Difference between revisions of "DiffusionImaging"

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__NOTOC__
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#REDIRECT [[MitkDiffusion]]
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<!-- #acl [[JanHering]],[[PeterNeher]],[[MbiEditorGroup]]:read,write -->
 
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= MITK Diffusion =
 
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[https://www.mitk.org/wiki/MitkGit direct link to source code]
 
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[[#Downloads|direct link to download section]]
 
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[[Media:DiffusionImaging$MITK_DIsmall.png|DI_App|Icon|align="right"]]
 
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The MITK Diffusion application offers a selection of image analysis algorithms for the processing of diffusion-weighted MR images. It encompasses the research of the [http://www.dkfz.de/en/mbi/projects/neuroimaging.html Neuroimaging Group] in the Division Medical and Biological Informatics at the German Cancer Research Center (dkfz).
 
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<pre><nowiki>#!wiki caution
 
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'''Features & Highlights'''
 
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* Tensor and q-ball reconstruction
 
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* Glyph visualization
 
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* Quantification and partial volume clustering of tensor and q-ball images
 
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* Global fiber tractography, visualization, and tract post-processing
 
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* Brain network statistics and visualization (connectomics)
 
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* Interactive exploration of Tract-based spatial statistics (TBSS) results
 
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* Intra-voxel incoherent motion (IVIM) estimation
 
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</nowiki></pre>
 
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The MITK Diffusion application is based on the [https://www.mitk.org/wiki/ResearchPlatform MITK research platform] and the most of it is open-source. Solely the tract-based spatial statistics viewer and the brain network statistics module were not released yet, mainly due to some major internal changes expected in the near future. The available code is embedded into the source code of MITK as a module and can be accessed through the [https://www.mitk.org/wiki/MitkGit public git repository].
 
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== Version ==
 
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The current stable version is the MITK Diffusion 2012 release.
 
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== Changelog ==
 
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A list of the major changes from the 2011 to the 2012 release of MITK Diffusion.
 
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{| border="1" cellpadding="2" cellspacing="0"
 
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|<style="width: 28%; text-align: center;vertical-align: middle;"|2>| '''Connectomics'''
 
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|align="left" |Added global clustering computation
 
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|-
 
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|colspan="2" align="left" | Added generator for synthetic networks
 
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|-
 
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|<style="width: 28%; text-align: center;vertical-align: middle;"|4>| '''Fiber Processing'''
 
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|align="left" |much more information about the selected fiber bundle is displayed 
 
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|-
 
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|colspan="2" align="left" | extraction of fibers passing through a 3D ROI (mitkSurface, STL mesh) is possible
 
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|-
 
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|colspan="2" align="left" | fiber smoothing using spline interpolation added
 
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|-
 
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|colspan="2" align="left" | fiber coloring by scalar map added
 
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|-
 
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|<style="width: 28%; text-align: center;vertical-align: middle;"|3>| '''Gibbs Tracking'''
 
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|align="left" |tracking results can be saved automatically 
 
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|-
 
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|colspan="2" align="left" | major bug that caused only few fibers to be reconstructed was fixed
 
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|-
 
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|colspan="2" align="left" | input of gfa image is not needed anymore
 
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|-
 
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|<style="width: 28%; text-align: center;vertical-align: middle;">| '''Stochastic Tracking'''
 
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|align="left" |gui completely refactored
 
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|-
 
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|<style="width: 28%; text-align: center;vertical-align: middle;"|3>| '''mitkFiberBundleX'''
 
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|align="left" |mitkFiberBundle is replaced by mitkFiberBundleX which is essentially a vtkPolyData which results in a much better performance and easier handling 
 
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|-
 
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|colspan="2" align="left" | fiber bundle are saved as vtkPolyData
 
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|-
 
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|colspan="2" align="left" | old xml based fiber files can still be loaded and are automatically converted into the new mitkFiberBundleX
 
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|<style="width: 28%; text-align: center;vertical-align: middle;"|3>| '''ODF Details'''
 
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|align="left" |refactored gui
 
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|-
 
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|colspan="2" align="left" | tensor data is displayed
 
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|-
 
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|colspan="2" align="left" | normalization of the ODFs is applied correctly
 
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|<style="width: 28%; text-align: center;vertical-align: middle;">| '''Partial volume analysis'''
 
