to export a Vinci program file and in a text-editor replace data set and session specifics (names, paths, etc.) by place holders. See RunStudy.txt for details.

• Qt 4.7.1 - now uses the newest version of Nokia's Qt libraries.
  CAVEAT: Our nightly tests detected slightly different pixel sets for some ROIs (up to four pixels), which according to Nokia were due to fixes in the Qt raster engine and/or the graphics items' bounding box, so ROIs may have slightly different statistics after this update.

• Update - Vinci Options - Vinci deleted some of its options during installation and de-installation since Vinci 3.63.0. - Hopefully FIXED.
• SaveImage - Redo - the Vinci program file export of SaveImage did not always contain correct XML syntax. - FIXED.
• InfoView - Text Selection - you could not select text in the InfoView. - FIXED.
• PlotsView - Show - you could not hide an imported plot curve (context-menu entry Import). - FIXED.

Vinci 3.73.0, December 10 2010

• LoadDICOM - Export/Anonymization - a button for this new feature can be found in the bottom left corner of the DICOM specific part of the LoadView. You can select one or more DICOM sets (you may need "Browse Dir" to scan a directory tree for DICOM files first), then use this new feature to write all associated DICOM data into a new directory: files will be renamed and VINCI can automatically create a zip-archive with the exported data. Exported data can be anonymized: "Patients Name", "Referring Physician" and other DICOM entries can be individually selected and overwritten ("x-ed out") - our approach for anonymization does not change any internal DICOM structures: the file length stays constant, only selected text data is overwritten, thus all remaining DICOM data remains unchanged and compatible.
• LoadDICOM - Dump Option - select a DICOM data set, then use this function (the button can be found in the bottom left corner or the DICOM specific part of the LoadView) to convert any DICOM file into a textual representation. We use the Offis DCMTK toolkit (http://dicom.offis.de), for this dump option, however, all other DICOM data is handled by our own engine for fast parsing of DICOM data to display image data. A suitable file (the first slice file of the selected DICOM series) is now pre-selected automatically (a good method to check whether a DICOM file has been anonymized properly). If you press the SHIFT-key when using this new option, the DICOM dump is written as an XML file (".xml" is appended to the orginal DICOM file's name).
• LoadDICOM - Selection from Load History - a DICOM data set usually consists of several slice files. VINCI uses the first of these files to identify a data set, and this file is also saved in the Load History (accessible through the triangular button below "Browse" in the top part of the LoadView dialog). If you select a DICOM file from the Load History and press "Load", VINCI will now automatically look for DICOM data sets in the directory of that file if required.
• LoadDICOM - Better Handling of DICOM CDs - scanning DICOM CDs for DICOM data sets is now significantly faster as VINCI has become better at ignoring files that do not contain DICOM data. The number of directories which will be analyzed in a directory tree has also been increased.
• LoadDICOM - Improved Reporting - DICOM CDs with many (unnecessary) directory levels will now create less noise in the VINCI log.

• LoadView - Speckle Image - the Speckle Image plugin now handles a new series type with file names img.[0-9]*.sc* and format as of img.[0-9]*.sc files.
• LoadView - Speckle Image - the Speckle Series First and Last Frame settings are now saved in the Vinci project file.

• Report Tool - LoadView - in order to create faster reports, the LoadView now gets closed during the computation for fast-loading image types like Speckle, Analyze, NIfTI and Paravision.
• Report Tool - Speckle Series - if the scatterplot is about to get computed for a speckle series with restricted range, i.e. whose first frame is not the very first frame of the whole series or whose last frame is not the last frame of the series, the report tool now asks the user whether he would like to continue or cancel the operation.

• LoadDICOM - orientation P/F - DICOM data sets acquired in this orientation were mirrored in x-direction (observed with MPRAGE MRI studies), a nasty bug, sorry. Thanks to A. Thiel and to N. Galldicks for reporting this. - FIXED.
• LoadDICOM - pixel_size_z - now uses the method implemented in Vinci 2.x: averages over the distances between slice locations and uses this value if it is inconsistent with the slice distance (another DICOM parameter), this problem was observed with PET/CT studies. Older VINCI DICOM summaries will be updated automatically. Thanks to W. Eschner and M. Hoevels for reporting this bug. - FIXED.
• LoadDICOM - InfoView - fixed some typos; now also displays the DICOM separator "^" in a more human readable fashion (as ", ") in names, etc.
• LoadDICOM - original color window - now extracts the DICOM data set's original color window (if given) and uses the WindowCenter and WindowWidth parameters for certain studies. This only worked partially so far. - FIXED.
• LoadDICOM - DICOM summary - VINCI caches information about files in DICOM directories in "VinciDCx.xml" summary files. In some cases, these files were assumed to be out-dated and unnecessarily re-created. - FIXED.

• OrthoDisplay - Double-Click Zoom - when you have an OrthoDisplay with a measure item on one OrthoPart and a profile item on another OrthoPart, and you move a measure grip, and afterwards a profile grip, and then tied to double-click on the profile's OrthoPart to get a Zoomed OrthoView, the double-click did not work. - FIXED.
• OrthoTools - OrthoDisplay Spin - when you spinned through the OrthoDisplays too fast Vinci might have crashed. - Hopefully FIXED.

• Load Speckle - Find Comment - could not find the current frame of the series if it was the first frame. - FIXED.

• Report Tool - Speckle Series - a scatterplot of a speckle series always started with time equal to zero for the first frame of the frame range, even it was not the very first frame of the whole series. - FIXED.

• PlotsView - Multi-Axis - a PlotsView with a single top and right axis was not correctly saved into the Vinci project file; thus, it might have got re-created with the axis titles drawn over the axis numbers. - FIXED.

• Multi-Frame Movies Tool - WMV MPEG-4(3) - if you did not install Microsoft's encoder package wmencoder71.exe, and tried to create an WMV MPEG-4(3) movie, Vinci would crash after displaying the message Unable to initialize Writing (Unknown error). - FIXED.

Vinci 3.72.0, December 03 2010

• PlotsView - Paste - you can now paste previously copied scatterplots, undo/redo incl. If Vinci finds a copied link to a graphics item or image buffer it asks whether you would like to
  • keep these links alive (which is only sensible when pasting scatterplots from within the same instance of Vinci);
  • remove these links; or
  • cancel the operation.

• PlotsView Properties - Multi-Axis - you can now view and change all properties of all used axis; undo/redo incl.
• PlotsView Properties - Window Title - you can now undo/redo changes of the PlotsView windows title.

• Save Stryker/Leibinger Plugin - this plugin has been ported from Vinci 2.x (finally, Moritz) and is not part of Vinci's main distribution.

• LoadView Speckle - Invisible Helper Images - the helper images (to compute difference and quotient images) are no longer loaded into visible Vinci image buffers. Thus, difference and quotient images are loaded faster and the helper images no longer pollute the list of all images.
• Speckle Series - Frame Link by Time - so far, frame links were implemented to show the same frame number for all images in the frame link. Now Vinci provides for image frames linked by absolute and relative time.
  When linked by absolute time, the program looks for the absolute time of the next frame to show and for all other images in the frame link, it shows the frame that is next to the given absolute time value.
  When linked by relative time, the program computes the time between the frame to show next and its first frame and for each image in the frame link adds this relative time interval to the absolute time of its own first image. With this absolute time again, it shows the frame that is next to this time value, as above.

• Boosted Undo/Redo - repetitve actions are normally collected into an undo/redo sequences. Where applicable, we now replaced these sequences by the direct jump to the start- or endposition.

• PlotsView - Crosshair - activating the crosshair independently for the x- and y-axis did not work correctly. - FIXED.
• PlotsView - Fonts - undo/redo of font changes did sometimes not show immediately. - FIXED.
• PlotsView - Shortcuts - mouse mode shortcuts were active even on a locked PlotsView. - FIXED.
• PlotsView - Save Project - Vinci crashed when you deleted profiles whose scatterplots were visible on a locked PlotsView and saved the project file. - FIXED.
• PlotsView - Multi-Axis - when you imported two scatterplots with different title only the title of the first scatterplot did show on the axis; and when you changed the axis for the second scatterplot, the new axis kept the title of the first. - FIXED.

• PlotsView Properties - Save Project - the PlotsView Properties dialog did not get re-created at the correct position from Vinci's project file. - FIXED.

• LoadView Speckle - Changing Series - when you loaded a Speckle image from another series while you had activated Difference to Given or Quotient with Given, the difference and quotient were computed correctly to the first image of the new series but the corresponding edit field still showed the old reference image's file name. - FIXED.
• LoadView Speckle - Undo Load - undo load might have crashed when you loaded an image from another Speckle series. - FIXED.

• LoadView MicroPET - Range - loading a range of MicroPET image frames with start frame greater one did not work correctly. - FIXED.

• Frame Link Checkbox - LoadView Speckle and Multi-Frame Movie Tool - activating frame links did not immediately show the correct frames of the linked images. - FIXED.

• OrthoView - Fusion Update Bug - an, infact, unfused display showing image buffer zero got drawn fused with image buffer one (having some previous reslicing state) if the image buffer zero was fused on another display with image buffer one (since Vinci 3.60.0). - FIXED, thanks to W. Eschner.
• SaveView - Change Geometry - you could not enter pixel sizes with float values manually i.e. with the keyboard; but changes via the adopt button worked correctly. - FIXED.
• Image Based Calculations - Different Pixel Size - after you used images with equal dimension but different pixel size you could not close Vinci anymore. - FIXED.
• Irritating Warnings - since Vinci 3.68.0, the program has shown some irritating warnings on unixoid systems like QMetaObject::invokeMethod: No such method VMainWindow::xmlUse(QString,void*). - FIXED.

Vinci 3.71.0, November 19 2010

• PlotsView - Multi-Axis - in the context menu of the PlotsView scatterplot table, the new submenus Change X-Axis and Change Y-Axis offer these new options:
  • Existing X- / Y-Axis - to show the scatterplot with another already existing X- or Y-axis;
  • New Bottom / Top Axis - to show the scatterplot with its own new bottom or top X-axis;
  • New Left / Right Axis - to show the scatterplot with its own new left or right Y-axis.
  If an axis looses its last associated scatterplot it gets deleted automatically. Exception: an empty PlotsView has a default left and bottom axis, as before. The axis title is black if the axis is the one and only axis in PlotsView or it is associated with more than one visible scatterplot; the axis title has the color of its one and only visible scatterplot else. An axis will not draw if it has no visible scatterplots.
  CAVEAT: The PlotsView Properties dialog still works only on the first X- and Y-axis. All other axis are scaled automatically, so far. This is work in progress.
• PlotsView - Import - in the context menu of the PlotsView, you can now choose the new Import entry to load tab-separated X<TAB>Y data to show in the PlotsView. The file can contain two comment lines (starting with '#') with tab-separated entries for the axes' titles and units (in square brackets). This is work in progress.
• PlotsView - Frame Linked Cut - in the context menu of the PlotsView you will find the new entry Frame Linked Cut. If activated, the PlotsView in cut mouse mode will load synchronized frames not only of all images associated with a visible scatterplot but also of all images in the frame link of each of these associated images. The menu entry is only enabled if the PlotsView synchronizes with images in a frame link.
• PlotsView - Line Mode - in this mode (previously called Connected Points), the scatterplots are drawn as lines; if switched off, the plots have now additional dots at their nodes, instead of dots alone. The dot thickness (first start of Vinci-) default has been reduced to one pixel. You can change the dot thickness yourself in the Vinci options dialog in the Extras main menu.
• PlotsView - Copy [N] ... Alt+N - the menu entry Copy [N] ... Alt+N to copy the scatterplot values to the clipboard as tabulator-separated X<TAB>Y table will now prepend the output with up to two comment lines containing the axis' titles (if not both empty) and units (in square brackets). This is the same format which is used in the new context menu entry Import to load external plot-data, see above.

• PlotsView - Zoom - a zoomed PlotsView may sometimes not have got re-created correctly from the Vinci project file. - FIXED.
• PlotsView - Lock - un-locking one PlotsView did not lock all other open PlotsViews. - FIXED.
• PlotsView - Copy/Export/Print - the dot thickness was not correct (far too small) in the print output or print preview - FIXED.

• PlanesView - VOI Edit in Pen Mode - on PlanesView showing coronal or sagittal displays, mouse marked voxels did not show on the correct plane if added or erased off of the crossmarker plane. - Sorry, FIXED.

• LoadView Speckle - Frame Link - whether usable or not, the checkbox was always enabled at start up. - FIXED.

Vinci 3.70.0, November 05 2010

• Report Tool (ROI TACs) - Frame Link - the tool provides a new checkbox frame link, which is enabled if the tool is working on an OrthoDisplay that shows an image with a frame Link.
  If activated the tool will open an additional report tool or uses an appropriate open one for every image in the frame link, and with them computes the plots and tables with as many threads as you have cores on your computer. So when you have e.g. a dual core machine the tool will only start two threads at a time. Afterwards, the additionally opened tools are closed again.
• Multi-Frame Movie Tool - Frame Link - you can now make movies of the fused frames of multiple synchronized Speckle series. Just activate a new checkbox frame link, which is enabled if the tool is working on an OrthoDisplay that shows an image with a frame Link.
  Hint: Make sure to deactivate the checkbox if you do not need it, as the load of all images of the frame link may slow down movie making considerably.

• LoadView Speckle - Frame Link - this new checkbox allows to switch on and off the frame link synchronized load in a Speckle series; unsynchronized scrolling is the new default.
• LoadView Speckle - Find Comment Combobox - in the (editable) combobox you can now choose a frame from the list of all commented frames and the plugin will immediately jump to the chosen frame.
• LoadView Speckle - Re-Open - when closed and re-opened again, the Speckle load-plugin will now automatically connect to the first suitable series.

• Open Project - Menu Entry - the file dialog now opens in the directory of the previously loaded project file.

• Load MicroPet plugin - the plugin did not recognize the unit information for the keywords (pixel_size_x, y, z); instead it always used cm as units. - FIXED.
• Load MicroPet plugin - the plugin did use the new format pixel sizes in x and y, but the old format pixel size in z direction. - Sorry, FIXED.

• Load DICOM plugin - the plugin could not always load images from a Vinci (2.x and 3.x) project file. - Hopefully FIXED.
• Load DICOM plugin - the plugin did not correctly work on big endian machines. - FIXED.

• Load Speckle plugin - if you changed to a Speckle series in another directory but of the same type you always got the message [...]is no Speckle file of the chosen filter[...] - FIXED.

• Save Image - after saving a computed image the image buffer's file name entry did not change to the file name of the saved image - FIXED.

• Magic Tool - Synch Zoom - synchronizing the zoom factor of all images may also have changed the zoom factor of the image shown in the OrthoDisplay of the tool if the image was in a link channel - FIXED.
• Drag and Drop - Synch Zoom - synchronizing the zoom factor of an image may also have changed the zoom factor of the drag source image if it was in a link channel - FIXED.

Vinci 3.69.0, October 22 2010

• Speckle Series - Frame Links - you can activate so-called frame links for images belonging to a Speckle Series with the new frame link button, which is the third from the right in the Ortho info line, carrying the stylized f-icon. Active frame links are indicated by a full stylized f-icon.
  Frame linked Speckle series always show the same frame when you:
  • move or click on the LoadView slider,
  • click on the move forward and backward buttons,
  • press the find button to skip to a previuosly commented image.

• Report Tool - TAC 3D-Text-Template - you can now export 3D TACs for a Speckle series with the new special Speckle template for text-output.

• Image NaN Values - VOI Image - NaN areas when used with a VOI image were labeled as background; they are now labeled as outside.

• LoadView Speckle - Change Reference Frame - the color parameters are no longer reset to their default when you insert a new reference frame for the computation of a difference or quotient image and when you change the Gaussian filter radius.
• LoadView Speckle - Current Frame Button - this new button makes the current frame the reference frame for the options Difference to Given or Quotient with Given if one of these options is active without reset of the color parameters; it works as if you copy-paste the current frame yourself.

• Copy/Export/Print - Image Transparency - with activated image transparency, fused images always got drawn with full opacity. - FIXED.

• LoadView Speckle - Create Speckle OrthoView - did create an OrthoView of constant size 768x512, independent of the image dimension. - FIXED.
• LoadView Speckle - Undo Options - setting an option did only work if another option was already set. - FIXED.
• Report Tool - Replacing Speckle series - the report tool may have crashed when you replaced one Speckle series by another in the LoadView. - FIXED.
• PlotsView - Synch Frames/Images - synchronization of frames might have crashed if used with more than one Speckle series. - FIXED.

• Image NaN Values - Palette Index - Image NaN values got the maximum palette number on some machines (e.g. Solaris); they now get zero and can be transparent in png-file output. - FIXED.
• Image NaN Values - Out of Area - Out of the image area Vinci showed zeroes even if configured to use Nan values. - FIXED.

• Vinci About Page - MiniZip - the minizip license was not correctly linked to the Vinci About-Page. - FIXED.
• Vinci Update - Vinci Demo Data - the program closed even when errors occured; so you may not have been able to read the messages in time. - FIXED.
• Drawing Objects Base Image - No Items-Icon - was missing in Vinci 3.68.0. - FIXED.
• Extras - Load Test Project - did not work in Vinci 3.68.0. - FIXED.

Vinci 3.68.0, October 8 2010

• ROI Center - Show/Hide - you can now show/hide the center of a ROI's bounding rectangle. Just toggle the ROIs new Show Center property in the OrthoDisplay context menu Work on First Selected or in the ROI Define tool. The center is hidden by default.
• ROI Define Tool - ROI Center Positioning - you can now move the center of a ROI to given image voxel coordinates.

• Images with NaN values - ROI Statistics - Vinci now ignores image NaN values in the ROI analysis. See below for details:
  • ROI Define Tool - The results for #pixels, surface and volume now also show the percentage of the non-NaN image values.
  • Group Define Tool - The single value results for #pixels, surface and volume now also show the percentage of the non-NaN image values. The ROI contents is not shaded at NaN image values.
  • ROI Evaluate Table - The column TH [%] shows the percentage of the non-NaN image values of each ROI; if you defined a real threshold, the column shows the percentage of the non-NaN image values within the threshold. For images with NaN image values, the table exports to the clipboard and to a file contain the comment The image has NaN values that are ignored in the statictics.

• Images with NaN values - VOI Statistics - Vinci now ignores image NaN values in the VOI analysis. See below for details:
  • VOI Define, VOI Manipulation and VOI Operation Tool - The results for #voxels and volume now also show the percentage of the non-NaN image values. VOIs are shaded at NaN image values.
  • VOI Evaluate Table - The column TH [%] shows the percentage of the non-NaN image values of each VOI. For images with NaN image values, the table exports to the clipboard and to a file contain the comment The image has NaN values that are ignored in the statictics.

• Image Volume Arithmetics - Division - you can now produce result images with explicit values NaN at voxels with a division by zero; you had to replace NaN values by a number (like zero) till now.
  BEWARE: Not all image formats (e.g. ECAT 7) can save NaN image values.

