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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<!-- #acl All:read -->
 
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= MITK Diffusion =
 
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=== Quicklinks ===
 
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* '''Sourcecode''': [https://www.mitk.org/wiki/MitkGit Wiki-Page with instructions] and [http://http://mitk.org/git/?p=MITK.git;a=summary  web interface] of the Git repository
 
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* '''Download Section''' is [[#Downloads|here]]
 
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----
 
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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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* Synthetic data generation
 
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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. 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 2013.03 release.
 
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== Changelog ==
 
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* Based on the [[MITK-ReleaseNotes-2013-03|MITK 2013.03 Release]]
 
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* New features in '''FiberFox'''
 
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** Fiber Definition
 
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*** Added functions to copy, translate, rotate and scale fibers including the corresponding fiducials
 
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*** Fiducial alignment with voxel grid
 
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*** Fiber definition with only two ROIs
 
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* Signal Generation
 
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** Extended diffusion models: Stick, Zeppelin, Tensor, Ball, Astrosticks, Dot
 
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** Extended two-compartment model to four-compartment model
 
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** Realistic simulation of relaxation effects. Parameters: T2 (per compartment), TE, T2' and line readout time
 
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** Explicit definition of fiber radius used for the calculation of compartment volume fractions
 
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** Changed the relative parameter SNR to the absolute parameter noise variance
 
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** Removed internal signal normalization --> double voxel size in one dimension results in twice the signal strength
 
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* Complete refactoring of the Fiberfox help page
 
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* Fiber Processing View reodered and splitted into separate views: '''Fiber Processing''' and '''Fiber Extraction'''
 
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* Modularization of the Diffusion Module into
 
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** '''new submodules''' DiffusionCore, FiberTracking, Connectomics, Quantification
 
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* New, user defined visualisation properties for connectomics networks added
 
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* Several bugs fixed in both registration views
 
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== User manual ==
 
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The user manual for the MITK Diffusion 2013.13 application can be found [https://www.mitk.org/download/releases/MITK-Diffusion-2013.03/documentation/ here].
 
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== Media ==
 
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'''Publication:''' ''[http://www.schattauer.de/en/magazine/subject-areas/journals-a-z/methods/contents/archive/issue/1594/manuscript/18261.html MITK diffusion imaging]'', In Methods Inf Med 2012 Oct 11;51(5):441-8<<BR>>
 
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'''Authors:''' Fritzsche KH<sup>1</sup>, Neher PF<sup>1</sup>, Reicht I<sup>1</sup>, van Bruggen T<sup>1</sup>, Goch C<sup>1</sup>, Reisert M<sup>2</sup>, Nolden M<sup>1</sup>, Zelzer S<sup>1</sup>, Meinzer HP<sup>1</sup>, Stieltjes B<sup>1</sup><<BR>>
 
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'''Institution:''' <sup>1</sup>German Cancer Research Center, Heidelberg, Germany<<BR>><sup>2</sup>University Hospital Freiburg, Department of Radiology, Medical Physics, Freiburg, Germany
 
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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 2013.03 ( Release date: ''04-04-2013'' )
 
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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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Tested systems
 
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* Windows 7, Windows Vista
 
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* Ubuntu 12.04 and newer
 
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* OS X 10.6 (Snow Leopard), OS X 10.8 (Mountain Lion)
 
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The OS X 10.6 installer is compatible with OS X 10.7 (Lion) so there is no dedicated disk image build under 10.7.
 
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=== Available installer ===
 
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{| border="1" cellpadding="2" cellspacing="0"
 
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|  '''Windows'''
 
−
|  Vista, Windows 7
 
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|  [http://mitk.org/download/releases/MITK-Diffusion-2013.03/windows/MITK-Diffusion-2013.03.00-win32.exe  MS Windows (32 bit) installer ]
 
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|  [http://mitk.org/download/releases/MITK-Diffusion-2013.03/windows/MITK-Diffusion-2013.03.00-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-2013.03/linux/MITK-Diffusion-2013.03.00-linux32.tar.gz  Ubuntu (32 bit), tar.gz archive ] 
 
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|  [http://mitk.org/download/releases/MITK-Diffusion-2013.03/linux/MITK-Diffusion-2013.03.00-linux64.tar.gz  Ubuntu (64 bit), tar.gz archive ]
 
−
|-
 
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|  '''Mac OS X'''
 
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|  OS X 10.6 and newer
 
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|  [http://mitk.org/download/releases/MITK-Diffusion-2013.03/macos/MITK-Diffusion-2013.03.00-10.6.dmg  10.6 OS X disk image ]
 
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|  [http://mitk.org/download/releases/MITK-Diffusion-2013.03/macos/MITK-Diffusion-2013.03.00-10.8.dmg  10.8 OS X disk image ]
 
−
|}
 
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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_2012_12|MITK Diffusion 2012.12]]
 
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|  21 Dec 2012
 
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|-
 
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|  [[#Release_2012_09|MITK Diffusion 2012.09]]
 
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|  02 Oct 2012
 
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|-
 
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|  [[#Release_2012|MITK Diffusion 2012]]
 