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|  Export of clustering result as image is now possible
 
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|<style="width: 28%; text-align: center;vertical-align: middle;"|2>| '''Preprocessing'''
 
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|align="left" |the number of gradients of the selected image can be reduced while preserving an equal distribution of the gradients (as far as possible)
 
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|colspan="2" align="left" | the gradient directions can be displayed as pointset
 
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|<style="width: 28%; text-align: center;vertical-align: middle;">| '''Q-Ball Reconstruction'''
 
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| removed erroneous numerical reconstruction method
 
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|<style="width: 28%; text-align: center;vertical-align: middle;">| '''Segmentation'''
 
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|align="left" |fast interactive 3D interpolation added
 
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|}
 
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== User manual ==
 
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You can access the MITK Diffusion online documentation [http://mitk.org/download/releases/MITK-Diffusion-2012/documentation/html/index.html here]
 
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== Media ==
 
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'''Publication:''' ''MITK-DI - A new diffusion imaging component for MITK.'' In Deserno TM, Handels H, Meinzer HP, Tolxdorff T (eds). Bildverarbeitung für die Medizin 2010. Heidelberg: Springer (2010) 246-250  <<BR>>
 
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'''Authors:''' Fritzsche KH<sup>1</sup>, Meinzer H-P<sup>1</sup><<BR>>
 
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'''Institution:''' <sup>1</sup>German Cancer Research Center
 
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== Downloads ==
 
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Version 2012 ( Release date: ''07-05-2012'' )
 
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=== Requirements ===
 
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Additional system specific requirements:
 
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* Windows
 
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** If you have problems running the Windows application, please install the Microsoft Redistributable Packages for VS 2008: [http://www.microsoft.com/download/en/details.aspx?amp;displaylang=en&id=5582 32 bit] or [http://www.microsoft.com/download/en/details.aspx?amp;displaylang=en&id=2092 64 bit]
 
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* Linux
 
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** the minimal OS version changed to '''Ubuntu 11.04''' because the compiler version available in 10.04 does not provide features needed by MITK
 
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** the [http://qt.nokia.com/downloads Qt framework], version 4.6.2 or later
 
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Tested systems
 
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* Windows 7, Windows Vista
 
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* Ubuntu 11.04 and newer
 
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* OS X 10.6 and newer
 
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=== Available installer ===
 
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{| border="1" cellpadding="2" cellspacing="0"
 
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|  '''Windows'''
 
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|  Vista, Windows 7
 
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|  [[ http://mitk.org/download/releases/MITK-Diffusion-2012/installers/windows/MITK-Diffusion-2012-win32.exe | MS Windows (32 bit) installer ]]
 
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|  [[ http://mitk.org/download/releases/MITK-Diffusion-2012/installers/windows/MITK-Diffusion-2012-win64.exe | MS Windows (64 bit) installer ]]
 
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|-
 
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|  '''Linux'''
 
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|  Ubuntu 11.04 and newer
 
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|  [[ http://mitk.org/download/releases/MITK-Diffusion-2012/installers/linux/MITK-Diffusion-2012-Linux32bit-Build_07_05_2012.tar.gz | Ubuntu (32 bit), tar.gz archive ]] 
 
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|  [[ http://mitk.org/download/releases/MITK-Diffusion-2012/installers/linux/MITK-Diffusion-2012-Linux64bit-Build_07_05_2012.tar.gz | Ubuntu (64 bit), tar.gz archive ]]
 
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|-
 
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|  '''Mac OS X'''
 
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|  10.6 Snow Leopard and newer
 
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|colspan="2" | [[ http://mitk.org/download/releases/MITK-Diffusion-2012/installers/macos/MITK-Diffusion-2012.dmg | OS X disk image (.dmg) ]]
 
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|}
 
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=== Testing data ===
 
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A set of data for testing the functionality of the mitkDiffusion application is available [http://mitk.org/download/releases/MITK-Diffusion-2012/mitkDiffusion2012DemoData.tar.gz here].
 
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== Contact ==
 
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If you have questions about the application or if you would like to give us feedback, don't hesitate to [http://www.dkfz.de/en/mbi/people/Klaus_Fritzsche.php contact us].
 
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----
 
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= MITK Diffusion - Release Archive =
 
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This section collects links and information for all released versions of the MITK Diffusion Application, but for the newest.
 