• Vinci Options - Interpolation outside of Images - in the Vinci options dialog's general tag you can now determine whether the values outside of all images are zero (default) or NaN.

• Maximum Image Matrix Size now 2048 - Vinci now supports the image matrix size and 3D sampling dimension in a range up to 2048; so now you can see images greater than 1024 pixels uncut.
  BEWARE: Graphics Items saved into an Vinci project on an image with matrix size greater than 1024 will not get re-created at the same positions with older versions of Vinci.

• Qt 4.7.0 - now uses newest version of Nokia's Qt libraries.
• Visual Studio 2010 - now built with the latest MS C/C++ compiler on WINDOWS.
  We found differences when comparing MMM results. The differences were insignificant in all our test cases, i.e. they were in the range of the precision limits that MMM was configured to observe.
• ZLib 1.2.5 - Vinci now uses the newest Zlib library on Windows, (C) 1995-2010 Jean-loup Gailly and Mark Adler.
• MiniZip 1.1 - we replaced the sources of the Zip project with the sources of the MiniZip contribution to ZLib 1.2.5, (C) 1998-2010 - by Gilles Vollant - version 1.1 64 bits from Mathias Svensson.

• VOI Analysis - Standard Deviation - the computation of the standard deviation did not include the first voxel. - Sorry, FIXED.
• ROI Analysis - Standard Deviation in Non-Native Image Units - the computation of the standard deviation in non-native preferred image units was wrong. - Sorry, FIXED.

• Report Tool - Generating Plots - the PlotsView flickered during creation of a scatter plot if used in non-MDI-mode, which is default on the MAC. - FIXED.
• Report Tool - Speckle Series - switching to another OrthoDisplay showing a second Speckle series may have caused an open Speckle LoadView to crash. - FIXED.
• Report Tool - Speckle Series - switching to another frame mode or changing frames may have caused an open Speckle LoadView to crash. - FIXED.
• Report Tool - Speckle Series - the tool crashed when you tried to create a report of a Speckle series that had no Speckle Image List. - FIXED.

• Speckle Image - in Non TruePixel Mode - after changing the 3D-sampling mode of a Speckle image to next-neighbor or trilinear interpolation, showing another Speckle frame changed 3D-interpolation back to TruePixel mode and disrupted the image's cut position. - FIXED.

• Mouse Mode - Polygon (Line) - polygons in line mode could not be closed by double click since Vinci 3.66.0, only by pressing the space key. - Sorry, FIXED.

• Vinci Update - tar file-error - as the setup-file grew and grew, the error message "tar-file; update will close" may lately have appeared on some unix machines. This was due to a time-out interval, that may have been too small to de-tar the file. We now increased it from 10 to 20 seconds.
  If you have this problem you will have to update from the web site once. - Sorry, FIXED.

Vinci 3.67.0, August 20 2010

• Standard Movies - Fusion Fade Out - standard movies of a fused image now starts with fusion fading, just as in Vinci 2.x.
• Standard Movies - Annotations - Patientname, -ID, -DOB and an arbitrary description string can be displayed in the movie. Furthermore, the distance in [mm] from the initial cut-position is included in the lower left corner of the currently processed OrthParts.
  You can choose a suitable font family, just press the font button. CAVEAT: only font family and size are used, all other font properties are ignored.

• VHist Workflow-Step - PlanesView Copy/Export/Print - copy to clipboard and the export of PlanesView as BMP-, PNG- SVG- and PDF-files is now handled as VHist workflow step, i.e. (a) the exported files are accompanied by flat image VHist files and (b) the export step is appended to project VHist file if the general VHist settings in Vinci's options dialog approve.
  The flat image VHist files are based on the possibly existing VHist file of a source image if PlanesView shows only one image. If PlanesView shows more than one image existing source image VHist files are embedded. The workflow step describes the chosen options of the Copy/Export/Print dialog and the source images in detail and contains a project file of Vinci's state at the time of the export.
  Furthermore, Vinci will generate or add to a project's VHist file. The workflow step describes options of the Copy/Export/Print dialog and the source images in detail (embedding the VHist files of the latter if they happen to exist).

• VHist Files - Workflow Steps - a VHist file that is created in a workflow step now will be deleted when and where the workflow step is undone.

• Standard Movies - Fused Images - the reslicing animation did not include fused images. - FIXED.
• Standard Movies - Sagittal Reslicing - the reslicing animation of the sagittal display was mixed with coronal components. - FIXED.
• Standard Movies - Splashscreen description - was partly wrong. - FIXED.

• Image VHist Files - Computed Images - computed images are always new image buffers as they are produced in Image Based Calculations and Image Volume Filter; they should therefore always have new VHist files and never append to any existing VHist files that happen to have the correct name. - FIXED.
• VHist Files - Temporaries - temporarary VHist files were never removed during Undo. - FIXED.
• VHist Files - Saving Non-Temporaries - When you saved the image or project after a normal VHist workflow step using non-temporary VHist files, the VHist file created during the workflow step unnecessarily gets backuped by itself during the save of the image or project. - FIXED.

• Copy/Export/Print - SVG Copy to Clipboard - did not work correctly. - FIXED.
  SVG via clipboard can be used e.g. with Inkscape.

• PlanesView - Show Crossmarker - the menu entry and shortcut could not activate a crossmarker switched off in the Vinci project file. - FIXED.
• PlanesView Copy/Export/Print - SVG-Export - Vinci version and date were not right-aligned; Licensee was not right-aligned if shown under the PlanesView displays. - IMPROVED.
• PlanesView Copy/Export/Print - Image Transparency - toggling the image transparency changed the number of displays. - FIXED.
• PlanesView General Properties - Copy/Export/Print Button - did not work. - FIXED.
• PlanesView - Shortcut P - the shortcut P, to switch between VOI Edit modi, did not work in Vinci 3.66.0. - FIXED.

Vinci 3.66.0, August 6 2010

• PlanesView Copy/Export/Print - this new dialog provides multiple export options:
  You can copy a PlanesView to the clipboard (as image, or svg-xml-text), export it into a file (in BMP-, PNG-, PDF-, and SVG-format), or send it directly to the printer if you like (we also have a print preview). The dialog features a live-preview of the various export options.
• PlotsView Copy/Export/Print - the menu entry is now at the end of PlotsView's context menu to have Copy/Export/Print at identical menu positions in OrthoDisplay, Planes- and PlotsView. For corresponding reasons, the shortcut has been changed to ALT+C.

• Vinci Drawing Objects - Precise Positioning - we implemented some features to enable precise positioning of Vinci Drawing Objects, e.g. measures.
  • Image Zoom - Graphics Items Stay in Place - Vinci Drawing Objects will now keep their position relative to the image during a mouse-induced zoom operation of the image.
  • Image Zoom - No Movement Limitations - Vinci Drawing Objects can now move without limitations on zoomed images. On unzoomed images the center of a Vinci Drawing Object cannot leave the display, as before.
    BEWARE: Of course, ROIs are still only evaluated on the displays; so a ROI that is partly outside of the display may get evaluated only on the inside part of the display, and a ROI that is completely outside of the display may not be evaluated at all.
  • Graphics Items - Transparent Handles - you can temporarily make item grips transparent. Simply press the SHIFT key on the item in focus.
  • E.g. Precise Measure Positioning - You are now able to zoom into an image, precisely position both ends, re-check the exact positioning with transparent grips, and unzoom again. You may even like to press the image reslicing undo in the OrthoDisplay info line to just undo the zooming while leaving the measure's positioning untouched.

• Analyze Image - Data Type RGB24 - the Analyze image load plugin can now read images with RGB24 data type. The image's float values are calculated in the simplest way: (red+green+blue)/3.0; i.e. iso-weighted and without prior gray-scale gamma correction.

• OrthoView Menu - Inverse Color Table, White-based Color Table - in OrthoView's main menu, the entries Inverse Color Table with shortcut I and White-based Color Table with shortcut W have been re-activated. They work on the image buffer of the OrthoDisplay under the mouse pointer or on the first OrthoDisplay if the mouse is over no OrthoDisplay.

• Measures - Rotation - the profiles part of a measure item can now rotate.

• Mac only: NSAutoreleaseNoPool - Vinci showed a number of warnings about (minor) memory leaks when started with a console output. - FIXED.

• OrthoView / PlotsView - Copy/Export/Print - may not have been completely visible on small screens. - FIXED.
• OrthoView - Maximize to Small Slice - when you saved a Vinci project with Vinci not in maximized size, re-loaded the project and tried to maximize the saved OrthoView, it would only re-appear as an about 100 pixel wide slice on the right border of the screen that you could not pull greater again. - FIXED.

• Load MicroPET - Range of Frames - did always stop at the second frame with the error message "The file size is [not] what it should be". - FIXED.

• TruePixel Mode Zoom - Undo/Redo - may not have worked correctly or crashed for images with non-homogenous matrix size. - FIXED.

• Mouse Mode - Polygon (Line) - polygons in line mode could not be created with the mouse since Vinci 3.48.0. - Sorry, FIXED.
• Annotations - After Editing on Screen - after editing an annotation item on the screen, it did no longer show the selection rectangle. - FIXED.
• Profiles - Rotation - rotation of a profile did change its length. - FIXED.

Vinci 3.65.0, July 23 2010

• Reslicing Tool - All - you can now choose between all image buffers in the project, the tool's OrthoView, in the red, green, blue or no link channel; undo/redo inclusive.

• Vinci Program File - Export - the new entry Export Vinci Program File... in the Edit menu exports a given set of redo-commands in form of a so-called Vinci Program file (*.vprog), - just as the Export-button in the Undo/Redo-View does.
• Vinci Program File - Run - the new entry Run Vinci Program File... in the Edit menu runs a given Vinci Program file from within Vinci using the stdout-, strerr-pipe interface; the python-script RunVinciProgram.py in Vinci's external/python-directory has changed accordingly to cover its new and previous usages just by calling it with appropriate options.

• Python-Examples - QCom*.py - the Python scripts QCom.py and QComBench.py in Vinci's bin-directory have been rewritten to cover all their features in one file including some additional but up-to-now internal usages, just by calling appropriate options; previously, different features needed commenting/un-commenting different parts of the code.
  The new script QComMinimal.py shows the simple structure of QCom.py when reduced to command-line-only usage.

• VHist Workflow-Step - Image Volume Filter - the image VHist file of the filtered image is based on the possibly existing VHist file of the source image. The workflow step describes the filter method and the source image in detail and contains a project file of Vinci's state at the time of the calculation.
  Furthermore, Vinci will generate or add to a project's VHist file. The workflow step describes the filter method, the filtered image and the source image in detail (embedding the VHist file of the latter if it happens to exist).

• Report Tool - Protocol File - Vinci did not correctly recognize relative protocol file paths on unixoid platforms. - FIXED.

• Save Project As - Pack and Go - did not change the image paths in the generated Vinci project file in Vinci 3.64.0. - Sorry, FIXED.
• PlotsView - Moving Cross - did not work since Vinci 3.45.0. - Sorry, FIXED.

• Copy/Export/Print - Image Transparency - with open PlanesView, switching image transparency crashed Vinci. - FIXED.

• File Associations (WINDOWS) - Vinci Program Files *.vprog - Vinci Program Files (*.vprog) did only start via double click in the external python directory. - FIXED.
• Vinci Program File - RunVinciProgram.py - did not handle correctly relative and absolute paths in project and log-file. - FIXED.

• Measure in Group - Selection - clicking on a measure that is part of a graphics item group did sometimes only select the measure, not the group as a whole. - FIXED.
• Measure in Group - Move via Profile - moving the whole group by clicking on the profile of the measure did not work correctly. - FIXED.
• Group (e.g. Measure) in Group - Creation - when - via the OrthoDisplay context menu entry New Drawing Object/Group Item - you created a new group with another group as member that had no bounding rectangle (e.g. a measure), and afterwards immediately shifted the group, the member group without bounding rect did not move correspondingly. - FIXED.

Vinci 3.64.0, July 9 2010

• Speckle Image - In Any Image Buffer - you can now use the Speckle load plugin to load Speckle images into any image buffer; this was restricted to image buffer zero, so far. Accordingly, the so called Speckle helper images, just loaded to compute Speckle difference or quotient images, are no longer restricted to the image buffers one and two.
• Speckle Image - Vinci Project File - difference, quotient and filter image properties are now saved into and re-created from the Vinci project file.

• Speckle Plugin - Synch with Image Buffer - you can use the new OrthoDisplay context menu entry LoadView as during Load (see below) to re-synch the LoadView Speckle plugin with any Speckle image (except the Speckle helper images, see above). After that you can zip through the corresponding Speckle series with the LoadView, switch options, etc., just as before, when there was only one Speckle series loaded in a project.
• Speckle Plugin - Create Speckle OrthoView - does no longer close all other OrthoViews.
• Speckle Plugin - Switch Image Options - does no longer reduce the number of OrthoDisplays.

• LoadView as during Load - the new OrthoDisplay context menu entry LoadView as during Load changes the LoadView back to the plugin and settings it had while it loaded the OrthoDisplay's image buffer.

• VOIs and TruePixel Mode - VOIs were not supposed to be created or even analyzed for an image in TruePixel mode. Thus, till now, you could only use VOIs with 2D- or Speckle-images if you changed from default TruePixel mode to, say, NextNeighbor interpolation after loading the image.
  We now aim at tearing down that limitation. But this is work in progress. Please do not hesitate to tell us any remaining inconsistencies in this regard.

• Qt 4.6.3 - Vinci now uses the latest Qt libraries on Solaris as well.

• TruePixel Mode - PlanesView InfoLine - PlanesView may have crashed for images in TruePixel mode with non-homogenous dimensions. - FIXED.
• TruePixel Mode - Linked Zoom - may not have worked correctly or crashed for images with non-homogenous matrix size. - FIXED.
• TruePixel Mode - Image Deletion - when you deleted an image buffer with non-homogenous matrix size, then changed the OrthoDisplay to an empty image buffer, and changed back to the previously deleted one, Vinci crashed. - FIXED.

• ECAT7 Load Plugin - Sum over some Frames - redo load of a summed image (summed over some frames) did always sum over all frames. - FIXED.
• ECAT7 Load Plugin - End Bed - a multiframe image's end bed position was not correctly re-created from the load history. - FIXED.

• Speckle Image - Graphics Items - newly generated Vinci Graphics Items on a Speckle Image saved in a Vinci project file could not be re-created correctly since Vinci 3.53.0. - Sorry, FIXED.

Vinci 3.63.0, June 28 2010

• Vinci Extras - File Associations (WINDOWS) - as in Vinci 2.x, Vinci 3.x now allows the user to manage (create and remove) File Associations for the Vinci project file and common Vinci image formats in a dialog. Just start the new menu entry Extras/File Associations.
  Only the administrator can create file associations for all users, and he cannot create them for himself alone. File assosciations created as normal user precede administrator settings for all users. When deleted, the settings for all users are used again.
• Vinci 3.x - File Associations (WINDOWS) - You can now start Vinci Program Files (*.vprog) simply by a double click.
• Vinci Installer - File Associations (WINDOWS) - the installer has a new checkbox (switched on by default) that makes Vinci create file associations for the Vinci project file and common Vinci image formats. The uninstaller recreates pre-existing file associations of other programs.
  Beware: Of course, there can only be one version of Vinci (2.x, or 3.x) associated with a given file extension. We did not implement precedences of Vinci 3.x over 2.x or v.v. So, the last Vinci installed will win.
• Vinci Installer - User Installation (WINDOWS) - we changed to the newest version (2.46) of the Nullsoft installer system (NSIS). On WINDOWS 7 with User Access Control in default settings, as on WINDOWS XP before, you can now install Vinci and the Vinci Demo Data as normal user in your home directory.

• MMM - Save Registration Result File - with this new checkbox you can save MMM registration results into an XML file. Use it with fixed file name to adopt the same transformation to other images via the Reslicing Tool. Without fixed file name the result file has the unique form as in Vinci 2.x.

• Qt 4.6.3 - Vinci now uses the latest Qt libraries on the WINDOWS, Linux and Mac platforms.
  We again added the patch that let the color spinbox show its current color on WINDOWS Vista and WINDOWS 7.

• Vinci Installer - Minimal Configuration crashed (WINDOWS) - Vinci installed in minimal configuration - i.e. without plugins - did complain about incorrect MD5 checksums for the missing plugins and denied to start. - FIXED.

• Report Tool - Cuts - spinbox was nearly always disabled. - Sorry, FIXED.
• Reslicing Tool - Redo "Add to ..." - did not work - FIXED.

Vinci 3.62.0, June 2 2010

• Reslicing Tool - implemented now; undo/redo inclusive. See Vinci's online Help for more information: Reslicing Tool.

• Link Channels - Green and Blue - Vinci 3.x now supports all three link channels of Vinci 2.x.

• Fusion Tool - Implicit Linking - in case that the fused images is not in the same link channel as the base image the fusion tool now asks whether it should make them so, i.e. adopt or ignore given link channel settings, or link them in a meta link channel, see below.
  If you agree to adopt link settings and the base image is already in some link channel the fused image will join it. Otherwise, the base image will join the fused image's link channel. If you ignore given link settings all images' link settings remain unchanged.
  CAVEAT: As you can now decline automatic linking, fused images can now be in different link channels. In this case, the link icon in OrthoDisplay's info line can only show the link channel of the fusion base image!
• Fused Display - Meta Link Channel - a meta link channel is a link channel in cut-synchronization-only mode (for now) that can contain images and color-coded link channels as a whole. In contrast to the latter which are project-owned, a meta link is OrthoDisplay-owned, and usually used with a fused OrthoDisplay.
  If in the process of fusion, images (or if they are linked their link channels) are inserted into a meta link channel, all cuts of one image will promote to all images and link channels in the meta channel. Images and color-coded link channels in a meta link channel have a black-bordered link icon in the OrthoDisplay info line.
• OrthoDisplay InfoLine - Link Menu - the new menu entry Meta Channel lets you freely toggle the OrthoDisplay's meta channel on a fused display and switch off the meta channel on any display showing an image meta-linked link channel; undo/redo inclusive.

• Save Vinci Project File - Invisible VOIs - when saving a VOI image and project, invisible VOIs may not have got saved. As preliminary fix, VOIs are made temporarily visible during save. So for now, VOIs are always saved as visible in the Vinci project file. - FIXED.
• VOI Define - Toggle Visibility - when making an overlapped VOI visible again, it is first drawn above the overlapping VOI(s). - FIXED.

• OrthoDisplay - Fusion Tool - the tool did always start with activated Cut Synchronization Only. - FIXED.
• OrthoDisplay - Contours Tool - the tool did get re-created from a Vinci 2.x project - FIXED.
  CAVEAT: Vinci cannot re-create the Contours Tool fron projects saved by previous Vinci 3.x versions.