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|  07 May 2012
 
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|-
 
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|  [[#Release_2011|MITK Diffusion 2011]]
 
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|  02 Nov 2011
 
−
|}
 
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<span id="Release_2012_12"></span>
 
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== Release 2012.12 ==
 
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Release date: '''21-12-2012'''
 
−
 
 
−
=== Requirements ===
 
−
 
 
−
Additional system specific requirements:
 
−
* Windows
 
−
** 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]
 
−
* Linux
 
−
** the [http://qt.nokia.com/downloads Qt framework], version 4.6.2 or later
 
−
 
 
−
Tested systems
 
−
* Windows 7, Windows Vista
 
−
* Ubuntu 11.04 and newer
 
−
* OS X 10.6 (Snow Leopard), OS X 10.7 (Lion)
 
−
 
 
−
=== Available installer ===
 
−
 
 
−
{| border="1" cellpadding="2" cellspacing="0"
 
−
|  '''Windows'''
 
−
|  Vista, Windows 7
 
−
|  [http://mitk.org/download/releases/MITK-Diffusion-2012.12/windows/MITK-Diffusion-2012.12.00-win32.exe  MS Windows (32 bit) installer ]
 
−
|  [http://mitk.org/download/releases/MITK-Diffusion-2012.12/windows/MITK-Diffusion-2012.12.00-win64.exe  MS Windows (64 bit) installer ]
 
−
| 
 
−
|-
 
−
|  '''Linux'''
 
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|  Ubuntu 11.04 and newer
 
−
|  [http://mitk.org/download/releases/MITK-Diffusion-2012.12/linux/MITK-Diffusion-2012.12.00-linux32.tar.gz  Ubuntu (32 bit), tar.gz archive ] 
 
−
|  [http://mitk.org/download/releases/MITK-Diffusion-2012.12/linux/MITK-Diffusion-2012.12.00-linux64.tar.gz  Ubuntu (64 bit), tar.gz archive ]
 
−
| 
 
−
|-
 
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|  '''Mac OS X'''
 
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|  OS X 10.6 and newer 
 
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|  [http://mitk.org/download/releases/MITK-Diffusion-2012.12/macos/MITK-Diffusion-2012.12.00-OSX-10.6-mac32.dmg  10.6 OS X disk image ]
 
−
|  [http://mitk.org/download/releases/MITK-Diffusion-2012.12/macos/MITK-Diffusion-2012.12.00-OSX-10.7-mac64.dmg  10.7 OS X disk image (.dmg)]
 
−
|  [http://mitk.org/download/releases/MITK-Diffusion-2012.12/macos/MITK-Diffusion-2012.12.00-OSX-10.8-mac64.dmg  10.8 OS X disk image (.dmg)]
 
−
|}
 
−
 
 
−
<span id="Release_2012_09"></span>
 
−
== Release 2012.09 ==
 
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Release date : '''02 Oct 2012'''
 
−
 
 
−
=== Requirements ===
 
−
 
 
−
Additional system specific requirements:
 
−
* Windows
 
−
** 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]
 
−
* Linux
 
−
** the [http://qt.nokia.com/downloads Qt framework], version 4.6.2 or later
 
−
 
 
−
Tested systems
 
−
* Windows 7, Windows Vista
 
−
* Ubuntu 11.04 and newer
 
−
* OS X 10.6 (Snow Leopard), OS X 10.7 (Lion)
 
−
 
 
−
=== Available installer ===
 
−
 
 
−
{| border="1" cellpadding="2" cellspacing="0"
 
−
|  '''Windows'''
 
−
|  Vista, Windows 7
 
−
|  [[ https://www.mitk.org/download/releases/MITK-Diffusion-2012/installers/windows/MITK-Diffusion-2012.09-win32.exe | MS Windows (32 bit) installer ]]
 
−
|  [[ https://www.mitk.org/download/releases/MITK-Diffusion-2012/installers/windows/MITK-Diffusion-2012.09-win64.exe | MS Windows (64 bit) installer ]]
 
−
|-
 
−
|  '''Linux'''
 
−
|  Ubuntu 11.04 and newer
 
−
|  [[ https://www.mitk.org/download/releases/MITK-Diffusion-2012/installers/linux/MITK-Diffusion-2012.09-linux32.tar.gz | Ubuntu (32 bit), tar.gz archive ]] 
 
−
|  [[ https://www.mitk.org/download/releases/MITK-Diffusion-2012/installers/linux/MITK-Diffusion-2012.09-linux64.tar.gz | Ubuntu (64 bit), tar.gz archive ]]
 
−
|-
 
−
|  '''Mac OS X'''
 
−
|  OS X 10.6 and newer 
 
−
|  [[ https://www.mitk.org/download/releases/MITK-Diffusion-2012/installers/macos/MITK-Diffusion-2012.09-10.6.dmg | 10.6 OS X disk image ]]
 
−
|  [[ https://www.mitk.org/download/releases/MITK-Diffusion-2012/installers/macos/MITK-Diffusion-2012.09-10.7.dmg | 10.7 OS X disk image (.dmg)]]
 
−
|}
 
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<span id="Release_2012"></span>
 
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== Release 2012 ==
 
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Release date : '''07 May 2012'''
 
−
 
 
−
== Changelog ==
 
−
 
 
−
A list of the major changes from the 2011 to the 2012 release of MITK Diffusion.
 