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{| border="1" cellpadding="2" cellspacing="0"
 
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| '''Available Versions'''
 
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|  '''Release date'''
 
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|-
 
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|  [[#Release_2011|MITK Diffusion 2011]]
 
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|  02 Nov 2011
 
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|}
 
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<span id="Release_2011"></span>
 
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== Release 2011 ==
 
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Release date : '''02 Nov 2011'''
 
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=== Requirements ===
 
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Additional system specific requirements:
 
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* Windows
 
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** If you have problems running the Windows application, please install the Microsoft Redistributable Packages for VS 2008: [http://www.microsoft.com/download/en/details.aspx?amp;displaylang=en&id=5582 32 bit] or [http://www.microsoft.com/download/en/details.aspx?amp;displaylang=en&id=2092 64 bit]
 
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* Linux
 
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** the [http://qt.nokia.com/downloads Qt framework], version 4.6.2 or later
 
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** the tar.gz archive needs to be extracted into a folder whithout whitespaces in the path
 
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=== Documentation ===
 
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You can access the MITK Diffusion 2011 online documentation [http://mitk.org/download/releases/MITK-Diffusion-2011/documentation/html/index.html here]
 
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You can download the MITK Diffusion information brochure [http://mitk.org/download/releases/MITK-Diffusion-2011/documentation/pdf/refman.pdf here] (PDF)
 
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=== Available Installer ===
 
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<pre><nowiki>#!wiki comment
 
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* Windows : '''Vista''', '''Windows 7'''
 
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  * [[ https://www.mitk.org/download/releases/MITK-Diffusion-2011/MITK-Diffusion-2011_Windows_32Bit.exe | MS Windows (32 bit) installer]]
 
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  * [[ https://www.mitk.org/download/releases/MITK-Diffusion-2011/MITK-Diffusion-2011_Windows_64Bit.exe | MS Windows (64 bit) installer]]
 
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* Linux : '''Ubuntu 10.04 and newer'''
 
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  * [[https://www.mitk.org/download/releases/MITK-Diffusion-2011/MITK-Diffusion-2011_Ubunu_10.04_32Bit.tar.gz | Ubuntu (32 bit), tar.gz archive ]]
 
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  * [[https://www.mitk.org/download/releases/MITK-Diffusion-2011/MITK-Diffusion-2011_Ubunu_10.04_64Bit.tar.gz | Ubuntu (64 bit), tar.gz archive]]
 
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* Mac OS X : '''10.6 Snow Leopard and newer'''
 
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  * [[https://www.mitk.org/download/releases/MITK-Diffusion-2011/MITK-Diffusion-2011_OSX.dmg|OS X disk image (.dmg)]]
 
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</nowiki></pre>
 
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The installer is available for platforms enlisted in the table. Support for other systems is only experimental.
 
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{| border="1" cellpadding="2" cellspacing="0"
 
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|  '''Windows'''
 
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|  Vista, Windows 7
 
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|  [[ https://www.mitk.org/download/releases/MITK-Diffusion-2011/MITK-Diffusion-2011_Windows_32Bit.exe | MS Windows (32 bit) installer]]
 
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|  [[ https://www.mitk.org/download/releases/MITK-Diffusion-2011/MITK-Diffusion-2011_Windows_64Bit.exe | MS Windows (64 bit) installer]]
 
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|-
 
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|  '''Linux'''
 
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|  Ubuntu 10.04 and newer
 
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|  [https://www.mitk.org/download/releases/MITK-Diffusion-2011/MITK-Diffusion-2011_Ubunu_10.04_32Bit.tar.gz  Ubuntu (32 bit), tar.gz archive ]
 
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|  [https://www.mitk.org/download/releases/MITK-Diffusion-2011/MITK-Diffusion-2011_Ubunu_10.04_64Bit.tar.gz  Ubuntu (64 bit), tar.gz archive]
 
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|-
 
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|  '''Mac OS X'''
 
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|  10.6 Snow Leopard and newer
 
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|colspan="2" | [https://www.mitk.org/download/releases/MITK-Diffusion-2011/MITK-Diffusion-2011_OSX.dmg OS X disk image (.dmg)]
 

Latest revision as of 12:35, 24 August 2018

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