• Save Link State - Undo - did not work correctly. - FIXED.
• Clear ImageBuffer - Undo - after undo the OrthoDisplay infoline did not always show the correct link icon. - FIXED.
• Link All - Re-use reslicing parameter of this image... - did not use the reslicing parameter of the given image, but always the parameters of the first image in the link channel. - FIXED.

Vinci 3.61.0, May 12 2010

• Protocol - Export - you can now export a given set of redo-commands in form of a so-called Vinci Program file (*.vprog).
  A Vinci Program file is an XML-file that contains one VinciVersion entry that denotes the Vinci version that created the file and an arbitrary number of Protocol entries. The first three entries recreate the Vinci environment, load the project file, and make the LogView log into a file. The following entries are the redo-commands that were present when the user exported the protocol.
  Hint: Users who want to script Vinci can now easily find the necessary VinciScript commands. Just do what you like to script in the Vinci user interface and afterwards export the Vinci Program file.
• External Python - RunVinciProgram.py - a new Python program that runs a given Vinci Program file. So, you can re-run a previous Vinci session, as long as the necessary VinciScript commands have already been implemented.

• LoadView - Replacement Path - if an image file is not found in the expected location, Vinci now opens the Replacement Path dialog. Here you can type in the image's correct path, choose the path from a list of previously used paths, or just browse for the image. You may want to use the same new path for all of the following images, i.e. as long as they exist in the chosen replacement path.

• Analyze Image - Multiframe-Handling - Vinci can now load Analyze multi frame images.
• Analyze Image - Frame-Mode: Sum - Vinci can now sum consecutive frames of an Analyze multiframe image directly in the load plugin.
• NIfTI Image - Frame-Mode: Sum - Vinci can now sum consecutive frames of a NIfTI multiframe image directly in the load plugin.

• Save Analyze Image - Vinci can now save images in the Analyze 75 format (float, int16 and uint8 data types are supported). CAVEAT: patient orientation is not a well-defined property for Analyze images and is a well-known problem. If you have a choice, use the NIfTI image format instead which is Analyze compatible and was designed to address this issue.

• OrthoDisplay - Copy/Export/Print Dialog - the new button Image Transparency makes the image's internal color handling so-called alpha-channeled while in the dialog. In this mode you can export (as *.png-file) and print the image with transparent image background (color palette number zero).
• OrthoDisplay - Sync Zoom - you can now Drag & Drop zoom parameters from one OrthoDisplay's image to another OrthoDisplay's image.

• InfoView - Contributors - list completed with Zip, MD 5 and TinyXML.

• Save DICOM - this plugin is temporarily not available due to major maintenance. In certain circumstances the plugin created incomplete DICOM files (only meta header information). We apologize. Work in progress.

• File Name Comparison - defaulted to case-insensitive comparison for WINDOWS and case-sensitive comparison on other platforms. This was not correct for most MAC computers. The necessary case-sensitivity of the file name comparison is now explicitly tested at program startup. Vinci temporarily creates a file __CaseSensitivity__.aaa and afterwards tries to read the file __casesensitivity__.AAA. - FIXED.

• MMM - Redo crashed - FIXED.
• ECAT7 Load Plugin - Sum & Avg Image - redo load did not work. - FIXED.
• SaveView - Redo - the SaveView did not save the plugin title and settings for redo. - FIXED.

Vinci 3.60.0, April 30 2010

• VHist Integration - Vinci can now generate and view VHist files. The VHist project remains an OpenSource project independent of Vinci. It defines a file format specification that allows to embed arbitrary binary data (with structured meta-information and multiple facilities for validation) as documentation of workflows. VHist includes a platform independent reference implementation of essential features, used here. The format conforms to the PDF and other open standards, is self-describing and particularly suited as an image or meta-image format in the context of multi-modality and functional imaging. VHist can be used on top of existing workflows without the need to change major applications.
  VHist files can be viewed with any PDF-browser, e.g. Acrobat Reader. Alas, some pdf-viewers (e.g. Preview on the Mac) only open VHist files if you add .pdf to the file names.
• Vinci VHist Handling - Vinci now uses part of the VHist reference implementation to generate new and append to given VHist files on image and Vinci project file level. By default, Vinci assumes images to have VHist files with names <image file name>.vhist for images and <project file name>.vhist for project files. You can change these default file names via the menu: just open Edit/New Project VHist file for projects and in the context menu of an OrthoDisplay open New Image VHist file for a particular image. Vinci can work directly with the default VHist file names (default action) or work with temporary files which will be renamed to the default names whenever an image or project is saved.
  In order to not overly disturb users with newly generated files, by default, Vinci does only work with already existing VHist files, so, in fact, does nothing, if you do not happen to have them. You may want to activate VHist option (b), see below, to make Vinci also create new VHist files.
  You cannot generate (or add to) VHist files with the lite version of Vinci.
• Vinci Options - VHist - Vinci's Options dialog features this new tag to fine tune Vinci's VHist usage or switch it on (default) and off completely.
  Here you can determine independently for images and projects
  (a) that Vinci only adds to already existing VHist files (default), or
  (b) also creates new ones;
  (c) that Vinci uses temporary VHist files - carrying the suffix YYYY.MM.DD.hh.mm.ss.vhist encoding the current date and time instead of just the default names; or
  (d) that always the user is asked which VHist files to use.
  Beware: As temporary VHist files cannot exist already, option (a) and the use of temporaries are mutually exclusive.
• Intended Workflow-Steps - by and by, Vinci will add more and more -so called- workflow steps to your image and project VHist files in the following kind of situations:
  (a) when Vinci generates a new image,
  (b) when Vinci changes an image (which only happens when you edit VOIs),
  (c) when Vinci creates a file, and
  (d) when Vinci exports to the clipboard.
• Implemented Workflow-Step - Images Based Calculations - if no or more than two images are involved in the calculation, Vinci will generate a new image VHist file for the resulting image. The workflow step will describe the specific calculation and the involved images in detail (embedding their VHist files if they happen to exist) and contain a project file of Vinci's state at the time of the calculation.
  If only one image is involved, Vinci will base the image VHist file for the result image on a possibly existing VHist file of the involved image. The workflow step will describe the specific calculation and the involved image in detail and contain a project file of Vinci's state at the time of the calculation.
  Vinci will further generate or add to a project VHist file. The workflow step will describe the specific calculation, the result image and the involved image(s) in detail (embedding the VHist files of the latter if they happen to exist).
  Of course, you have to chose VHist option (b) to create new VHist files at all, see above.
• View working VHist files - Vinci uses part of VHist's VHistzard to show the VHist files Vinci is working on.
  In order to view the project VHist file, just open the menu entry Edit/Show Project VHist file, to view an image's VHist file open Show Image VHist file in the context menu of an OrthoDisplay showing the image in question.
• View external VHist files - open the menu entry Edit/Show VHist file to browse for any given VHist file and show it in VHist's VHistzard; or just by drag & drop the VHist file on Vinci.

• New Online Help System - you can now use the new "Vinci Online Help" entry in the Help menu to open Vinci's online help. The "?"-buttons (active on some toolboxes, e.g. "Talairach") will open the corresponding part of the documentation. You can use the icon in the top left corner to navigate to the index page. Work on more help topics is in progress.

• Drag & Drop of image files - if an image file is dropped onto any of Vinci's windows, Vinci will cycle through all available Load plugins and try to find one that is suitable for loading that file (this works well for a wide range of file formats). The LoadView now treats the Load Flat image plugin differently (see below). There is another exception: if the file is dropped onto the top part of the LoadView, Vinci will not load the file but only insert the file's path into the LoadView. You can also drop Vinci Project files.
• Load Flat Image revisited - this plugin will now open files with arbitrary names. However, as the Flat Image plugin has generally no way of deciding whether a particular file is suitable for loading (and which configuration of parameters to use), it is now handled differently from Vinci's other Load Plugins: if the Flat Image plugin has been selected in the LoadView, Vinci assumes an advanced user who wants to re-apply the current settings to the next file dropped on Vinci. CAVEAT: working with flat files is strongly discouraged for routine usage - it is usually easy to create a small interfile text file with the required meta information and this prevents many sources of potential errors when handling binary image data without header information (good scientific practice).

• Vinci Update - Minimize - on the MAC, due to technical reasons, the Vinci update dialog starts as top level application. It now features a minimize button to click it out of the way.

• InfoView - Basic Info - Vinci now shows the matrix size and the so called matrix pixel size.
  The latter is the pixel size on the three perpendicular matrix size planes that are the result of 3D-sampling and reslicing of the image to three perpendicular sampling dimension size planes that are afterwards zoomed (2D) to the matrix size planes. The 2D-zoom uses a high resolution bi-spline algorithm if the 3D-sampling was tri-linear and pixel-reduplication if the sampling was next-neighbor or TruePixel.
  The value shown so far as pixel size was the matrix pixel size for three fixed 256x256 matrix size planes and the value shown now is the matrix pixel size for the actually used matrix size planes.
• Magic Tool - Matrix Pixel Size - Vinci now shows the matrix pixel size, described above. The Zoom Factor so far was the x-component of the 3D-Size Factor shown in the InfoView. It is now the minimal value of the 3D-Size Factor and explicitly renamed as Minimal Size Factor. The 3D-Size Factor is a dimensionless floating-point number that is defined as:
  (a) <Size Factor> := <sampling dimension> / 256.0, in TruePixel 3D-interpolation mode;
  (b) <Size Factor> := <sampling pixel size> / 1.0 mm, in tri-linear and next-neighbor mode.

• Image Based Calculations - the functions msum and mavg did not support the calls with no given start- and endframe. - FIXED.
• Image Based Calculations - the functions msum and mavg did not work in Vinci 3.54.0. - FIXED.
• VinciScript - external/python - the script RunImageCalc.py crashed during usage of the mathematical standard functions and the functions msum and mavg. - FIXED.

• Vinci Project File - Load - if the files are greater than 500 kB the user can decide whether to load a Vinci project file or not. Alas, Vinci might have crashed if the load was cancelled. - FIXED.
• External Python - Vinci_Image(T) - due to a missing import library, python may have crashed in the classes Vinci_Image and Vinci_ImageT if the computation failed. - FIXED.
• External Python - Examples - on the MAC, the examples could not communicate with Vinci. - Sorry, FIXED.
  BEWARE: On the Mac, the return value of StartMyVinci() is wrong, so far. The examples RunMMMJob.py and ReapplyMMMTrafo.py, depending on this value to find the demo data images, will still not work.
• Simplified User Interface - Default Project - the default project file was not part of the WINDOWS, Linux and Solaris-distributions. - Sorry, FIXED.

• Save ECAT7 - after saving an image as ECAT7-file Vinci left the file pointer open, so the image could not be deleted from within (e.g. during undo) or from outside of Vinci, until Vinci was closed. - FIXED.
• Save ECAT7 - undo did only correctly recreate the situation before the save if the image file did already exist. - FIXED.

Vinci 3.54.0, April 19 2010

• Animation Tools - Standard Movies - this tool is now available for the Linux and Solaris versions of Vinci.
• Animation Tools - Movie Formats - additionally to Vinci's WINDOWS release (see version 3.52.0), Vinci's Linux and Solaris releases can now create Ogg/Theora movies, Copyright (c) 2002-2009, Xiph.org Foundation. You can play Ogg/Theora movies directly in VLC on all platforms. For the WINDOWS Media Player you'll need to install an additional plugin, though.
  INTERNALS for Linux and Solaris: By default, Vinci uses it's own libraries of the Ogg 0.6.0 and Theora v 1.1.1; if you want or need to use the system libraries, instead, just remove the four Ogg/Theora libraries in Vinci's bin-directory.
  The MAC platform is not supported, so far. This is work in progress.

• Drag & Drop for Vinci Project Files - you can now drop Vinci Project files onto any Vinci window (in addition to most image files).

• VinciScript - external/python - we improved the structure of the Python classes by changing to explicit dependencies and getting rid of global variables. The examples were changed accordingly. As Vinci's communication protocol did not change, old example scripts should continue to run. However, the use of the old class structure is discouraged.

• Load MicroPet plugin - now supports additional systems, UINT16 data and new keywords (pixel_size_x, y, z).

• Image/Project paths containing "&" characters - were not treated correctly in Vinci: special care must be taken of the "&" character when used in an XML file (such as a Vinci project file). In particular, older Vinci 2.x project files were saved incorrectly causing Vinci 3.x to crash in some circumstances. Vinci 3.x now uses a heuristical approach when encountering certain XML syntax errors and should be able to restore Vinci 2.x project files with this problem. This was a particularly nasty bug (sorry, Delphine). A word of caution: using spaces, "German umlauts" and, generally, non-ASCII characters in file or directory names is usually not a good idea. - FIXED.
• MicroPET - Units/Study Time - were not set in Vinci 3.x. - FIXED.

• Vinci About - Contributions - the links did not always open the license texts. - Hopefully FIXED.
• Simplified User Interface - Save Project - saving a newly created project in Simplified User Interface mode did not invoke the SaveAs-Dialog. - FIXED.

• OrthoTools - Color Spinbox - in WINDOWS Vista and WINDOWS 7, the color spinbox, used in many tools to show and change the color of an specific object, did work in that you could use it to change the color, but it always showed White as the object's current color. Due to Nokia's patch the problem is now - FIXED.
• Report Tool - Computation cancelled - if you had no write permission in the directory of the image you were analyzing the tool tried to write the current project file and the computation result into your home directory. This almost certainly went wrong due to a missing "/" in the path. - FIXED.

Vinci 3.53.0, March 22 2010

• Speckle Image - Graphics Items - Vinci 3 can now re-create Vinci Graphics Items on a Speckle Image saved in a Vinci project file written with Vinci 2.x.

• Speckle Ratio - Build-in Palette - Vinci 3 features the new build-in palette Speckle Ratio, which is the palette Ratio with a gray middle.
• Speckle Plugin - Difference to Given / to Previous - the slider now allows to show the difference image of the given image with itself (i.e. a zero-image).
• Speckle Plugin - Quotient to Given / to Previous - the slider now allows to show the quotient image of the given image with itself (i.e. an image filled with 1.0 everywhere).

• Vinci About - Contributions - we added a section that lists external software contributions to Vinci with direct links to their individual copyright notices.
• ZLib 1.2.4 - Vinci now uses the newest Zlib library, (C) 1995-2010 Jean-loup Gailly and Mark Adler.

• Annotation Objects - Generic Substitution - annotation objects with generic texts substituted according to the currently shown image frame did not always update when you changed the image frame, e.g. in the Report Tool, Multi-Frame Movies Tool or the Speckle Image LoadView frame slider. - FIXED.

• Speckle Calibration - Mouse Mode - was not available in the release version of Vinci. - Sorry, FIXED.
• Speckle Display - Copy / Paste - copying ROIs at mouse position from a squared OrthoDisplays to the (by default non-squared) Speckle OrthoDisplay and v.v. did not work. - FIXED.
• Vinci 2.x project file - Speckle Image - Vinci might have crashed if you loaded a Speckle Image via the Loadview and moved the mouse in the empty (dark gray) display area not filled with image data - FIXED.
• Speckle Plugin - Color Defaults Quotient - the color defaults for quotient images did not change for the new *.sc-type Speckle images - FIXED.

• VOI Manipulation - VOI Editing - in Vinci 3.52.0, VOI editing on the reference image might have been impossible. - FIXED.

• OrthoDisplay Props - Spin-Boxes - the image sampling resolution and image matrix size did not update after loading a Speckle image. - FIXED.

• MicroPET - Frame Number - the addtional image info test was not set for MicroPET multi-frame images. - FIXED.

Vinci 3.52.5, March 11 2010

• Simplified User Interface - this new option can be enabled in the "Extras" menu (Vinci will remember this setting between sessions). It forces a new default project ("simple.vpx") which will have just one OrthoDisplay (initially in cut mode in addition to crossmarker and text mode).

• (Mac only) Improved Finder Support - Vinci will now open NIfTI (.nii, .nii.gz), ECAT (.v) and other images if a file with a suitable extension is dragged onto the Vinci icon or onto the OrthoView.

• OrthoDisplay Props - Spin-Boxes - the image sampling resolution and image matrix size spinboxes did not work correctly since 3.50.0. - Sorry, FIXED.

• Graphics Items - Handles - graphics items of images with non-homogenous matrix size had non-homogenous sizes of the handles of the bounding rectangle. - FIXED.

Vinci 3.52.0, March 9 2010

• Threshold Tool - implemented now.
• Threshold Tool - Main Differences to the Vinci 2.xx versions
  • Undo/Redo - Complete - for all tool operations.
  • Overlapping VOIs - are saved in the Vinci project file.
  • Help - you can now open a html help-page via the ?-button at the tool's top.

• Animation Tools - Movie Formats - the movie tools can now create Ogg/Theora movies in a high and low quality profile, Copyright (c) 2002-2009, Xiph.org Foundation. Our implementation is restricted to the WINDOWS platform, so far. This is work in progress.
• Animation Tools - Movie Formats - the movie tools can now create all the Vinci 2.x Quicktime and WMV movie formats.
• Animation Tools - Format Description - the movie tools provide a movie format description field with usage recommendations and additional informations for every movie format.
• Standard Movies - Cancel - you can abort standard movie creation now; just press the new cancel-button on the splashscreen dialog.

• VOI Operations - Vinci now uses faster algorithsms to edit irregular VOIs and to unite, intersect and subtract irregular VOIs.

• Image Values - List - you can now get a list of image values at the current mouse position over all OrthoDisplays of a given OrthoView. Just press the new shortcut key V on any OrthoDisplay.
  The list is shown in the LogView and put on the clipboard with system locale settings for direct import into the spreadsheet program of your choice.

• OrthoView - OrthoTools - if you worked with several OrthoTools, deleted one created another, and saved the session in a Vinci project file and re-loaded the project, not all of the OrthoTools might have got re-created. - FIXED.
• OrthoView - ShortCut P - pressing the shortcut key P on a display that did not show a VOI image as Drawing Objects Base Image led to a crash. - FIXED.

• VOI Tools - VOI Image Overload - the VOI tools (VOI Define, VOI Manipulation and VOI Operations) crashed if you overloaded the currently used VOI image. - FIXED.
• VOI Tools - VOI Image Save - the VOI tools did not re-initialize their VOI image lists after a VOI image got saved and thus kept the * in front of the saved VOI image file name. - FIXED.
• VOI Tools - VOI Rename - the rename edit field showed unchanged (i.e. xmlified) VOI names and renaming a VOI with the rename-button did not xmlify the contents of the edit field. - FIXED.
• VOI editing - Initialization - when entering VOI Edit mode, the program checks if the image is cut well within a voxel, i.e. not on or near a voxel border. This check did not work properly for all images. - Sorry, FIXED.

• Graphics Items - Move to Forground/Background - did not work correctly for groups (and measures) since Vinci 3.47.0. - Hopefully FIXED.
• Analyze Image - Clones - some Image Arithmetic results of Analyze images were saved as real NIfTI images but still with wrong file extension (Analyze .img instead of NIfTI .nii) and were thus not loaded again. - Sorry, FIXED.
  HINT: You can repair already saved images and projects simply by changing the image file extensions to .nii and matching the project files in a text editor of your choice.

