DiffusionImaging

MITK Diffusion

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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 Neuroimaging Group in the Division Medical and Biological Informatics at the German Cancer Research Center (dkfz).

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'''Features & Highlights'''

 * Tensor and q-ball reconstruction
 * Glyph visualization
 * Quantification and partial volume clustering of tensor and q-ball images
 * Global fiber tractography, visualization, and tract post-processing
 * Brain network statistics and visualization (connectomics)
 * Interactive exploration of Tract-based spatial statistics (TBSS) results 
 * Intra-voxel incoherent motion (IVIM) estimation

The MITK Diffusion application is based on the 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 public git repository.

Version

The current stable version is the MITK Diffusion 2012 release.

Changelog

A list of the major changes from the 2011 to the 2012 release of MITK Diffusion.

2>| Connectomics	Added global clustering computation
Added generator for synthetic networks
4>| Fiber Processing	much more information about the selected fiber bundle is displayed
extraction of fibers passing through a 3D ROI (mitkSurface, STL mesh) is possible
fiber smoothing using spline interpolation added
fiber coloring by scalar map added
3>| Gibbs Tracking	tracking results can be saved automatically
major bug that caused only few fibers to be reconstructed was fixed
input of gfa image is not needed anymore
Stochastic Tracking	gui completely refactored
3>| mitkFiberBundleX	mitkFiberBundle is replaced by mitkFiberBundleX which is essentially a vtkPolyData which results in a much better performance and easier handling
fiber bundle are saved as vtkPolyData
old xml based fiber files can still be loaded and are automatically converted into the new mitkFiberBundleX
3>| ODF Details	refactored gui
tensor data is displayed
normalization of the ODFs is applied correctly
Partial volume analysis	Export of clustering result as image is now possible
2>| Preprocessing	the number of gradients of the selected image can be reduced while preserving an equal distribution of the gradients (as far as possible)
the gradient directions can be displayed as pointset
Q-Ball Reconstruction	removed erroneous numerical reconstruction method
Segmentation	fast interactive 3D interpolation added

User manual

You can access the MITK Diffusion online documentation here

Media

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 <
> Authors: Fritzsche KH¹, Meinzer H-P¹<
> Institution: ¹German Cancer Research Center

Downloads

Version 2012 ( Release date: 07-05-2012 )

Requirements

Additional system specific requirements:

• Windows
  • If you have problems running the Windows application, please install the Microsoft Redistributable Packages for VS 2008: 32 bit or 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 Qt framework, version 4.6.2 or later

Tested systems

• Windows 7, Windows Vista
• Ubuntu 11.04 and newer
• OS X 10.6 and newer

Available installer

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	10.6 Snow Leopard and newer	10.6 OS X disk image available soon	[[ http://mitk.org/download/releases/MITK-Diffusion-2012/installers/macos/MITK-Diffusion-2012.dmg | 10.7 OS X disk image (.dmg) ]]

Testing data

A set of data for testing the functionality of the mitkDiffusion application is available here.

Contact

If you have questions about the application or if you would like to give us feedback, don't hesitate to contact us.

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MITK Diffusion - Release Archive

This section collects links and information for all released versions of the MITK Diffusion Application, but for the newest.

Available Versions	Release date
MITK Diffusion 2011	02 Nov 2011

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: 32 bit or 64 bit
• Linux
  • the 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 here

You can download the MITK Diffusion information brochure here (PDF)

Available Installer

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 * 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 and newer'''
   * [[https://www.mitk.org/download/releases/MITK-Diffusion-2011/MITK-Diffusion-2011_OSX.dmg|OS X disk image (.dmg)]]

The installer is available for platforms enlisted in the table. Support for other systems is only experimental.

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	Ubuntu (32 bit), tar.gz archive	Ubuntu (64 bit), tar.gz archive
Mac OS X	10.6 Snow Leopard and newer	OS X disk image (.dmg)