−
 
 
−
{| 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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|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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|-
 
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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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|-
 
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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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|-
 
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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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|-
 
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|colspan="2" align="left" | the gradient directions can be displayed as pointset
 
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|-
 
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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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|-
 
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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
 
−
|}
 
−
 
 
−
=== Requirements ===
 
−
 
 
−
Additional system specific requirements:
 
−
* Windows
 
−
** 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]
 
−
* Linux
 
−
** the minimal OS version changed to '''Ubuntu 11.04''' because the compiler version available in 10.04 does not provide features needed by MITK
 
−
** the [http://qt.nokia.com/downloads Qt framework], version 4.6.2 or later
 
−
 
 
−
Tested systems
 
−
* Windows 7, Windows Vista
 
−
* Ubuntu 11.04 and newer
 
−
* OS X 10.6 (Snow Leopard), OS X 10.7 (Lion)
 
−
 
 
−
=== Documentation ===
 
−
 
 
−
You can access the MITK Diffusion online documentation [http://mitk.org/download/releases/MITK-Diffusion-2012/documentation/html/index.html here]
 
−
 
 
−
=== Available installer ===
 
−
 
 
−
{| border="1" cellpadding="2" cellspacing="0"
 
−
|  '''Windows'''
 
−
|  Vista, Windows 7
 
−
|  [[ http://mitk.org/download/releases/MITK-Diffusion-2012/installers/windows/MITK-Diffusion-2012-win32.exe | MS Windows (32 bit) installer ]]
 
−
|  [[ http://mitk.org/download/releases/MITK-Diffusion-2012/installers/windows/MITK-Diffusion-2012-win64.exe | MS Windows (64 bit) installer ]]
 
−
|-
 
−
|  '''Linux'''
 
−
|  Ubuntu 11.04 and newer
 
−
|  [[ 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 ]] 
 
−
|  [[ 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 ]]
 
−
|-
 
−
|  '''Mac OS X'''
 
−
|  OS X 10.6 and newer 
 
−
|  [[ http://mitk.org/download/releases/MITK-Diffusion-2012/installers/macos/MITK-Diffusion-2012_10_6.dmg | 10.6 OS X disk image (.dmg)]]
 
−
|  [[ http://mitk.org/download/releases/MITK-Diffusion-2012/installers/macos/MITK-Diffusion-2012_10_7.dmg | 10.7 OS X disk image (.dmg) ]]
 
−
|}
 
−
 
 
−
<span id="Release_2011"></span>
 
−
== Release 2011 ==
 
−
Release date : '''02 Nov 2011'''
 
−
 
 
−
=== Requirements ===
 
−
 
 
−
Additional system specific requirements:
 
−
* Windows
 
−
** 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]
 
−
* Linux
 
−
** the [http://qt.nokia.com/downloads Qt framework], version 4.6.2 or later
 
−
** the tar.gz archive needs to be extracted into a folder whithout whitespaces in the path
 
−
 
 
−
=== Documentation ===
 
−
 
 
−
You can access the MITK Diffusion 2011 online documentation [http://mitk.org/download/releases/MITK-Diffusion-2011/documentation/html/index.html here]
 
−
 
 
−
You can download the MITK Diffusion information brochure [http://mitk.org/download/releases/MITK-Diffusion-2011/documentation/pdf/refman.pdf here] (PDF)
 
−
 
 
−
=== Available Installer ===
 
−
 
 
−
The installer is available for platforms enlisted in the table. Support for other systems is only experimental.
 
−
 
 
−
{| border="1" cellpadding="2" cellspacing="0"
 
−
|  '''Windows'''
 
−
|  Vista, Windows 7
 
−
|  [[ https://www.mitk.org/download/releases/MITK-Diffusion-2011/MITK-Diffusion-2011_Windows_32Bit.exe | MS Windows (32 bit) installer]]
 
−
|  [[ https://www.mitk.org/download/releases/MITK-Diffusion-2011/MITK-Diffusion-2011_Windows_64Bit.exe | MS Windows (64 bit) installer]]
 
−
|-
 
−
|  '''Linux'''
 
−
|  Ubuntu 10.04 and newer
 
−
|  [https://www.mitk.org/download/releases/MITK-Diffusion-2011/MITK-Diffusion-2011_Ubunu_10.04_32Bit.tar.gz  Ubuntu (32 bit), tar.gz archive ]
 
−
|  [https://www.mitk.org/download/releases/MITK-Diffusion-2011/MITK-Diffusion-2011_Ubunu_10.04_64Bit.tar.gz  Ubuntu (64 bit), tar.gz archive]
 
−
|-
 
−
|  '''Mac OS X'''
 
−
|  10.6 Snow Leopard and newer
 
−
|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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