Vinci 3.51.1, March 5 2010

• Qt 4.6.2 (2) - now also MacOS X uses the latest Qt libraries.

• Animation Library missing - this bug only affected the MacOS X platform: our animation library was not part of the distribution due to a technical problem. We apologize.

Vinci 3.51.0, February 19 2010

• Multi-Frame Movies - Frames per Second - introduced a new spinbox to change the up-till-now constant rate of 10 fps (frames per second) of the movies. Introduced the field Motion Factor which shows the corresponding fast-motion factor of the movie, based on the current frame's duration: MotionFactor = FramesPerSecond * FrameDuration.
  BEWARE: The motion factor may change during a movie if the individual frames have different duration.

• MicroPET - Load Plugin - the new button Header (re-)reads the header information of the current MicroPET image.

• Qt 4.6.2 - Vinci now uses the latest Qt libraries on the WINDOWS, Linux and Solaris platforms.
  We added a patch to fix the problem on the WINDOWS platform that sometimes let dialogs and context menus first appear as shadowy outlines and not become fully visible or let the program stop processing completely until you moved the mouse.

• Analyze Image - Clones - VOI images, Arithmetic and Gaussian-Filter results of Analyze images were saved as real NIfTI images but with wrong file extension (Analyze .img instead of NIfTI .nii) and were thus not loaded again. - FIXED.
  HINT: You can repair already saved images and projects simply by changing the image file extensions to .nii and matching the project files in a text editor of your choice.

• ECAT7, HRRT, MicroPET - Multi-Frame Movie - when you wrote a movie in the multi-frame movie tool the operation might have stopped after the first frame unless you moved the mouse, see above. - FIXED.
• ECAT7, HRRT, MicroPET - Multi-Frame Image - when you tried to load an invalid image frame in the multi-frame movie or report tool and afterwards deleted the image, Vinci did not delete the image's ROIs. - FIXED.

• MicroPET - Multiframe Image - Vinci did always load the first frame in the multi-frame movie tool. - FIXED.
• MicroPET - Frame Number - the frame number logged in Vinci 3.x as "frame id: xx" was one less than logged in Vinci 2.x as "frame: xx". - FIXED.

Vinci 3.50.1, February 12 2010

• Animation Plugin - tools - the Multi-Frame Movies- and the Standard Movies-Tool may not have appeared in the tools list due to an library initialization problem. - FIXED.
• Standard-Movies - Quicktime - writing Quicktime movies does only work if a current version of the Quicktime player is installed. And it did presumely not run on WINDOWS system newer than XP, so far. - FIXED.

Vinci 3.50.0, February 10 2010

• Multi-Frame Movies - Quicktime, WMV, MP4 - the Multi-Frame Movies Tool now supports the creation of movie files in Quicktime- (lossless PNG and high quality H.264) on MAC and WINDOWS, WMV- (high and low quality) on WINDOWS XP and higher and MP4- (high quality H.264)-format on WINDOWS 7 and WINDOWS Server 2008 R2. Just press the Record-button denoted by the usual icon to write a multi-frame movie. Writing Quicktime movies requires the installation of a current version of the free Quicktime Player. WMV-creation may require the installation of an appropriate encoder on older (before 2008) WINDOWS systems. You cannot write movies with the "lite" version of Vinci.
  The existing interface to view memory-based movies (generated "on-the-fly" by showing consecutive frames of a multi-frame image or Speckle series directly within VINCI) has been extended and now features infinite loops, fast- and slow-motion, adding of an annotation item that shows the image's additional text, which usually adds information about the individual frames.
  The movie part of the tool is only available for the WINDOWS and MAC platforms, so far.

• Standard-Movies - WMV- and MP4-Format - Vinci 3.x now supports the creation of MP4- (H.264)-movies on WINDOWS 7 and WINDOWS Server 2008 R2. Like Vinci 2.x, Vinci 3.x now supports WMV-movies on WINDOWS XP and higher with a high and low quality profile. Writing Quicktime movies requires the installation of a current version of the free Quicktime Player. WMV-creation may require the installation of an appropriate encoder on older (before 2008) WINDOWS systems. You cannot write movies with the "lite" version of Vinci.
  The tool is only part of the WINDOWS and MAC distribution, so far.

• Speckle Calibration - Mouse Mode - implemented now; for Ortho- and PlanesView usage.
  In order to calibrate a Speckle image, enter the new Speckle Calibration mouse mode, draw with the mouse a line of known length on the image, enter its real length in [mm] in the presented dialog and press Ok. The image's pixelsize will be changed accordingly for the current Vinci session and a new calibration file CAL.DAT will be written into the directory of the Speckle series to re-use the calibration in future Vinci sessions.

• VOI editing - Initialization - when entering VOI Edit mode, the program now checks that the image is not cut on or near a voxel border, as the user painted or encircled voxels may get edited on the wrong image plane in this case. The program allows the user to cut in the corresponding voxel center instead.
• Fusion Tool - Selected Image - the label field for the fused image now displays the image index number in front of the image file name.
• Image-Based Calculations - Abort - the user can now abort a running calculation by pressing the Abort-button, i.e. the cancel-button that has a different caption during a calculation.

• InfoView - Speckle Image - the InfoView did not show basic image information for Speckle images. - FIXED.

• MicroPET - Multiframe Image - Vinci did ignore the frame information so far. - Sorry, FIXED.

• PlanesView InfoLine - Mouse Modes - in TruePixel mode, Vinci offered mouse modes in the PlanesView infoline that had no visual effect in the PlanesView displays. - FIXED.
• Color-Legend - Image Min-, Max-Tooltips - did sometimes close immediately. - FIXED.
• Image-Based Calculations - Timeout - the python sub-process did timeout after 60 seconds which may have been too short a period for special calculations and/or machines; set to 60 minutes now. - FIXED.

Vinci 3.48.1, January 27 2010

• Installing License Files - when trying to install a new license file, the file browser only displayed grayed entries so the new license file (lic*.xml) could not be selected. This, for a change, was not our own bug but related to a minor change in Qt 4.6.1 and affected only the Mac OS X platform. Sorry, FIXED.

Vinci 3.48.0, January 26 2010

• ROI Define Tool - Create Mirrored - you can now create mirrored ROIs (rectangles, ellipses and polygons) in the ROI-Define Tool. The ROI is mirrored relative to a profile named _MirrorAxis if present; else it is mirrored relative to the vertical middle axis of the display.
• Measure Tool - you can now open a html help-page via the ?-button at the tool's top.

• Polygon ROIs - quietly ignore duplicate vertices while loading a polygon from file or pasting it into a scene.

• Magic Tool - the tool tip of the Create Measure icon said you would create profiles. FIXED.

Vinci 3.47.0, January 22 2010

• Measures and Measure Tool implemented now; undo/redo inclusive.

• Graphics Groups - Vinci now propagates several tasks to the parent group if it has de-activated Show Bounding Rect.
  • Selection in Group Tool - after selection of a group member by mouse.
  • Move Restrictions - Context Menu - Move Freely, Move Vertically, and Move Horizontally.
  • General Properties - Context Menu - Set ToolDef, Set SaveVpx.
  • Open Tool - Context Menu - now Vinci offers to open the group tool, if no member or the group itself is selected.

• Graphics Item - Annotation - the default color is changed from white to a very light gray, so as to make it visible while editing on a really white background.

• Qt 4.6.1 - Vinci now uses the latest Qt libraries on all platforms.

• Load NIfTI - crash while trying to cope with an unknown image orientation. FIXED.

• PlanesView - Transaxial View - an image shown in TruePixel mode was always cut at the last plane since Vinci 3.30.0. Sorry - FIXED.
• PlanesView - Maximum Number of Displays - Vinci crashed when you exceeded the maximum number of displays (1024). - FIXED.

• ROI Define Tool - Show All - the button was disabled in the release version. FIXED.
• Profile in PlotsView - for an image in TruePixel mode, if you switched on Automatic Unit Transformation the x-axis showing [mm] was wrongly scaled. Sorry, - FIXED.
• Graphics Items - Move to Background and Move to Forground did not work in Vinci 3.46.0 if exactly two items were present. FIXED.

• Graphics Group - Deletion - deleting a group with Delete Members activated and Show Bounding Rect de-activated led to a crash. - FIXED.
• Graphics Group - Copy/Paste - when you copied a group with de-activated Show Bounding Rect and pasted it the system produced in fact as many copies of the whole group as the group had members. - FIXED.
• Graphics Group - Undo Member Deletion - did not always re-construct the member order - FIXED.
• Graphics Group - Member Selection - the selection state of group member were not re-created from the Vinci project file. - FIXED.
• Graphics Group - Member Deletion - you could not delete a selected group member of a group with Delete Members activated with the <Del>-key. - FIXED.
• Graphics Group - Selection - a group with de-activated Show Bounding Rect did not re-create its selection state. - FIXED.

• External Python - small changes in the interface.
• Python Example - RunMMMJob.py - script waited indefinitly for MMM due to a typo.

Vinci 3.46.0, December 2 2009

• Standard Movies Tool - implemented now; only WINDOWS and Mac OS X so far.
  The tool will write a QuickTime PNG movie (lossless compression; can be viewed on Apple MacOS X, Windows (QuickTime Player) and recent versions of Linux) of the target OrthoDisplay's current image (and optional fusion/contour layers) by scrolling through the standard axes. The animation will start at the current cut position. The plugin displays bounding boxes which can be adjusted by mouse and indicate the extent of the animation's movements in each of the standard axes. CAVEAT: the interface is still preliminary and the current flavour of movies requires VLC or a similar player on MacOS Snow Leopard (work in progress).

• PlotsView Copy/Export/Print - this new dialog provides multiple export options:
  You can copy the PlotsView contents to the clipboard (as image, or svg-xml), export it into a file (in BMP-, PNG-, PDF-, and SVG-format), or send it directly to the printer if you like (print preview inclusive); the plot fits to the page. The dialog features a live-preview of the various export options.
• OrthoDisplay Copy/Export/Print - the image of an OrthoDisplay now fits to the page.
  

• Reset Image buffer - now sets the sampling dimension to the image's default matrix size.
• ROI Evaluation Tool - now handles groups correctly (see below).
  For multi-result operations (Individual Evaluations and Sequential Differences) the name column displays the group name in square brackets before the ROI member name; for single result operations (Global Union, Global Intersection and Global Difference) only the group name is shown. The table includes the column Operation and shows it by default if it contains any groups.
• ECAT7 Image - Load - unnecessary warning removed in multi-bed mode; now logs information about bed positions and bed planes.

• ROI Evaluation Tool - did inadvertently contain groups in the evaluation table, the numbers listed where random in Vinci 3.45.1. FIXED, see above.

• Zooming in Next-Neighbor/TriLinear Interpolation mode - might have left the image plane for sampling dimensions unequal 256, which was especially unpleasant while zooming 2D-Images. FIXED.
• Undo/Redo after Double-Click Zooming - might have left an offset. FIXED.
• OrthoDisplay Copy/Export/Print - the image of a Zoomed OrthoDisplay did not fit into the preview window. FIXED.

• New OrthoTool - may have got created outside of the workspace, thus being invisible. FIXED.
• Annotation - Creation by Mouse - did not work since Vinci 3.40.0. Sorry - FIXED.
• ECAT7 Image - Load - may have crashed in multi-bed mode. - FIXED.

Vinci 3.45.1, November 16 2009

• Load Speckle Image - the following options are implemented now: difference to previous image, difference to a given image, gaussian filter, and new and only in Vinci 3.x: quotient with previous image, quotient with a given image. The color table Ratio for the two new options is ranged between 0.5 and 2.0 with gamma correction especially set so as to make the image value 1.0 the white center of the legend.
• Load Speckle Image - the plugin features three new buttons that open dialogs to edit color parameters, i.e. Color Table, minimum, maximum and gamma correction for normal, difference and quotient images resp. The entries are used when you load an image with the LoadView Load-button.
  The default color table for difference and quotient images is Ratio, for normal images Speckle Rainbow. The default minimum for new type difference images is -0.1 (-40.0 for old type), for quotient images it is 0.5, for normal images the minimum is fixed to zero. The default maximum for new type difference images is +0.1 (+40.0 for old type), for quotient images it is 2.0, for normal images the maximum is fixed to about 232.033 for old type images and set to the maximum of the image last loaded with the LoadView Load-button else. The default value for gamma correction is true for quotient images and disabled else.
• Load Speckle Image - complete undo/redo now.

• MP4A maskless - the final version of the MP4A tool has now been cleared of all experimental features and provided with comprehensive online documentation, acess via the ?-button at the tool's top. In addition, two default parameters of the previous release have been changed in order to implement our new policy of reference mask generation.
  This plugin is only available internally or with a special license file.

• PlotsView - TACs - TAC scatterplots are now saved in the Vinci project file.
• PlotsView - scatter plots - you can now delete scatterplots; undo/redo inclusive.

• ROI Evaluate Tool - implemented now, undo/redo inclusive. You can open it in the Files/Automate menu, entry ROI Report, and via the Show All button in the ROI Defines tool.
  Pressing the Compute button displays the ROI statistics of all ROIs in table format; results can be copied to the clipboard and exported into a tabulator-separated .TXT-file.

• Report Tool - TAC - the tool now generates so called frame activity curves, i.e. plots the mean value of a ROI or VOI evaluation against the image frame number, for image types known to have no frame time information.
• Report Tool - TAC - you can now generate frame activity curves for Analyze, NIfTI and Paravision frame series, Paravision echo number and slice package series, and Speckle frame series without time information.
• Report Tool - TAC - while computing the time activity curve, the tool needs no longer show the whole plot but a constant number of the latest vertices. At the end or on cancellation it always shows the whole plot.

• Load 2D-Image - 2D-images are now loaded with sampling dimension equal to the image matrix size by default.
• Zoomed OrthoDisplay - images with non-cubical image matrix-size (e.g. 2D- and Speckle images) can now zoom into a non-quadratic Zoomed OrthoDisplay adapted to the image's optimal matrix size.
  The size of the Zoomed OrthoView is now limited by the screen size, instead of the fixed value 1024.
• OrthoDisplay Props - images with non-cubical image matrix-size (e.g. 2D- and Speckle images) can now change back to their optimal sampling dimension and image matrix size in the tool.

• LoadView - as already with Qt's own file dialog, you can now load two or more images at once.
• Ortho Tools - re-opening an already open tool now brings it to the front.

• Reslicing Addition - did neglect a small offset which is important for rotated images with different voxel size:
  • Reslicing Tool - adapted accordingly; alas, results will change slightly, but look better when using MMM result files on already resliced images. - FIXED.
  • Reset Link Channel - adapted accordingly. - FIXED.
  • MMM Reslicing - adapted accordingly; alas, results will change slightly, but look better when MMM works on already resliced images. - FIXED.
  • Synch Reslicing in Drag & Drop - adapted accordingly. - FIXED. Synch Reslicing in the Magic Tool has already been ok.
• Reset Link Channel - for two images, Reset Link Channel did not always work correctly for both images. Sorry, FIXED.

• LoadView - Analyze Image - reading the last frame may have crashed for images with UINT16 data - FIXED.
• LoadView - NIfTI Image - reading the last frame may have crashed for images with UINT16 data - FIXED.

• Multi-Frame Movie Tool - Last Frame - in auto-run mode, the tool did not show the last frame of an image series - FIXED.
• Multi-Frame Movie Tool - Start Frame - did always open with frame number one of the image series instead of its start frame, which maybe frame zero - FIXED.
• Multi-Frame Movie Tool - Analyze Mirroring - running a multi-frame Analyze image, the tool did not use the mirroring parameters originally used in the Analyze load plugin - FIXED.

• PlotsView - slow plotting - generating TACs may sometimes have slowed down without visible cause; hopefully FIXED.
• VOI Evaluate Tool - the tool was not accessible via the Files/Automate menu. FIXED.

Vinci 3.41.0, October 14 2009

• Load Speckle Image - new plugin to load Speckle Images; no options yet (work in progress).
  As with Vinci 2.x, this plugin is only available internally or with a special license file.
• Load Speckle Image - Main Differences to the Vinci 2.xx versions
  • New Speckle Series - the plugin now recognizes a new Speckle series without help from the user; thus, the combobox from which the user chooses a series is disabled now.
    Simply load an speckle image from another directory, the plugin does the rest.
  • ROIs on a Speckle Image no longer get deleted when changing to another Speckle Series.
  • Milli Seconds - absolute time and time differences of frames are now read with milli seconds precision.
  • Raw Speckle Data - the plugin now loads raw speckle data files into Vinci image buffers, where the raw image series of such a file will become a series of z-planes in the image buffer.
  • Progress Bar - the plugin displays a progress bar while (re)creating a speckle image list.

• Load Flat Image - Vinci now initializes the plugin with the Vinci 2.x defaults.
• Image Matrix Size - Auto-Adaption - auto-adaption of the image matrix size can be fine-tuned in the Vinci-Options dialog now.
  It is by default switched off for all 3D-Image types. It is likeswise switched off by default while loading old project files i.e. projects written with Vinci 3.40.0 and before (see also below). It is by default switched on for 2D-Images (i.e. images loaded with the 2D-Image plugin) and Speckle Images.

• Image Matrix Size - an image with matrix size different from the default was not correctly re-created from Vinci project file, independent of the image's format type. - Sorry, FIXED.
• Contours - for images with matrix size greater than 256, contours had broken lines when seen on a 256-pixel display. - FIXED.
• Contours - for images with matrix size 256, contours may have been blatantly false when shown on an image with matrix size greater than 256. - FIXED.
• Vinci Project - after loading one Vinci project, the image matrix size was no longer correctly adapted to image's maximal dimension coordinate. - FIXED.
  To assure that projects written with Vinci 3.40.0 are not involuntarily corrupted concerning image matrix size settings, Vinci 3.41.0 will keep to the default image matrix size while loading older projects (see above).

• TruePixel Move - moving an image with sampling dimension greater than 256 with the mouse did not work correctly. - FIXED.
• TruePixel Cut - cutting an image on a display with the mouse also changed the cutting plane in the vertical direction. - FIXED.

• DICOM Image - image matrix size was adapted to image's maximal dimension coordinate only for images with less than 10 slices, so far. - FIXED.
• DICOM Image - Vinci could not re-create two DICOM images from the same DICOM directory from one Vinci project. - FIXED.

• ROI move via handles - still there were situations where a newly created ROI could only grow in one direction, either horizontally or vertically. - We hope it's finally FIXED now.
• OrthoDisplay Props - the tool always showed TruePixel mode as image sampliung method. - FIXED.
• OrthoDisplay Props - the image sampling dimension was not updated correctly in the combobox when changed in the spinbox for values less than 128. - FIXED.

