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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).

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
  • Synthetic data generation

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

Version

The current stable version is the MITK Diffusion 2013.09.04 release.

Changelog

  • Redesign of the segmentation plugin
  • Based on MITK 2013.09 Release

    • Update of many third party libraries
    • support for Visual Studio 2012
  • Improvement of usability and workflow of several perspectives
    • New motion correction view
    • Tensor and Q-ball reconstruction will now show a preview when thresholding based on the b0 image
    • Diffusion miniApps have been bundled in one binary
  • The 2013.09.04 bugfix includes important fixes improving the head motion correction stability and corrects an error in the MD calculation

User manual

Please refer to the user manual of MITK Diffusion 2013.03 or use the context help pages in the application.

Media

Publication: MITK diffusion imaging, In Methods Inf Med 2012 Oct 11;51(5):441-8
Authors: Fritzsche KH1, Neher PF1, Reicht I1, van Bruggen T1, Goch C1, Reisert M2, Nolden M1, Zelzer S1, Meinzer HP1, Stieltjes B1
Institution: 1German Cancer Research Center, Heidelberg, Germany
2University Hospital Freiburg, Department of Radiology, Medical Physics, Freiburg, Germany

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 2013.09 ( Release date: 10-10-2013 )

Requirements

Additional system specific requirements:

  • Windows
    • If you have problems running the Windows application, please install the Microsoft Redistributable Packages for VS 2010: 32 bit or 64 bit

  • Linux

Tested systems

  • Windows 7
  • Ubuntu 12.04 and newer
  • OS X 10.6 (Snow Leopard), OS X 10.8 (Mountain Lion)

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.

Available installers

Windows

Vista, Windows 7

MS Windows (32 bit) installer

MS Windows (64 bit) installer

Linux

Ubuntu 12.04 and newer

Ubuntu (32 bit), tar.gz archive

Ubuntu (64 bit), tar.gz archive

Mac OS X

OS X 10.6 and newer

10.6 OS X disk image

10.8 OS X disk image

Installers for the 2013.09.00 version can be found here

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.


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 2013.06

04 Jul 2013

MITK Diffusion 2013.03

04 Apr 2013

MITK Diffusion 2012.12

21 Dec 2012

MITK Diffusion 2012.09

02 Oct 2012

MITK Diffusion 2012

07 May 2012

MITK Diffusion 2011

02 Nov 2011

Release 2013.06

Release date: 04-07-2013

Changelog

  • Based on the MITK 2013.06 Release

  • Following the ITK support change in MITK, also MITK Diffusion now fully supports ITK4 ( the ITK3 support is discontinued )
  • New Features

    • new mini-applications for fiber direction extraction and evaluation
  • Over thirty bugs were fixed across the different modules and plugins

User manual

Please refer to the user manual of MITK Diffusion 2013.03 or use the context help pages in the application.

Downloads

Version 2013.06 ( Release date: 04-07-2013 )

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

Tested systems

  • Windows 7, Windows Vista
  • Ubuntu 12.04 and newer
  • OS X 10.6 (Snow Leopard), OS X 10.8 (Mountain Lion)

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.

Available installer

Windows

Vista, Windows 7

MS Windows (32 bit) installer

MS Windows (64 bit) installer

Linux

Ubuntu 12.04 and newer

Ubuntu (32 bit), tar.gz archive

Ubuntu (64 bit), tar.gz archive

Mac OS X

OS X 10.6 and newer

10.6 OS X disk image

10.8 OS X disk image

Release 2013.03

Release date: 04-04-2013

Changelog

  • New features in FiberFox

    • Fiber Definition
      • Added functions to copy, translate, rotate and scale fibers including the corresponding fiducials
      • Fiducial alignment with voxel grid
      • Fiber definition with only two ROIs
    • Signal Generation
      • Extended diffusion models: Stick, Zeppelin, Tensor, Ball, Astrosticks, Dot
      • Extended two-compartment model to four-compartment model
      • Realistic simulation of relaxation effects. Parameters: T2 (per compartment), TE, T2' and line readout time
      • Explicit definition of fiber radius used for the calculation of compartment volume fractions
      • Changed the relative parameter SNR to the absolute parameter noise variance
      • Removed internal signal normalization --> double voxel size in one dimension results in twice the signal strength

    • Complete refactoring of the Fiberfox help page
  • Fiber Processing View reodered and splitted into separate views: Fiber Processing and Fiber Extraction

  • Modularization of the Diffusion Module into
    • new submodules DiffusionCore, FiberTracking, Connectomics, Quantification

  • New, user defined visualisation properties for connectomics networks added
  • Several bugs fixed in both registration views

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

Tested systems

  • Windows 7, Windows Vista
  • Ubuntu 12.04 and newer
  • OS X 10.6 (Snow Leopard), OS X 10.8 (Mountain Lion)

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.

Available installer

Windows

Vista, Windows 7

MS Windows (32 bit) installer

MS Windows (64 bit) installer

Linux

Ubuntu 11.04 and newer

Ubuntu (32 bit), tar.gz archive

Ubuntu (64 bit), tar.gz archive

Mac OS X

OS X 10.6 and newer

10.6 OS X disk image

10.8 OS X disk image

Documentation

The user manual for the MITK Diffusion 2013.03 application can be found here.

Release 2012.12

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: 32 bit or 64 bit

  • Linux

Tested systems

  • Windows 7, Windows Vista
  • Ubuntu 11.04 and newer
  • OS X 10.6 (Snow Leopard), OS X 10.7 (Lion)

Available installer

Windows

Vista, Windows 7

MS Windows (32 bit) installer

MS Windows (64 bit) installer

Linux

Ubuntu 11.04 and newer

Ubuntu (32 bit), tar.gz archive

Ubuntu (64 bit), tar.gz archive

Mac OS X

OS X 10.6 and newer

10.6 OS X disk image

10.7 OS X disk image (.dmg)

10.8 OS X disk image (.dmg)

Release 2012.09

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: 32 bit or 64 bit

  • Linux

Tested systems

  • Windows 7, Windows Vista
  • Ubuntu 11.04 and newer
  • OS X 10.6 (Snow Leopard), OS X 10.7 (Lion)

Available installer

Windows

Vista, Windows 7

MS Windows (32 bit) installer

MS Windows (64 bit) installer

Linux

Ubuntu 11.04 and newer

Ubuntu (32 bit), tar.gz archive

Ubuntu (64 bit), tar.gz archive

Mac OS X

OS X 10.6 and newer

10.6 OS X disk image

10.7 OS X disk image (.dmg)

Release 2012

Release date : 07 May 2012

Changelog

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

Connectomics

Added global clustering computation

Added generator for synthetic networks

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

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

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

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

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

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 (Snow Leopard), OS X 10.7 (Lion)

Documentation

You can access the MITK Diffusion online documentation here

Available installer

Windows

Vista, Windows 7

MS Windows (32 bit) installer

MS Windows (64 bit) installer

Linux

Ubuntu 11.04 and newer

Ubuntu (32 bit), tar.gz archive

Ubuntu (64 bit), tar.gz archive

Mac OS X

OS X 10.6 and newer

10.6 OS X disk image (.dmg)

10.7 OS X disk image (.dmg)

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

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

Windows

Vista, Windows 7

MS Windows (32 bit) installer

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)