Vinci 3.40.0, September 30 2009

• Load Image - Vinci now loads images with the so-called image matrix size set to the smallest multiple of 256 (<= 1024) that is greater or equal to the maximal image dimension coordinate. The image matrix size determines the size of the final image slices that are used to evaluate ROIs and Profiles independent of the size of the display(s) on which they are later shown (see OrthoDisplay Props Help for details). It had the constant value of 256 pixels for each image until now.
  So, these changes will only effect images with at least one image dimension coordinate greater than 256, but, alas, you may get slightly different Profiles and ROI statistics for such images. In order to exactly re-produce old results, you can set the image matrix size back to its old default-value in the OrthoDisplay Props tool, see below.
  Images loaded via an old Vinci project, written with Vinci 2.x or version 3.37.0 and prior, are not affected.
• Load Image 2D - according to these changes Vinci 3.x now evaluates ROIs and Profiles on 2D image in full resolution. If you want to see the image in full resolution, however, you have to open a zoomed OrthoView (e.g. by double-clicking on the normal OrthoView) with the same size as the image matrix size and in the OrthoDisplay properties change the sampling resolution (and image matrix size) to meet the display size.
• Load high resolution 3D Image - according to these changes Vinci 3.x now evaluates ROIS and Profiles of e.g. 512-pixels MicroPET images in full resolution.

• Load Analyze Image - the plugin now activates LR mirroring by default, as in Vinci 2.x.

• OrthoDisplay Props - changes of the rendering / sampling parameters can be undone / redone now.
• OrthoDisplay Props - the tool now displays the image matrix size.
  Beware: The sampling dimension must be (and is ensured to be) less or equal to the image matrix size.
• OrthoDisplay Props - you can now open a html help-page via the ?-button at the tool's top.

• Vinci Options - Graphics Items - you can now define whether graphics item groups (GI Groups) by default a) delete their members if they are deleted themselves and b) change the color of their members if they change their own color.

• PlanesView - Zoom - PlanesView features three new zoom levels to shrink the display size to one half, one third and one quarter respectively.
• PlanesView - Plane Numers - the size of the font used to show the plane numbers will now remain constant during zooming.

• LoadVista plugin - should now handle images with "transversal" attribute correctly. More verbose output in the log and consistency checks for corrupted data have been added.

• DICOM image - the fix in Vinci 3.37.0 to read DICOM image from a Vinci project, in fact, made it impossible to read DICOM images directly in the loadview. Sorry - FIXED.
• DICOM image from Project - might have crashed due to a double use of the Vinci splashscreen - FIXED.

• PlanesView - startup - PlanesView may have crashed for big images or (now possible) big image matrix sizes - FIXED.
• PlanesView - invisible crossmarker - PlanesView may have crashed using the context menu if the crossmarker was switched off - FIXED.

• Changing Sampling3D - did sometimes change the current cut position - FIXED.
• Changing Sampling Dimension - did sometimes change the current cut position - FIXED.

• NIfTI Image - Auto-Save - newly created NIfTI image clones (like VOI images or image arithmetic-results) did not save automatically while saving the Vinci project - FIXED.
  The Save NIfTI plugin got renamed from NiFTI to NIfTI by the way.
• VOI Image - Auto-Save - did not work for image types that have no image save plugin - FIXED.
  These VOI images are now saved as interfile images.

• Vinci Close - a changed-project-warning was given if the projects contained Graphics Items or images as they save the time they were loaded into the project as part of their settings. - FIXED.
• Graphics Items Group - Bounding Rect - a switched off bounding rect may have had an offset when switched on again. - FIXED.
• Profiles - Undo - an undo of a translation after an undo of a rotation did not work correctly. - FIXED.
• Text Properties - Copy - copying an annotation object in the tool could not be redone. - FIXED.
• Graphics Items - Reshape with Handles - undo/redo did not immediately update the ROI statistics in their respective tools. - FIXED.
• Vinci Options - General - when you press the Default button to reset the Vinci startup project the changed startup project was not immediately displayed. - FIXED.
• Fusion Tool - the opacity sliders were not completely visible after choosing a fusion image or clicking the fusion button. - FIXED.

Vinci 3.37.0, August 14 2009

• InfoView - MicroPET Image - main info page added.

• Qt 4.5.2 - Vinci now uses the latest Qt libraries on all platforms.
• Qt Asserts - now Vinci gracefully ignores most internal warnings, instead of handling them as fatal errors leading to an instant program termination.

• InfoView - Paravision Image - the InfoView html-template file was not deployed for WINDOWS and Linux. - Sorry, FIXED.
• Load Interfile Image - loading images with data of type UINT8 may have crashed - FIXED.
• Load DICOM Image from project - may not have worked. - Sorry, FIXED.
• InfoView - DICOM Image - due to a case-sensitive search in the info-table, the InfoView page did not show all known information. - Sorry, FIXED.
• External - Python examples - did in fact expect to work with Vinci's debug version. - Sorry, FIXED.
• Contours - Switch off - switching off one or all contours may have crashed Vinci if a graphics item tool (e.g. ROI 2D Define) was open. - FIXED.
• Graphics Items - Scale by Mouse - was not always correctly undone/redone. - FIXED.
• ROI Polygon - Point Insertion - was not always correctly redone. - FIXED.
• ROI Ellipse - Perimeter - sometimes resulted in NaN since Vinci 3.28.0. - Sorry, FIXED.
• ROI - Translation/Rotation - undo/redo did not immediately update the ROI statistics in their respective tools. - FIXED.
• VOI Operations - may have crashed if the operation yielded no resulting VOIs. - FIXED.

• ROI Define Tool - did not immediately update the statistics results of the current ROI if the image interpolation mode changed. - FIXED.
• Groups Define Tool - did not immediately update the statistics results of the current ROI-only group if the image units or image interpolation mode changed. - FIXED.
• Groups Define Tool - did not immediately react if the image buffer in the tool's OrthoDisplay changed, was deleted, or the deletion undone, or if the image buffer was over-loaded, or the overload undone. - FIXED.

Vinci 3.36.0, July 24 2009

• Graphics Item Groups - you can now unite any given set of graphics items using the new Graphics Item Groups, or short GI Groups. GI Groups themselves are a new sort of graphics items which, in fact, means that groups can contain other groups. GI Groups show (by default) their own bounding rectangle. This and other group properties are managed in the new Groups Define tool, see below. The group members act as one item concerning selection, translation, rotation, copy, paste. Deletion of a group (by default) only deletes the group object itself not its member items; but you can change this in the Groups Define tool.
  New evaluation features - ROI Groups, i.e. GI Groups that only contain ROIs, can compute statistics on the union, intersection or difference of the areas of all ROIs, compute a table of the statistics of all individual ROIs and last but not least compute a table of the statistics on the pairwise difference of consecutive ROI group members.
  Constraints: - any graphics item can be in one and only one GI Group.
  The order of the graphics items in the list of group members is kept identical to the order of the graphics items in the image list and project list.

• Mouse and Menu Handling - complete undo/redo inclusive.
  • Creation - You can generate a new GI Group just by starting the OrthoDisplay context menu entry New Drawing Object/Group Item. It opens a dialog to directly choose the desired members with the currently selected graphics items preselected in the list.
  • Selection - If the group shows its bounding rectangle and you click inside the rect or on one of its members, the group's selection state is indicated by the different outlines of its bounding rect. The members themselves are de-selected so to not get distracted by too many selected items on the view.
    However, when the group does not show its bounding rectangle, you can, of course, only select it by clicking on one of its members. Here, the members themselves are shown as selected.
  • Translation - A selected group can be translated with the mouse as any other graphics item. All its members move synchronously.
  • Rotation - When a group shows its bounding rectangle, you can rotate it with the mouse at the bounding rect's rotation handles; when it does not show its bounding rectangle you can rotate it at the rotation handles of its members.
  • Copy Nothing special here: just select the group item and copy it, e.g. by pressing the shortcut CTRL-C (Cmd-C on MacOS).
  • Paste Nothing special here too. Note: the order of the members is kept identical.
  • Deletion Deleting a group (by default) only deletes the group object itself not its members; but you can change this property in the Groups Define tool.
  • Change Color Changing the color of the group (by default) only changes the color of the groups bounding rectangle. You can switch on color synchronization of all members in the Groups Define tool, though.
  • Working on individual Member items First deselect the group, then select an individual member with pressed CTRL key (Alt on MacOS). Afterwards you can do anything with this item as if it were not part of a group, e.g. translate and rotate it relative to the other members. Setting properties of a group member in their respective tools does, of course, not affect the other members.
    Note: Change OrthoPart, Move to Foreground and Move to Background always work on the whole group, even if changed for an individual member in its respective tool. The selection of individual group members is not saved in the Vinci project file.

• Groups Define Tool - complete undo/redo inclusive.
  • new - this button creates a new GI Group and opens a dialog to directly choose the desired members, with the currently selected graphics items preselected in the list.
  • delete - this button deletes the currently selected group. If the checkbox Delete Members is switched off (the default) only the group object itself gets deleted, otherwise also its members.
  • copy - copies the currently selected group.
  • paste - pastes a previously copied group onto the tool's OrthoDisplay.
  • rename - renames the currently selected group.
  • add - opens a dialog to choose the members, the currently selected graphics items are preselected in the list.
  • remove - the currently selected members are removed from the group.
  • up/down - the currently selected members are move up/down in the member list. The graphics items are moved up/down in the image and project list of all graphics items accordingly, which itself determines which item is drawn before which other item.
    Hint: As mentioned above, a call to Move To Foreground and Move to Background for individual ROIs that are members of a group, always work on the group as a whole, so these calls do not have influence on the order of the members.
  • Tool - this button opens the tool of the last of the selected members.
  • Show Bounding Rect - the checkbox determines whether the group's bounding rectangle is drawn or not. This influences the selection and mouse-induced translation and rotation as described above.
  • Delete Members - if this checkbox is switched off (the default) only the group object itself gets deleted, otherwise also its members.
  • Color - include members - if this checkbox is switched off (the default) a color change only afflicts the color of the group's bounding rectangle, otherwise also the color of all members.
  • Operation - for ROI groups, i.e. groups that only contain ROIs, you can here set a mode of evaluation.
    In Global Union, Global Intersection and Global Difference mode the tool computes the statistics on the union, intersection or difference of the areas of all members. In the mode Individual Evaluations the tool computes a table of the statistics of all individual ROIs. In the mode Sequential Differences the tool computes a table of the statistics on the pairwise difference of consecutive ROI group members.
  • Table Context Menus - the context menu of the table header allows to choose which of the following columns are visible: Member Number, Object Name, Number of Pixels, Average, Standard Deviation, Standard Deviation in %, Surface, Volume, Sum, Minimum, Maximum, Type; where Object Name, #Pixels, Average and Std. Dev. [%] are visible by default.
    The context menu of the table body allows to clear its current selection, to toggle between localized and standard English number format, and to export the currently selected rows of the table contents into the clipboard or a file in the directory of the evaluated image and filename combining the object name of the current group with _stat.txt.
  • shade - with this checkbox you can visualize the operation. In the global modes, the area that enters the calculation is shaded with the group's color, in table modes the individual areas are shaded with the individual ROI colors.
  • Help - you can open a html help-page with this text via the ?-button at the tool's top.

• ROI evaluation results - our internal tests showed that the ROI evaluation results on MS Windows changed minimally, i.e. less than 0.1 %. This is due to additional code in our ROI classes and some different compiler optimizations resulting from this.
• VOI Manipulation Tool - you can now open a html help-page via the ?-button at the tool's top.
• Modifier keys - Vinci often uses modifier keys to modify a standard behaviour (see item selection above). The typical keys on WINDOWS in these cases are SHIFT and CTRL and ALT. We now use consistently the SHIFT and ALT keys on MacOS.
  Note: In shortcuts for menu-entries CTRL on WINDOWS is replaced by the CMD key in MacOS.

• Graphics Item - Creation - sometimes the items resisted widening with the mouse - FIXED.
• MouseMode - Create Annotion - when you create an annotion by mouse Vinci complained that it could not generate the DontKnow toolbox since Vinci 3.29.0. - Sorry, FIXED.
• OrthoDisplay - Paste Objects (mouse pos) - a redo pasted the objects at the current mouse position when activating redo, not at the mouse position of the original paste. - FIXED.
• The Copy/Export/Print (OrthoDisplay) keyboard shortcut did not work on MacOS X. It is now Alt-C on all platforms.
• PlanesDisplay - Paste Objects (mouse pos) - a redo pasted the objects at the current mouse position when activating redo, not at the mouse position of the original paste. - FIXED.
• PlanesDisplay - Graphics Item Selection - did not always work as on the OrthoDisplay. - FIXED.
• Setting ToolsDef - with open tool may have crashed Vinci on non-WINDOWS machines. - FIXED.

Vinci 3.35.3, June 10 2009

• Talairach Tool - you can now open a html help-page via the ?-button at the tool's top.
• Load 2D Image - added plugins for SVG- and GIF-images.

• Missing Library - due to a missing Qt library, Vinci crashed immediately on most systems. Sorry, FIXED.

Vinci 3.35.0, June 9 2009

• Talairach Tool - tool implemented now; undo/redo inclusive. From the Vinci 1.98 documentation: The tool applies the Talairach proportional grid system transformation to compute the Talairach coordinates at the cursor position. They are displayed in the OrthoDisplay info line if you activate the Show Talairach coordinates checkbox (Talairach activation).
  • Talairach landmarks - you define a landmark by choosing it in the list, cutting the image at the appropriate position and pressing the Set button. The Find button shows already defined positions. You must define all of the following eight landmarks:
    AC - top-behind to the anterior commisure,
    PC - below the posterior commisure,
    left - most lateral point of the parietotemporal cortex (left hemisphere),
    right - most lateral point of the parietotemporal cortex (right hemisphere),
    anterior - most anterior point of the frontal cortex,
    posterior - most posterior point of the occipetal cortex,
    superior - highest, most superior (most dorsal) point of the parietal cortex,
    inferior - lowest, most inferior (most ventral) point of the temporal cortex.
    NOTE: The landmarks and the setting to show an image with Talairach or default image coordinates are saved in the Vinci project file.
  • Adopt Talairach landmarks - Talairach landmarks that you set in one image buffer can be re-used in any co-registered image buffer. You choose the image buffer in the drop down list and press the Adopt button. Talairach coordinates will be activated immediately.
    This is the preferred way to define Talairach landmarks on a PET image using the anatomical information from a co-registered MR study.
    CAVEAT: Make sure the two images are really co-registered; otherwise the displayed Talairach coordinates may be incorrect.
  • Find Position - you can input Talairach coordinates [mm], press the Find button and the image will be cut at the given position.
  • Undo/Redo - setting and deleting a Talairach landmark and deleting all Talairach landmarks can be undone/redone, as can Talairach activation and adoption of Talairach landmarks defined on a co-registered image buffer.
  • Restriction - the algorithm assumes that the interhemispheric fissure lies on a vertical plane while you set the landmarks.
    WARNING: Make sure this is exactly fulfilled; otherwise the diplayed Talairach coordinates may be incorrect.

• OrthoDisplay Copy/Export/Print - this new dialog provides multiple export options:
  You can copy an OrthoDisplay to the clipboard (as image, or svg-xml-text), export it into a file (in BMP-, PNG-, PDF-, and SVG-format), or send it directly to the printer if you like (we also have a print preview). The dialog features a live-preview of the various export options.

Vinci 3.34.0, May 15 2009

• QuickReslicer Tool - tool implemented now; undo/redo inclusive.

• Save Project - Pack & Go - Vinci now writes the Vinci project file and closes the Save Project dialog automatically if the image relocation works successfully, e.g. was not cancelled by the user.
• OrthoDisplay Properties - as in Vinci 2.xx, the tool now closes when you switch off the crossmarker via the OrthoDisplay infoline.

• Landmark Tool
  • Tab Order - defined now.
  • Shortcut Q - as in Vinci 2.xx, you can now open the tool with the shortcut Q.
  • Registration Quality - you are warned about a bad correlation of the landmarks if, after registration, the summed mean square distance of corresponding points exceeds twice the greater voxel-diagonal of both images.
    Until now Vinci used a fixed value of 5 mm which is appropriate for human brain image registrations only.

• OrthoTools - Change OrthoDisplay - an undo now also re-creates the tool state.

• OrthoTool Help
  • Landmark Tool - you can now open a html help-page via the ?-button at the tool's top.
  • Report Tool - you can now open a html help-page via the ?-button at the tool's top.

• OrthoTools - Change OrthoDisplay - no longer grabs the focus. So, when pressing a shortcut key e.g. <M>, the tool no longer tries to switch to OrthoDisplay <M> but the tool's OrthoDisplay changes to mouse-mode <M> (image move), as expected.

Vinci 3.33.0, May 8 2009

• Landmark Registration - tool implemented now; undo/redo inclusive.
• Landmark Registration - Main Differences to the Vinci 2.xx versions
  • in case of a landmark registration based on two points, our tests found one backward/forward flip when comparing Vinci 3 with Vinci 2 results. The algorithm aligns the two points on their common axis, though the rotation around this axis is, per se, undefined. If the user chooses to prepare for manual registration both images get resliced in a way that the common axis is shown perpendicular on the sagittal part of the OrthoDisplays. The user can then easily apply the missing rotation e.g. by visual inspection.
    CAVEAT: The direction of the common axis depends on the order of the two points going into the calculation. This order changed when porting Vinci 2 (using MFC) to Vinci 3 (using Qt). The usual Reset Link Channel on the reference image, after a full registration has been achieved manually, will, of course, result in the same final orientation.

• Qt 4.5.1 - Vinci now uses the latest Qt libraries on all platforms.

• MicroPET Image - Vinci 3 could not correctly load Vinci 2 project files containing MicroPET images and v.v. - FIXED.
  CAVEAT: Vinci 3.32.1 and versions before can no longer load project files containing MicroPET images written by Vinci 3.33.0.
• Online Update - [MacOS only] Vinci 3.32 crashed when trying to close the current instance. Either update from Vinci 3.31 or install manually, sorry. - FIXED.
• Flat Image - PatientName, DataUnits and ImageSettings were not correctly saved into the Vinci project file, nor into the LoadHistory - FIXED.
• Save Image - saving an image buffer may reset the OrthoDisplay's entry about Drawing Objects Base Image - FIXED.

Vinci 3.32.1, April 28 2009

• Save Interfile image - can now also save image data in 2-byte signed integer flavour.

• PlanesView - crashed since Vinci 3.30.0 when opened before any image is loaded. FIXED.
• Load 2D Image - the tool needs appropriate image formats plugins which were missing in the Vinci 3.32.0 release - FIXED.
• Load 2D Image - did reject correct file-extensions if they contained capital letters - FIXED.

Vinci 3.32.0, April 24 2009

• Load 2D Image - this new plugin can read 2D images in many popular formats, including PNG, TIFF and JPG. We currently convert colour to "grayscale" values.

• Load NIfTI image - it appears that Vinci consistently flipped one axis when loading image data, resulting in a mirrored left and right side. We apologize. FIXED.
• Save NIfTI image - it appears that Vinci consistently flipped one axis when saving image data, resulting in a mirrored left and right side. We apologize. FIXED.

Vinci 3.31.0, April 23 2009

• VOI Manipulation - new features; undo/redo incl.
  • Voxels in given ROI - you can now add or erase voxels lying in a given ROI, e.g. you can re-use a ROI previously drawn in Polygon mode, see below.
  • Delete Immediately - in Polygon mode, the polygons drawn to add or erase voxels no longer get deleted automatically after releasing the mouse button if you switch it off in the new delete immediately checkbox.
  • Plane Width - support for simultaneous editing (add/erase) in neighbouring planes in Polygon and the new Given ROI mode.
  • PlanesView - in Parts as already in Pen mode, you can edit VOIs on all PlanesView displays in parallel.
    INFO: This will not work for Polygon or Given ROI mode as ROIs can only be shown (drawn) on the Crossmarker display.

• Load Analyze Image - added new option "Set NaN values to zero" (now default) to the plugin.
• Load Flat Image - now also accepts image files with filenames that have a "numerical extension" such as "somepath/somefile.1234".

• PlanesView InfoLine - the image values shown in the PlanesView info line were still incorrect for displays smaller than the standard size (256 pixel) - FIXED.
• PlanesView Reslicing - crashed if done outside the dimension bounderies - FIXED.
• Image Rotation - mouse- or magic-tool-induced rotation of an or into an un-rotated image may have disrupted the sequence of planes on PlanesView if used with multiple slots - FIXED.
• Image Cut - undo/redo did not work for image cutting induced by a pressed mouse wheel - FIXED.
• SaveView - Browse Dialog - the Save button was nearly always grayed - FIXED.
• Rectangular ROIs - statistics may have wrongly stated that some rectangles have no pixels, since Vinci 3.28.0. Sorry - FIXED.

• VOI Manipulation
  • Zoomed OrthoView/PlanesView - VOI Editing in Polygon mode used shifted voxel positions - FIXED.
  • Activate Mouse Edit - undo/redo did not always work correctly - FIXED.

Vinci 3.30.1, April 10 2009

• Load DICOM plugin - a stupid bug caused Vinci to crash in certain circumstances when loading DICOM data (the bug was related to adding another column in the list of DICOM data sets and only affected Vinci 3.30.0), sorry. FIXED.

Vinci 3.30.0, April 9 2009

• VOI Manipulation - tool implemented now; undo/redo inclusive.
• VOI Manipulation - Main Differences to the Vinci 2.xx versions
  • Full Undo/Redo - you have full undo/redo for adding and erasing voxels, as well as in the tool editing settings.
  • PlanesView - you can edit VOIs on all PlanesView displays in parallel in Pen mode.
  • Plane Width - support for simultaneous editing in neighbouring planes in Pen mode.
  • Context Menu - you can change editing modi in the OrthoView and PlanesView context menu, so in principle, you can work without open VOI Manipulation tool.

• Rotation Center - image's rotation center is now shown on all displays in rotation mouse mode.

• Load DICOM plugin - a column "orientation" was added to the list of DICOM data sets.

• Vinci Close - when closing Vinci as already done when closing a project, you will now be asked whether you want to save the project, close without saving or cancel closing if the project has changed, or if not, just whether you really want to close or cancel closing.
• Ask even if Closing an Unchanged Project - this new option in the Vinci Options's General tag allows you to switch off the question whether you really want to close an unchanged project.
• Reset Startup Project - also in the Vinci Options's General tag, you can now reset Vinci's startup project - auto-loaded when starting the program - to the system default which is the project default.vpx in Vinci's bin directory.

• Save Project - the project name and path proposed for a not-yet-named project is now derived from filename and path of the first loaded image buffer (similar to Vinci 2x).
• Save Project - a new button allows to extract project name and path from filename and path of any chosen image buffer.

• PlanesView - mouse induced reslicing optimized for speed.
• Displays - optimized for memory usage.

• Application startup error - (Windows only) due to missing libraries, since Vinci 3.28.0; sorry, FIXED.

• PlanesView InfoLine - the image values shown in the PlanesView info line were always calculated in the image's cut plane, independant of the display on which the mouse cursor happened to linger - FIXED.
• PlanesView - may have crashed during reslicing on WINDOWS and LINUX since Vinci 3.28.0; sorry, FIXED.
• PlanesView General Properties - some spin boxes e.g. Number of Planes, Color of Plane Number, etc. did not allow single step action - FIXED.

• VOI Operations - the deletion of all VOIs (i.e. the last VOI) of a VOI subtraction computation crashed on UNIX. FIXED.

• Project Changed - check did not work correctly for some time now. FIXED.
• Moving Cross - did not appear at the position of the mouse cursor when started. FIXED.
• Moving Cross - did not disappear immediately when stopped. FIXED.

• OrthoView - copy to clipboard (right-mouse menu) only copied parts of the OrthoDisplay. FIXED.

• Load Bruker/Paravision - for some data sets the parameters slice orientation and read orientation are not interpreted correctly. The problem has been identified (thanks Michael D and Jan) and will be fixed shortly.

Vinci 3.29.0, March 27 2009

• Load DICOM
  • selection by double-clicking - you can now double-click on a DICOM data set in the list box in order to load it. If you want to load more than one data set, select the corresponding entries in the list box (use SHIFT and CTRL modifier keys for an extended selection) and click "Load".
  • added modality information - we extended the Vinci DICOM summary to include information on the modality of a DICOM data set. This is now also displayed in the first column of the list box.
  • clear list box before browsing - when changing to another directory tree of DICOM data, the list box will be cleared before new DICOM data sets are added to the list box.

• Save DICOM - experimental feature (advanced users only) for converting any image volume that can be read by Vinci into mainstream DICOM flavours (MR, CT, PETCT) - status: experimental.

• Options: Target Operating System - when running Vinci remotely on a Unix server using X11 on a MacOS X system, dropdown lists on toolboxes do not work properly. You can set "Mac" as the "target operating system" in the Help menu or Vinci's options (General tag) and a different kind of widget is used for toolboxes.

• Installer problem (Windows only) - some MS Windows systems require installing additional libraries provided by Microsoft at no cost (vcredist 2008 SP1). This is related to our compiler upgrade and affects all versions since Vinci 3.28.0. See the note on our download page.

• OrthoView - sometimes crashed during creation on UNIX systems. FIXED.

• VOI Images - with overlapping irregular VOIs were not saved properly. FIXED.
• VOI Paste - after undo of a paste of a VOI that overlapped, the overlapped VOI was not repainted correctly. FIXED.
• VOI Paste - did crash on Linux if the pixel sizes of the source and target image were not identical - FIXED.

• MMM Tool - might have crashed because it did not find the icons for the choose-image-buffer buttons. FIXED.
• Report Tool - TACs - has crashed after processing the last frame since Vinci 3.28.0. Sorry, FIXED.
• ROI/VOI Tools - the tool sometimes worked on another ROI/VOI than was color-marked as selected - FIXED.

• Load DICOM - did not always load the DICOM data set that was selected in the list box, in particular, when restoring the settings of a previous Vinci session. FIXED.

Vinci 3.28.0, March 20 2009

• Image-based Calculations - new functionality has been added, now using expressions like 1.3 * log( a ) or b/c ** (2/3) can be used where a, b, c refer to previously loaded image data. See technicalreference.htm in Vinci's doc directory for more information.
• Image-based Calculations - now deletes temporary images (i.e. in-between results).
• Image Arithmetic Tool - features a new exponentiation operation: a * A**b, where A denotes an image buffer, and a and b are real numbers.

• Bruker Paravision Images - where possible, Vinci will now inherit all properties (meta-information like patient id, acquisition parametes, etc) of Bruker Paravision source images in arithmetic operations.

• Qt 4.5.0 - Vinci now uses the latest Qt libraries on all platforms.
• Visual Studio 2008, SP1 - Vinci now uses the newest MS compiler version for the WINDOWS platform.

• Image Arithmetic Tool - did not correctly reset labels and default-values for image multiplication after scaling. Sorry - FIXED.
• Image-based Calculations - in certain circumstances, evaluating expressions with round brackets resulted in an error due to a stupid mistake when preparing the Python parameter list, sorry. FIXED.
• PlanesView - sometimes crashed during resize on UNIX and WINDOWS systems. FIXED.

Vinci 3.27.1, March 04 2009

• DiMI Vinci course - welcome to all participants of the fourth Vinci course, the first course to use Vinci 3.x during practical exercises. Thanks to all colleagues who offered to contribute and help with presentations, guided tours and practical exercises.

• Image-based Calculations - (first introduced in Vinci 1.93.0, March 2005) a flexible way to evaluate expressions involving image data assigned to variables (e.g. a: image buffer [0], b: image buffer [1], etc.). We support arithmetic operations and have defined some useful functions, e.g. for thresholding images. See technicalreference.htm in Vinci's doc directory for more information.

Examples:
• "a + b" - in this example, a new image buffer will be created by adding corresponding voxels of image buffers a and b. Subtraction, multiplication and division also work on a voxel-voxel basis (similar to array operations in the IDL language).
• "1.7 * a + 23.8" - in this example, a new image buffer will be created by multiplying all voxels of image buffer a with a constant factor (here: 1.7), then a constant (here: 23.8) is added to all voxels.
• "ge (a, 5.0)" - this will return a new image buffer of the same geometry as image buffer a, all voxels are set to one where corresponding voxels in image buffer a are greater or equal than a threshold value (here: 5.0), otherwise the voxels will be zero.
• "th_ue (a, 5, 10)" - this will return a new image buffer of the same geometry as image buffer a, voxels are set to a constant value (here: 10) where corresponding voxels in image buffer a are greater or equal than a threshold value (here: 5), otherwise the voxels values will be inherited from a.

• Pack And Go - the button in the SaveProject dialog is implemented now for all image types except DICOM and Paravision; work in progress.

• Load Bruker/Paravision Plugin - improved handling of 2D multi-echo data sets: we can now read individual echo images which are treated similar to "multi-frame" studies, and, as a consequence, can now be displayed as movies. Use the Multi-Frame Movie plugin (s.b.) for animations, or to efficiently load individual echo images. Reading of meta-information from header files has also been improved (taking up more suggestions from Michael D) this is reflected in the log.

• Multi-Frame Movies - this OrthoDisplay plugin (you can use the triangular "play" icon in an OrthoDisplay's title line as shortcut) can now be used to efficiently load individual frames of a multi-frame series. This should currently work well for certain types of NIfTI and Bruker Paravision data sets.

• Load DICOM Plugin - pressing either SHIFT or CTRL when clicking on the Dump button will open the native file browser instead of the one provided by the Qt framework (on the Mac platform, we use the native file browser as default). After browsing a directory tree for new DICOM data sets, we will now select the first new data set after all have been added to the listbox - good suggestion, Moritz.

• Vinci on Linux/Solaris
  • Absolute Path - in order to start Vinci on Linux and Solaris without using the start scripts provided with our distribution, you had to change to Vinci's bin directory first. Now, Vinci for Linux and Solaris is linked in a way that you can start it from any directory just by using its absolute path. On Mac OS, you could start Vinci using its absolute path right from its very first release; on MS Windows you can do this anyway.
  • Qt Config - you can now use the full functionality of qtconfig, Qt's own tool to easily change the look and feel of every Qt-4 program running on your Linux/Solaris machine.
    On the Vinci Options General page just press the new button qtconfig. For the changes to take effect, though, you have to re-start Vinci, or your other Qt-4 applications, resp.
• Vinci on Linux
  • Start Scripts - due to the changes mentioned above, we no longer need the startVinci.sh script in Vinci's bin directory, and could simplify the startVinci_<platform_id>.sh script to be a simple link to the Vinci program (now called vinci_<platform_id>), and change the all-user calling script vinci accordingly.
  • Installation - we changed from a binary all-in-one installer to a packed tar-ball and provide an installation script, viz. install.sh, see INSTALL.htm for details. Please note that we tried a ready-to-run ("out of the box") approach also for the Linux versions of Vinci, the install script is intended to make the installation process more transparent and circumvent occasional problems with the binary installer program.

• Analyze Image Relocation - did not copy the header file - FIXED.
• Stryker/Leibinger and Flat Image - the InfoView crashed when opened via the icon in the OrthoInfoLine if it were to show the image's Basic Info tag by default - FIXED.
• Linux installer - the binary all-in-one installer we have used for our Linux distributions crashed on some older distributions of Linux (it did work in text mode, though, thanks to R Kupers for the bug report). Starting with this version, the distribution takes a more "traditional" approach and uses packed tar-balls, s.a.
• Load Bruker/Paravision Plugin - 2D multi-echo data sets were not interpreted correctly: they were not displayed with correct dimensions and not sorted correctly into image volumes. FIXED.
• Vinci Lite crashed when closing. Thanks for the bug report, Dirk. - FIXED.
• Vinci Arithmetic Tool did not always work correctly after scaling - hopefully FIXED.

Vinci 3.26.0, February 19 2009

• Contours Tool - this important plugin allows to define iso-contours on an image buffer's histogram. These contours can then be displayed on one or more OrthoDisplays (in the top-most layer) which, in conjunction with the Fusion functionality, is the preferred way to evaluate a co-registration attempt's quality. Tool tips have been added to explain the most important parameters.
• Keyboard Shortcuts - as the Contours Tool and the Fusion Tool are required quite often for daily work, we have created keyboard shortcuts to open them: move the mouse cursor to an OrthoDisplay that shows suitable image data and press "K" (Contours) and "F" (Fusion), resp., to open the corresponding plugin.

• Drag and Drop - the OrthoDisplay name button (e.g. < A >) can now be dragged and dropped
  • onto another OrthoDisplay (to efficiently sync color and/or reslicing settings - be our guest, Heike)
  • onto the fusion tool - one of its image edit fields;
  • onto the report tool - one of its image edit fields;
  • onto the SaveView - start and end frame edit fields.

• Load Paravision (Bruker) Image - most changes are related to improved analysis of meta-information, more to come (thanks to Michael D for suggestions):
• New entries - added ACQ_scan_name, EXPNO, PROCNO to the list of data sets (new columns).
• Improved logging - streamlined output in the LogView.
• Distinction 2D/3D data set - will now write a suitable comment in the log (but not always act accordingly - work in progress).
• Data set selection - now full lines are selected, using alternating row colours.
• Native File Browser - you can now also use your platform's native file/directory browser, see "Load DICOM Image" below.

• Load DICOM Image - pressing either SHIFT or CTRL when clicking on the Browse button will open the native file browser instead of the one provided by the Qt framework (on the Mac platform, we use the native file browser as default).
• Color Tool - Sync - added some questions before starting the sync process.

• Drag and Drop - might have been indicated as possible where in fact it was not supported. FIXED.
• Load DICOM Image - removed some diagnostic output (leftovers from debugging). FIXED.

Vinci 3.25.0, February 11 2009

• New Scrollwheel Option - if the mouse is placed over an OrthoDisplay, using the scrollwheel while keeping SHIFT pressed will cut the current image buffer in a perpendicular way - which is useful for getting an overview of all slices in that direction. A new option in the OrthoView tab of the Options dialog (it has an entry in the Extras menu, on Macs it is called "Preferences" and can be found in the very first menu) now allows you to use scrolling without the additional SHIFT key.
• Fix Frames - a new feature available through the LoadECAT7plugin: ECAT7 multi-frame files can have less actual frame data than advertised in their main headers for several reasons. This can play havoc on some tools that expect frames to be consecutively numbered, starting with frame 1. You can now use the "Fix Frames" button to have Vinci create a new multi-frame file that replaces missing frames with "empty" images that will have suitable frame times. It is also a good method to generally check the consistency of multi-frame studies in terms of frame times.
• Load ECAT7 image - improved loading of ECAT7 files with missing frames: Vinci will now list all existing frames and make them available for loading/summing (you need to manually defined suitable intervals of consecutively numbered frames).
• Color Tool - the tool now contains some missing features of Vinci 2.x, like Max Cols, Sync, etc; undo/redo inclusive.
• The Vinci Config file on Unix machines (e.g. on Linux ~/.config/MPIfnF/VinciQ.<computername>.conf) is now saved with a shortened form of the computername i.e. the name without domain extension to provide for portable computers that may live in different domains and normally want to share one configuration file.

• Save Project - the "Browse" button did not open a file browser: sorry, Heiko. FIXED.
• The WINDOWS Setup started Vinci and showed the history file twice - FIXED.

Vinci 3.24.1, February 8 2009

• Install script - (MacOS X only) a new install script has been added to the standard installer (bottom right corner, start with a double-click). This optional method for automated installation will (cautiously keeping older versions) copy the current Vinci application to the "/Applications" directory (or to your home directory if you do not have sufficient write permissions), and update a "VINCI.app" in that directory: you can drag this placeholder application to the MacOS Dock (once), it will then always start the latest Vinci version.

• Qt warnings - some non-critical Qt-related warnings appeared in the Unix versions of Vinci (at console level). The offending source code has been mended. FIXED.

Vinci 3.24.0, February 6 2009

• Arithmetic Tool - the new scaling operation no longer scales the actual image minimum to a new minimum, but the so-called scale minimum, a value you can now enter in the third edit field. For PET-images the scale minimum should be set to 0, the default value.
  Where this is not appropriate, you can set it back to actual image minimum with the new button Set to Min next to the edit field.
  The image color table and gamma correction remain untouched, minimum and maximum are set according to the new image range.
  The scaling range is changed to 0 till 256.
  Some convenience functions: the selected operation is no longer set to a default value when you change the display. The default display for chosen image is now set to the display of the tool.
• LoadView - the plugin part is scalable now. This feature (thanks, Michael!) is particularly useful when working with directory trees containing many DICOM or Bruker Paravision data sets ("browsing").
• SaveView - the plugin part is scalable now.

• PlanesView - Copy to Clipboard - did only copy the currently visible part of PlanesView into the clipboard; it now copies the whole contents of the view. - FIXED.

Vinci 3.23.0, February 5 2009

• Arithmetic Tool - features a new operation for scaling an image into a given range; 0 to 255 by default.

Vinci 3.22.1, February 4 2009

• Load DICOM image - if available, will now include the patient's name, the protocol name and the study date in the title line when the image is displayed.

• Load DICOM image - did not load DICOM data sets from a Vinci project. FIXED.
• PlanesView - an ugly bug caused Vinci to crash in certain circumstances when using the PlanesView. This bug only affected the non-MDI version (default on the MacOS X platform). We apologize. FIXED.

Vinci 3.22.0, February 3 2009

• Vinci Options - dialog implemented now; undo/redo inclusive.
  You will find it in the Extras menu.
• InfoView - improved output (cosmetics) for image data of types DICOM, NIfTI, and Analyze; work in progress.

• Report Tool - TAC - Cancel button implemented now.
• Report Tool - TAC - removed unused edit field for Patlak Tool output.
• Report Tool - TAC - the default output path (i.e. the path of the currently used project file) is replaced by the user's personal folder if he lacks the necessary write-permissions.

• OrthoView Properties - introduced undo/redo for Zoom Level settings.
• Target Operating System - introduced undo/redo for settings.
• PlotsView Settings - we re-named the entries for consistency with the entries of the other views. Previous changes of the fonts will be lost. Sorry for the inconvenience.
• OrthoTools - can now scroll their OrthoView into view when clicking on them, unless you press the CTRL button during the mouse click.
  You can activate this behaviour under Extras/Vinci_Options on the OrthoView page. Just switch on Auto Scroll.

• Report Tool - TAC - the selected VOI image was not saved in the Vinci project file. - FIXED.
• Report Tool - TAC - a newly loaded VOI image was not inserted in the combobox of selectable VOI images. - FIXED.
• Report Tool - TAC - the output file edit field did not allow empty entries for text output which would only show in the log. - FIXED.
• Report Tool - TAC - the default output file name sometimes had no extension. - FIXED.
• The View Icons - did no longer apppear in MDI mode - FIXED.
• The Vinci History - has looked horrible in Internet Explorer and Firefox since Vinci 3.21.0, due to a glitch in the Vinci style sheets - FIXED.

Vinci 3.21.0, January 27 2009

• MP4A maskless Plugin - kinetic analysis of MP4A PET data independent of the Zuendorf mask. Voxel based Nonlinear Least Squares fit powered by a Gauss Newton solver. Built-in regional statistics. Template and atlases are part of the distribution. Error estimate "k3dev", optional k3r-correction.
  This plugin by C. Hohmann (PhD thesis) is currently only for internal usage.

• Report Tool - TAC - tool implemented now; undo/redo inclusive.
• Report Tool - Main Differences to the Vinci 2.xx versions
  • VOI TACs - you can now compute and plot time activity curves (TACs) for VOIs.
  • Text File Templates - text file output is formatted according to a template file.
    Some templates are predefined that format text files like in Vinci 2.xx.
  • Patlak Tool Compatible Output - patlak output is also formatted according to a template file.
    One template is predefined that produces the necessary format to boost our internal Patlak Tool.

• DICOM reloaded - the DICOM plugin now features a new user interface that takes advantage of some Qt features.
  The DICOM color window settings now initialize the Vinci image's color range.
• InfoView - improved output for image data of types DICOM, NIfTI, and Analyze.
• InfoView - the Vinci version history is now shown in the About entry of the InfoView, and the menu entry Update/Version History now opens the InfoView and no longer the standard browser to show it.

• VOI Statistics - due to unification of the algorithm of VOI and ROI analysis, VOI statistics may change very slightly.
  The Vinci test suite found changes in one of about 100 VOIs with relative differences less than 0.00001 on WINDOWS and SOLARIS; and no changes on our LINUX platforms.
• Default Font - the default font of dialogs, menus etc. is too small on Unix systems. We now initialize the user's ~/.config/Trolltech.conf file so as to use a sans serif font with 14 pt size if it is not already set.

• VOI Report - the Close button did not close the window but only delete its contents in MDI mode. FIXED.
• VOI Report - the floating point number results were in fixed format instead of compact format (%g) with 6 digits precision used for individual VOIs - FIXED.
• Loading Vinci Tests did not work for tests produced by Vinci 2.x that contained a wait-on-thread-finished command - FIXED.
• InfoView - when started from the OrthoDisplay info line, the InfoView has not expanded the corresponding image entry since Vinci 3.19.0. Sorry, FIXED.
• SaveView - the SaveView size did not automically adjust to the plugin size (since Vinci 3.16.3). - Sorry, FIXED.
• SaveView - switching on/off the SaveView options (e.g. Frames) did not automically change the plugin size (since Vinci 3.16.3). - Sorry, FIXED.

Vinci 3.20.0, January 16 2009

• Load Flat image - similar to the plugin in Vinci 2, this new plugin can be used to load image data where no suitable header information is available and needs to be provided manually. The plugin currently only supports 3D data and might later also support multi-frame series.
• Load Stryker/Leibinger image - a plugin for loading Stryker/Leibinger data has been added, this is similar to the corresponding plugin in Vinci 2 (introduced in Vinci 1.68 of Aug 2004), this is primarily of interest for stereotactical applications and to some extent for neuronavigation. This plugin requires a special license key, otherwise it will not appear in the list of load plugins.

• Load Micropet Image - the z pixel size was not set correctly: it was set to the transaxial_crystal_pitch but should have been half of that (thanks, Heiko). Sorry, FIXED.
• Load ECAT7 Image - resetted choices for Frame Mode and Frames before loading a file (thanks, Heiko). Sorry, FIXED.
• ROI2D Define, Text Define and Profile Tool - may have crashed since Vinci 3.19.0 during image overload (loading of an image in an already used image buffer). FIXED.
• PlotsView Properties - the Close button did not close the window but only delete its contents in MDI mode. FIXED.
• PlotsView Properties - the size did not automically shrink/expand according to the state of the more check box (since Vinci 3.16.3). - Sorry, FIXED.
• Project Save - on LINUX OrthoTools got switched on and off continously when using the menu entry File/Save Project (since Vinci 3.16.3). - Sorry, FIXED.

Vinci 3.19.2, January 12 2009

• LoadView - changing the Load Plugin could crash Vinci in certain circumstances. FIXED.
• LoadView - the LoadView size did not automically adjust to the plugin size (since Vinci 3.16.3). - Sorry, FIXED.

Vinci 3.19.1, January 9 2009

• New Web Site - the Vinci 3 web site is now available here: http://www.nf.mpg.de/vinci3.
• Multi-Frame Movie - this new plugin (open via toolbox menu in the OrthoView, or use the new "play" shortcut in an OrthoView's title line) allows to efficiently load the next frame of a multi-frame series: it has been optimized for speed, in particular for NIfTI images, so it is possible to view 4D-data efficiently as a movie (also for gzipped NIfTI files). Caching (this is done automatically) is only required for fast toggling between the first and the last frame of a series. This new plugin is currently limited to NIfTI, Analyze and Bruker Paravision images.
• Small Animal Imaging - the load plugins for MicroPET, Paravision, Analyze and ECAT data now use a more appropriate sampling pixel size when loading data from small animal imaging.
• Load Paravision Image - improved browsing function. It is now possible to select any frame of a multi-frame series.
• Load Analyze Image - a new plugin to load Analyze 7.5 data (it now uses the same backend as the NIfTI plugin).
• LoadView - more robust behaviour if a particular Load Plugin is not available.

• Load NIfTI plugin - did not display the correct number of frames when restoring a setting from the file history. FIXED.
• Zoomed OrthoViews - this problem only affected the Non-MDI window mode and caused zoomed OrthoViews (generated by double-clicking on an OrthoDisplay) to have a faulty position and/or size. FIXED.
• LoadView - changed z-order of widgets too frequently (flicker), a (cosmetic) problem that affected the Mac platform. FIXED.
• Save Project - when saving a project, Vinci did not always prevent the user from overwriting the default project (by forcing an initial "Save As"). FIXED.
• info.xml - the MacOS X version did not have a distribution-specific "info.xml" file which is needed to validate the checksums of libraries. FIXED.

Vinci 3.18.1, December 19 2008

• Magic Tool - Missing icons have been implemented (creation mode); all icons have tool tips now.
• Load MicroPET plugin - a plugin for loading data from the Siemens microPET and Focus line of systems has been added. This is still work in progress, not all features of the corresponding Vinci 2.x plugin are yet available.
• Load Paravision plugin - several improvements in the user interface but still not yet production level.
• Log View - the log now stops scrolling while you press the CTRL key and jumps to its bottom when you release the key again.

• VOI Tools - Undo of selection of first VOI did not work - FIXED.
• VOI Operations - Undo of Select None did close the VOI list for operations 1 and 2 - FIXED.
• Image Volume Filter - may have crashed since Vinci 3.15.0 - FIXED.
• Log View - the log did not always scroll to its bottom when text was added - FIXED.

Vinci 3.17.0, December 2 2008

• Multi-Window-Mode - sizing and positioning generally improved.
• Mac: open-event support - you can now use open -a vinci_317 <image file> to load image data into Vinci. If Vinci is already open, the frontmost instance will load the file, otherwise a new instance of Vinci is started. Vinci tries to automatically recognize the required load plugin.
• Bruker Paravision plugin - a plugin for browsing and loading image data from Bruker NMR systems, status: experimental.

• PlotsView Properties - did not re-create its position when loaded from Vinci project file - FIXED.
• Opening Vinci w/o Loading a Project - did not resize and position the program's main window, thus leading to a hidden title lines when saving on LINUX and restoring the project on WINDOWS - FIXED.
• Big Endian MD5 checks - on a big-endian machine Vinci complained about image changes when loading projects saved on little-endian machines (although the image data was not corrupted) - FIXED.
• Vinci Test - Compare Column Value File - could not cope with empty columns that were last in a line of text - FIXED.

Vinci 3.16.3, November 20 2008

• New OrthoView - OrthoViews will now get created and shown maximized.
• Multi-Window-Mode - size and positioning
  • MainWindow - OrthoView - improved start size and positioning.
  • PlotsView - improved default size and positioning.
  • InfoView - improved default size and positioning.
  • LogView - improved default size and positioning.
• Minimizing the Application - in multi-window mode, minimizing the application main window will now hide all sub-windows; when shown normal again the sub-windows will re-appear.

• Multi-Window-Mode problems
  • All Views covered the OrthoView - on WINDOWS without being able to get the OrthoView in front of the other views - FIXED.
  • Re-loading a PlotsView - from a Vinci project file crashed - FIXED.
  • Re-loading a PlotsView Properties - from a Vinci project file crashed - FIXED.
  • Re-loading a VOI Report - from a Vinci project file crashed - FIXED.
  • Changing 3D-Interpolations Mode in PlanesView crashed - FIXED.
• White Pixels - clicking on an OrthoDisplay or PlanesView showing an undefined image produced temporary white pixels - FIXED.
• Hide/Show OrthoView Colorbar - did not shrink/enlarge the OrthoView correctly - FIXED.
• Hide/Show OrthoDisplay OrthoParts - did not shrink/enlarge the OrthoDisplays correctly - FIXED.

Vinci 3.16.2, November 07 2008

• Load Image - if there are not enough OrthoDisplays to show a newly loaded image a new OrthoDisplay will now get created on-the-fly.

• Font Settings - PlotsView and Logger now feature better platform-specific startup font families and sizes. PlotsView now saves font families and sizes in the user-settings.
• LogView - Shortcuts - You can now use CTRL-Plus and CTRL-Minus on any platform to increase/decrease the font-size. On WINDOWS you have the old shortcuts CTRL-Y and CTRL-Shift-Y as well.
• Style Sheets - used in InfoView and History and Test-Report are now platform- and browser-specific.

Vinci 3.16.1, November 01 2008

• Load NIfTI Images - many optimizations now allow a movie mode for viewing compressed NIfTI. So far, no, or little caching of data is required.

• Load NIfTI Images - a particularly ugly bug in the plugin's initialization crashed Vinci in certain circumstances (e.g. at startup). FIXED.
• Directory Write Permissions - were not properly determined on WINDOWS since Vinci 3.15.1. Sorry - FIXED.

Vinci 3.16.0, October 29 2008

• Save ECAT7 Image plugin - implemented now.
• Vinci Script - Python - you now find examples to script Vinci with Python in external/python. We will shortly offer a user-friendly way of copying them to a suitable location.
• Drag & Drop - you can now drag image files onto Vinci: it will try to make an educated guess about the file type and open it.
• Window Management - improvements for Non-MDI mode.

• Load NIfTI Images - only the first frame/volume of a multi-frame NIfTI images was loaded (independent of the frame setting). This problem only affected the compressed flavour of NIfTI files (.nii.gz). FIXED.
• ECAT7 VOI Images - could be created but not saved, as there was no appropriate image save plugin. FIXED.
• PlanesView - crashed if you tried to open the context menu with no image loaded yet. FIXED.
• Second OrthoView at startup - one additional, empty OrthoView was created when opening Vinci. FIXED.
• Updater - downloaded the installer image but did not open it properly as the front most window on the Mac platform. FIXED.

Vinci 3.15.1, October 22 2008

• Installer (Mac OS X) - some Qt dependencies were not resolved properly. FIXED.
• LicenseMgr (Mac OS X) - "~" in file names was not mapped to the HOME environment setting. FIXED.

Vinci 3.15.0, October 15 2008

• Image Volume Arithmetics - tool implemented now; undo/redo inclusive.

• VOI Operations - tool implemented now; undo/redo inclusive.
• VOI Operations - Main Differences to the Vinci 2.xx versions
  • Separate Tool - the computation of intersection, union and difference of two VOI sets is no longer part of the VOI Manipulation tool.
  • New VOI Image - the resulting VOI image is no longer per se the first operand but can now be created during the computation; simply check the corresponding New button at the head of the tool.
  • Addition, Subtraction and Subtraction % - three newly implemented operations to get the algebraic sum or difference of two VOI images or the difference of two VOI images recalculated to their relative percentage, and afterwards create VOIs as the sets of voxels with the same image values.

• VOI Color Legend - VOI images now show the colors of their VOIs in the image color legend and the Color Tool.
• VOI Palette Handling - You can now gather VOI colors from a "normal" palette like Rainbow, Sokolow, etc. simply by choosing any of the given palettes in the Color Tool; undo/redo inclusive.
  The index range of non-empty VOIs will be scaled to the 256 color palette indeces.
• Sorting by VOI index - All VOI Tools can now switch to sorting by VOI index instead of fixedly sorting by VOI name; choose the desired sorting mode simply in the new list context menu.

• Vinci Settings - Vinci now saves its settings in different files for different machines, allowing for conflict-free simulteneous runs of Vinci on different machines with a common home directory of the user.
• Qt 4.4.2 - now uses the latest version of Trolltech's Qt library for WINDOWS and Linux.

• Work in progress - feedback desirable.
  • Multi-Window Mode - Vinci can now be run in multi-window instead of multi-document (MDI) mode; MDI mode is still default on WINDOWS, multi-window mode is the new default on linux and Mac. You can change the mode in the Extras menu.
  • Target-Platform - Vinci now tries to cope with differences between run and target platform concerning window sizes, positioning and framing. You can set the target platform in the Help menu; e.g. if Vinci runs on a linux system and gets displayed on WINDOWS set the later as target platform.
  • Visible Title Line - this menu entry tries to handle a situation when Vinci e.g. running on a linux system and displayed on WINDOWS, due to inherent differences in the window manegement, does not initially show its title line, so the program windows as such cannot be moved, maximized or minimized. The menu entry tries to shift the program window appropiately.

• Empty Vinci - Opening LoadView, SaveView or PlanesView in an empty Vinci crashed - FIXED.
• PlotsView Creation - as in VinciM the toolbar buttons now create views only if they do not yet exist, otherwise they are just brought to the front.
• PlanesView - Graphics Item Creation - crashed if not started via context menu on a display that did not show the crossmarker - FIXED.
• PlanesView Context Menu - when you opened the PlanesView context menu on a PlanesView that did not show the cut plane (crossmarker) crashed - FIXED.
• VOI Evaluate Tool - a redo of its creation via the VOI Define tool did not update its contents - FIXED.
• VOI Evaluate Tool - a redo of the change of the VOI image via the VOI Define tool did not update the contents - FIXED.

Vinci 3.14.1, August 5 2008

• Qt 4.4.1 - now uses the newest version of Trolltech's Qt library for WINDOWS and Linux.

Vinci 3.14.0, August 4 2008

• VOI Define Tool - now implemented, undo/redo inclusive. Alas, no interactive support yet. The number of VOIs is now unlimited.
  Boids can now overlap. Non-overlapping Boids are saved in a Vinci image containing the VOI index numbers, as in Vinci_M, overlapping Boids are saved in the Vinci project file as a list of indeces.
  You can now load a so called atlas description file after loading an images as Atlas, see below. Vinci, for now, understands two file types: classical .3DT-files from the MPIfnF 3D-Tool and .TXT files with lines in index<TAB>name format, which you can easily create by hand, or are given e.g. in the Montreal ICBM template. Lines starting with a hash (#) are considered to be a comment.
  As VinciQ can only has a save Interfile images, for now, you should only create VOI Image for Interfile images.
• VOI Evaluate Tool - now implemented. You can open it, as in the Vinci 2.xx series, in the Files/Automate menu.
  Pressing the Compute button displays the VOI statistics of all VOIs in table format; results can be copied to the clipboard and exported into a tabulator-separated .TXT-file.
  
• VOI Copy/Paste - now implemented, undo/redo inclusive.
  Beware: VOIs are uniquely defined by index; so if you try to paste a VOI with an already used VOI index, Vinci offers to delete the existing one, create the VOI with a different index, or cancel the operation.

• Load-Plugin - 3DTool Atlas - now implemented.
• LoadView - you can now load images as Atlas; which means that the images are loaded as index volume generating non geometrical VOIs (Boids) for each index (integer value) of the image; images with values less than zero or greather or equal 256 are considered to be float-images and loaded as such.

• Save Project (As) - one-level-undo and redo are implemented now. One-level undo means that when you save the project under a given name more than once, only the last save can be undone. Undo removes backup or newly created Vinci project files. Backup-Vinci project filenames get the extension ".backup.vpx".
  Vinci tries to save computed or changed images automatically while saving the Vinci project file. If some image files cannot be written or the user denies an image file to be overwritten the user can chosse whether to Continue or Abort saving, the first continues and asks the user to save the image himself, the last undoes already performed image-saving.
• Save Images (As) - one-level-undo and redo are implemented now. One-level undo means that when you save the image under a given name more than once, only the last save can be undone. Undo removes backup and newly created image files. Backup-image filenames are prepended by "backup.".

• Ortho Display - Color Tool - undo/redo is now implemented.
• Clear Image Buffer - undo is now implemented.
• Clear All Image Buffers - undo is now implemented.
• LoadView - you can now select more than one file for loading.
• Tab Order - defined for all dialogs now.
• Clear Protocol - the edit main menu features this new entry to empty Vinci's undo/redo stack (Protocol).
• Link Channel - when you insert an image into a link channel Vinci now syncs reslicing and zoom parameters while keeping the rotation center constant in display coordinates (instead of images coordinates), so that VOI resampling remains possible after the operation.
• InfoView ImageInfo - the image rotation center is now also shown in display coordinates.
• Auto Update - will propose an update path parallel to the current installation, starting with the next release.

• Magic Tool - the setting of the Details button will be remembered now.
• Magic Tool - the image rotation center is now also shown in display coordinates.
• Magic Tool - you can now call Reset Link Channel with respect to the image shown on the current OrthoDisplay.
• Magic Tool - the Sync Rsl button now syncs reslicing and zoom parameters while keeping the rotation center constant in display coordinates (instead of images coordinates), so that VOI resampling remains possible after the operation.
• Magic Tool - the All Images Synchronization operations Sync Rsl, Sync Zoom and Sync Color can be undone/redone now.

• ROI Define Tool - ROI surface and volume were not correct, due to integer instead of double value multiplication of the image pixel sizes. Sorry - FIXED.
• Graphics Item Selection - changing the current ROI, profile or annotation with the keyboard (e.g. with the arrow keys) did not change the displayed properties in their respective tools. - FIXED.
• Plots Axis - Tick Limits - were not always respected while computing the minimum and maximum for the axis; - FIXED.
• Version History - did no longer open after installation or update since using Qt 4.4.0 if the installation path included a blank; - FIXED.
• PlanesView Update - may have led to flickering of its displays since Vinci 3.13.0. - FIXED.
• OrthoDisplay Title Line - changing the image buffer on a fused OrthoDisplay does de-activate fusion, as in VinciM, but the display did not directly show the un-fused new image buffer. - FIXED.
• DICOM Image - load plugin did not present image files without file-extension in the Browse-button - FIXED.
• OrthoDisplay NFusion Tool did not always update its settings if the fusion was undone - FIXED.
• SaveView may have saved images with wrong dimension and pixelsize information in the header file - FIXED.

• ROI Define Tool - Undo - Vinci crashed when you undid the creation of a ROI in the ROI Define tool; - FIXED.
• Undo Graphics Item creation - Vinci crashed when you undid the creation of a ROI, profile or annotation in the respective tools. - FIXED.
• DICOM Image - load plugin did crash since Vinci 3.12.0 when trying to browse a directory. - Sorry, FIXED.
• Magic Tool - Set to Saved did crash when used without priorly saving a link state - FIXED.

• Save Link State - undo did not work - FIXED.
• Save Link State, Reset to Saved Link State and Reset Link Channel - did something (unexpected) when the image was not part of a link channel; the menu entries are blocked now - FIXED.
• Project Load - Linked Images - when you use a project with linked images and load another project Vinci might have crashed - FIXED.
• Project Load - Linked Images - when loaded a Vinci project with linked images some images might not have been included into the link channel - FIXED.

Vinci 3.13.0, May 21 2008

• License Dialog - features a an advanced button to show the used license file and the order of directories where the license file is searched for.

• zlib1.dll - was missing in the Vinci 3.12.0 WINDOWS release. Sorry - FIXED.
• Image Handling - image reslicing, especially cut, move and rotate, did no longer show instantaneously on the OrthoDisplay since Vinci 3.12.0. - FIXED.
• PlotsView Handling - mouse position and scatter plot may have got out of synch on all machines since Vinci 3.12.0. - FIXED.
• PlotsView Handling - mouse position and scatter plot may have got out of synch on slow machines during PlotsView move. - FIXED.
• Splash Screen - did start up without its proper contents visible since Vinci 3.12.0. - FIXED.
• Non-English System-Locale - may not have been ignored correctly on some LINUX machines (e.g. Debian 4.2.3), resulting in problemes for image load, ROI creation, etc. Sorry - FIXED.
• IpcManager Start - may have been so slow on some computers that the waiting timeout expires, especially when the programs were run in niced mode on LINUX. We extended waiting time from 3 to 10 seconds. - Hopefully FIXED.

Vinci 3.12.0, April 30 2008

• Windows Vista ready - all automated tests now also run on Windows Vista.
• Windows 64 ready - Vinci has been tested with Windows Vista 64-bit enterprise. We have observed differences in ROI evaluations when comparing 32-bit and 64-bit editions of Vista, these differences should be insignificant in most cases.

• Qt 4.4.0 - now uses newest version of Trolltech's Qt library for WINDOWS and 64bit-Linux. We have observed differences when comparing Qt 4.4.0 and Qt 4.3.4 ROI rendering and statistics, these differences should be insignificant in most cases.
• Visual Studio 2008 - now built with the new MS C/C++ compiler.

• License Dialog - in the main menu entry "Extras" you can now import the Vinci License File so that it is automatically placed in the correct directory and given the correct name.
• Inter Process Communication now uses new code for event handling and waiting that does no longer contribute to the processor load and is considerably faster.
• PlanesView - Skip Planes - shifting the start plane can change individual planes again in order to be able to find the cut plane (i.e. the plane with the crossmarker) if it got lost by cutting on the OrthoDisplay.

• Application failed to initialize - on some computers Vinci failed to initialize since 3.02.0 without prior installation of some MSVC runtime DLLs using the program vcredist_x86.exe - FIXED.
• PlanesView may have crashed on WINDOWS Vista due to a missing variable re-initialization - FIXED.

• Vinci Test Environment - in the main menu entry "Extras", you can now interactively create, load and run Vinci Test Scripts, and load project files of given Test Configuration files. This is work in progress.
  Vinci expects the directory of all files used or created during the tests, the so called Test Root Directory, to be named Vinci_Test and placed in a folder parallel to the Vinci installation directory (i.e. in the MPIfnF folder). Test projects (*.vpx) and test scripts (*.vtx) are expected in sub-directories named Reference_XXX of Vinci_Test. Here, XXX stands for the Vinci version the test is created with, e.g. 312 for this version of Vinci. Test Configuration files (*.xml) are expected in a sub-directory called RunQ.
  Creating a new test involves to enter test mode, do something in Vinci e.g. loading an image, create reference files, do something else e.g. reslice the image, create again some reference files, and so on, and finally exit test mode.
  During test creation images that are used in the tests are automatically copied to sub-folders called Data/<image type> if not already present there, references to their original position are automatically replaced by references to the test environment.
  Reference files can be the OrthoDisplay or PlanesDisplay color- or float matrix, value lists, xml-based property lists of all kind of internal objects. You typically generate them using the copy to clipboard buttons or menu entries which feature special functionality in test mode. The reference files are placed parallel to the test project and test script i.e. in the Reference_XXX directory.
  Running a given test means, your actions are redone and new reference files are generated in the so called Test Output directory and compared with the original files. The test output folder is given by the sub-folder MPIfnF/Vinci_Test_WorkQ of the directory defined in the environment variable APPDATA on WINDOWS and HOME on Linux.

Vinci 3.11.0, April 4 2008

• PlanesView - General Properties Dialog is implemented now.
• PlanesView - context menu is implemented now.
• PlanesView - Display of Grahics Items can be switched off now. Simply choose the option No Items in the sub-menu Use Drawing Objects Of of the context menu.

• PlanesView - Main Differences to the Vinci 2.xx versions
  • Cut plane In most cases the planes stay at their positions. More generally: If the number of displays or skipped planes changes, at least the center display (i.e. the first display of the center row) will show the same plane.
    The cut plane will now be re-centered only if an image buffer is exchanged, an image's 3D-sampling changes from or to TruePixel mode or the PlanesView shows slices of a different OrthoPart.
  • PlanesView - Skip Planes - shifting the start plane now skips planes to let the display with the cross marker always show the cut plane.

• Ortho-Toolboxes now hide / show if the parent OrthoView gets de- / activated.
• Image Overload can be undone now.
• Gauss Plugin undo/redo implemented.
• OrthoDisplay - Display of Grahics Items can be switched off now. Simply choose the option No Items in the sub-menu Use Drawing Objects Of of the context menu or the corresponding OrthoDisplay Info Line button.

• PlanesView - Images in TriLinear/Next Meighbour Mode - the cut plane (identified by the cross marker) may have been offset by up to half a plane compaired with the cutplane shown in an OrthoDisplay - FIXED.
• PlanesView - Fused Images - images were shown with a relative plane offset if the fused image was the reference image - FIXED.
• PlanesView - changing the sampling mode of an image buffer to or from TruePixel mode did not de-/activate the mouse mode shortcuts - FIXED.
• PlanesView - Double Click - a graphical text item did not enter edit mode if double-clicked on; the PlanesView was zoomed instead. - FIXED.

Vinci 3.10.0, March 4 2008

• PlanesView - implemented now; the PlanesView tools, the context menu and the info line template button remain for the next Vinci version.

• PlanesView - Main Differences to the Vinci 2.xx versions
  • 3D-Sampling Mode - PlanesView shows images in their inherent 3D sampling mode now.
  • Mouse Modes - Images in non-TruePixel 3D-sampling mode can be fully resliced on all displays; image in TruePixel mode can be cut on all displays as before (movement and rotation would not change the displayed slices anyway, in TruePixel mode).
  • Graphics Items - The display with the current cut plane shows the graphics items also displayed on the OrthoDisplay.
  • Complete Undo/Redo - all changes can be undone/redone now.

• AMPkin v 1.04 (svn revision 1470) - adapted to changes in Vinci interface; first version for global release, now able to read beyond 31 ECAT 7 frames, intermediate interfile images can be read back into Vinci.
• View creation - we have now undo/redo for opening of all Vinci view types.
• OrthoView - we have now undo/redo for toggling of Moving Cross and Cross Marker.

• The OrthoView Tools Menu has only contained the color tool since Vinci 3.07.0, the rest of the tools has appeared at the bottom of the OrthoView menu. - FIXED.
• Mouse Mode: Polygon (Draw) did not allow to draw smooth polygons in Vinci 3.09.0. - FIXED.
• The OrthoView Info Line showed wrong image coordinates for under-sampled images, - FIXED.
• Under-sampled images saved into Vinci project file by Vinci_Q were not correctly handled by Vinci_M, - FIXED.
• The Fusion Tool crashed if fusion were activated with an undefined image, - FIXED.

Vinci 3.09.0, January 25 2008 (internal prerelease)

• Annotations and Text Define Tool - creation, movement and general handling of annotation objects are implemented now.
• Annotations can be edited on the OrthoDisplay - you can enter edit mode by double clicking the text item and activate your changes by clicking beside it (de-selection) or pressing Return.

• Vista Image - Vinci can now read boolean and bit data types.

• DICOM plugin - a major rewrite of the DICOM import engine. Now support Siemens MOSAIC and other flavours. Still experimental.
• DICOM to NIfTI - an extension of Vinci's DICOM engine. Can be scripted using Python. Still experimental.

• Update - now installs on LINUX into the default directory proposed by the setup program.
• Setup - on LINUX allows to install a 64bit version of Vinci alongside a 32bit version in the same (home) directory.
• Desktop Icon - is now version and platform specific on LINUX.

• ROI Scaling did use the scene instead of the item coordinate system, thus did not work if the items were rotated by about 90 degrees - FIXED.
• ROI type change - undo did not work in 3.08.0. FIXED.
• Newly created selected ROI did not use the correct cursorform - FIXED.
• Changing an graphics item's orthopart did only always reflect in it's tool if it was loaded in selected state from a project file - FIXED.

• Overwrite Images during project save - infact, the image was saved when you pressed cancel and the saving cancelled when you pressed overwrite. FIXED.
• Arrow Mouse Mode - Vinci crashed when entering Arrow mouse mode (e.g. by pressing the SPACE key) before changing to any other mouse mode. FIXED.
• <line>...</line> framed strings from Vinci_M were not de-framed - FIXED.
• License files (created on WINDOWS) but delivered by a MAC mail tool may have been rejected as invalid - FIXED.

Vinci 3.08.0, December 11 2007 (internal prerelease)

• ROI Define Tool - All Planes Statistics implemented now.

• PlotsView - after initialization, the color of a profile's scatterplot is now independant of the profile's color.
• PlotsView - showing/hiding a profile's scatterplot is now independant of its Process property.

• PlotsView - hiding a scatter plot would sometimes shrink the PlotsView header area inappropriately - FIXED.
• Changing the ROI Type did not change the Vinci XML-target type - FIXED.
• Changing the ROI Type reset the rotation angle - FIXED.

Vinci 3.07.0, December 5 2007 (internal prerelease)

• Profiles and Profiles Tool - creation, movement and general handling of profiles are implemented now.
• PlotsView and PlotsView Properties - implemented now.

• PlotsView - Main Differences to the Vinci 2.xx versions
  • Unlimited Number of Profiles - you can now show an unlimited number of profiles in the PlotsView. If there are more then 10 profiles the header gets scrollable.
  • Profiles Hide/Show - you can hide profiles temporarily in the Plotsview using the context menu in the PlotsView header area.
    Hidden profiles can be shown again by re-activating them in a context menu shown in a small empty area below the profiles or at the bottom of the header scrollarea if you have more then 10 profiles.
  • Zoom and Move - you can zoom (enlarge/shrink the plot window) by drawing a rubberband with the mouse or just click on the Plotsview in zoom mode; you can move the plots around with the mouse in move mode.
    You can activate these mouse mode in the PlotsView context menu, the PlotsView main menu, the toolbar, or with the usual shortcuts (Z for zoom-in, U for zoom-out and M for move) and reset them with Space for arrow mode.
  • Complete Undo/Redo - all changes to axis-settings can be undone/redone now.

• Vinci Update - the Vinci online updater installed Vinci on linux in a directory with the name of the updating Vinci version instead of the downloaded version - FIXED.
• ROI Define Tool - the graphics item association of an OrthoDisplay (accessed via the OrthoDisplay Infoline button Change Drawing Objects Base Image) did not (immediately) reflect in the items list of the tool - FIXED.

Vinci 3.06.0, November 20 2007 (internal prerelease)

• MP4A plugin - this conservative version 2 (svn version=1142) has new functionality for analyzing and filling bad voxels.
• Viinspector plugin - new plugin for viewing the numbers stored in a Vinci Image Volume.
• Parametrics plugin - new plugin for generating parametric images of correlation coefficients.

• Load DICOM plugin - can now load some new DICOM flavours including some types of Siemens MOSAIC data. Beta-Version.
• Save NIfTI image plugin - new plugin that save images in NIfTI format. It supports data types FLOAT32, INT16 and UINT8.
• Load NIfTI image plugin - new plugin that loads images in NIfTI format. It supports data types FLOAT32, INT16 and UINT8. In contrast to Vinci 2.x, this version also works for data sets that use an Sform but not a Qform entry to specify patient orientation.

• Graphics Items - translation, scaling and the movement of individual points is now limited in a way that the center of the item's bounding rectangle remains inside the display.
• ROI items - movement can be restricted to vertical or horizontal translation in the context menu of an individually selected item.
• ROI Defines Tool - creation of ROIs in the tool (new button) can now be undone/redone.

• MMM Tool - due to over-optimization the tool's image reslicing was no longer immediately reflected on the display since Vinci 3.04.0. Sorry, - FIXED.
• Magic Tool - due to over-optimization Single Image Reslicing was no longer immediately reflected on the display since Vinci 3.04.0. Sorry, - FIXED.
• OrthoDisplay Context Menu - Vinci crashed if you right-clicked below the area of the displays, - FIXED.
• Graphics Item Deletion Undo did not always re-create the objects in their original order of creation, - FIXED.
• Graphics Item Cut Undo - the OrthoDiplay object complained about a missing DoNothing xml handler, - FIXED.
• Orthodisplay Properties - did only allow extending the OrthoDisplay with empty image buffers - FIXED.

• ROI Define Tool - when you switched ROI thresholding on/off the tool did not always update the statistics nor activate/deactivate threshold minimum and maximum edit fields - FIXED.
• ROI Define Tool - changing the image buffer in the OrthoDisplay did not reinitialize the ROI list in a tool that works on the display - FIXED.
• Vinci Graphics Items - clearing an image buffer did not delete its graphics items - FIXED.

Vinci 3.05.2, October 17 2007 (internal prerelease)

• InfoView implemented - displays full information for images of type ECAT7, Interfile and HRRT, so far.

• ROI Rectangle and Ellipsoid could not be created using their respective mouse modes. Sorry, FIXED.
• Vinci Update complained wrongly about not being able to log its download request. FIXED.

• AMP kinetics - the plugin is not part of this release.

Vinci 3.04.2, October 2 2007 (internal prerelease)

• ROIs implemented - VinciQ now provides ROI rectangles, ellipses and polygons.
• ROIs - Main Differences to the Vinci 2.xx versions
  • Statistics - Area - ROI statistics may have (slighty) different results as the ROI regions (due to rounding differences) may include other pixels at the border.
  • Statistics - Zoomed OrthoView - ROI statistics now have the same results on zoomed (e.g. 768 pixel square) as on standard 256 pixel square OrthoDisplays.
  • Display bound ROIs will be no longer supported.
  • Paste & Subscribe will be no longer supported.
  • Outward evaluation will be no longer supported.
• Opening URLs - the user will no longer be requested to provide the path to his preferred web browser.

• AMP kinetics - the plugin is not part of this release.

Vinci 3.03.1, July 3 2007 (internal prerelease)

• MP4A kinetics plugin added (svn version=857)

Vinci 3.02.0, June 15 2007 (internal prerelease)

• Our New Installer Builder on Linux produces 3 MB smaller setup programs.
• Visual Studio 2005 - we use the new Service Pack 1; thus the program will be delivered with a new manifest file and runtime DLLs.
• Graphics Items Selection Rubberband implemented.

Vinci 3.01.1, June 8 2007 (internal prerelease)

• DICOM Images plugin did show the error message XML-tag "_NotifySubscribersNewImages" not processed for target type "LoadView" instead of the actual image. FIXED.
• OrthoDisplay Properties - the foreground color spin box wasn't fully visible any more. FIXED.
• OrthoDisplay Properties - may have complained about invalid XML in the log when opening. FIXED.
• Color Spin Box spins colors red-blue-swapped compared to VinciM. FIXED.
• CrossMarker Color appeared red-blue-swapped compared to VinciM. FIXED.
• Test Results Accumulated Time did show wrong number of minutes. FIXED.

Vinci 3.01.0, June 6 2007 (internal prerelease)

• The Mouse Wheel - used on a display - now cuts through an image if the shift or ctrl key is pressed or the mouse wheel itself is pressed.
• Moving Cross now implemented on OrthoDisplays.
• Qt 4.3.0 - newest library version now used for WINDOWS and 64bit-Linux.

• Memeory Leaks found by the software package valgrind - FIXED.

Vinci 3.00.3, May 31 2007 (internal prerelease)

• Parametrics Plugin now with shuffle button.

Vinci 3.00.2, May 25 2007 (internal prerelease)

• Parametrics Plugin now remembers its settings: Input File and Compute what selection.

• Package Validation did not name the offending files, - FIXED.

Vinci 3.00.1, May 24 2007 (internal prerelease)

• ECAT7 Images - the ECAT 7 load plugin can now handle multiframe files.

• ECAT7 Images - load problems with parametrics plugin FIXED.

Vinci 3.00.0, May 24 2007 (internal prerelease)

• First Release
• Main Differences to the Vinci 2.xx versions
  • Link Channels - In Vinci 2.xx an OrthoDisplay was in a link channel and so automatically all images visible in it (i.e. including fused images). So images were synchronously resliced if and only if they were visible in a linked OrthoDisplay.
    In Vinci 3.xx the images themselves are in a link channel which makes reslice images synchronously even if they are not currently visible on any OrthoDisplay.
    As before, if you select the link mode in the OrthoDisplay info line all images currently visible there (i.e. including fused images) will enter the link channel.