Difference between revisions of "DiffusionImaging"

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== Publications ==
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== References ==
  
 
[1] Fritzsche, Klaus H., Peter F. Neher, Ignaz Reicht, Thomas van Bruggen, Caspar Goch, Marco Reisert, Marco Nolden, et al. “MITK Diffusion Imaging.” Methods of Information in Medicine 51, no. 5 (2012): 441.
 
[1] Fritzsche, Klaus H., Peter F. Neher, Ignaz Reicht, Thomas van Bruggen, Caspar Goch, Marco Reisert, Marco Nolden, et al. “MITK Diffusion Imaging.” Methods of Information in Medicine 51, no. 5 (2012): 441.

Revision as of 10:42, 20 July 2017

DiffusionImaging$MITK DIsmall.png

MITK Diffusion

Quicklinks


The MITK Diffusion application [1,2] offers a selection of image analysis algorithms for the processing of diffusion-weighted MR images. It encompasses the research of the Division Medical Image Computing at the German Cancer Research Center (dkfz).


Features & Highlights

  • Support for most established image formats, such as DICOM, NIFTI, and NRRD
  • Tensor and Q-ball reconstruction
  • Intravoxel Incoherent Motion (IVIM) analysis
  • Fiber tractography and fiber processing
    • Global tractography [3]
    • Interactive (similar to [4]) deterministic and probabilistic peak, ODF and tensor streamline tractography
    • Machine learning based tractography [5]
  • Brain network statistics and visualization (connectomics)
  • Fiberfox: simulation of diffusion-weighted MR images [6]
  • Command line tools for most functionalities

The MITK Diffusion application is based on the MITK research platform and is completely open-source. The code is embedded into the source code of MITK as a module and can be accessed through the public git repository.


Version

The current version is MITK Diffusion 2017.07 based on the MITK commit hash 2bda849ee86a362583ee3d2beb4baaca038bd8a5.

This is a beta release based on the current master branch of MITK that features cutting edge developments and has not been tested extensively! The next stable release of this application will be based on the next stable release of MITK. Many but not all modules available in MITK are included in this beta release. If you encounter any bugs, please report them in our bugtracking system or use the MITK-users mailing list. We are grateful for any feedback!


User manual

Please refer to the user manual of MITK Diffusion 2017.07 or use the context help pages in the application (F1).


References

[1] Fritzsche, Klaus H., Peter F. Neher, Ignaz Reicht, Thomas van Bruggen, Caspar Goch, Marco Reisert, Marco Nolden, et al. “MITK Diffusion Imaging.” Methods of Information in Medicine 51, no. 5 (2012): 441.

[2] Fritzsche, K., and H.-P. Meinzer. “MITK-DI A New Diffusion Imaging Component for MITK.” In Bildverarbeitung Für Die Medizin, n.d.

[3] Neher, P. F., B. Stieltjes, M. Reisert, I. Reicht, H.P. Meinzer, and K. Maier-Hein. “MITK Global Tractography.” In SPIE Medical Imaging: Image Processing, 2012.

[4] Chamberland, M., K. Whittingstall, D. Fortin, D. Mathieu, und M. Descoteaux. „Real-time multi-peak tractography for instantaneous connectivity display“. Front Neuroinform 8 (2014): 59. doi:10.3389/fninf.2014.00059.

[5] Neher, Peter F., Marc-Alexandre Côté, Jean-Christophe Houde, Maxime Descoteaux, and Klaus H. Maier-Hein. “Fiber Tractography Using Machine Learning.” NeuroImage. Accessed July 17, 2017. doi:10.1016/j.neuroimage.2017.07.028.

[6] Neher, Peter F., Frederik B. Laun, Bram Stieltjes, and Klaus H. Maier-Hein. “Fiberfox: Facilitating the Creation of Realistic White Matter Software Phantoms.” Magnetic Resonance in Medicine 72, no. 5 (November 2014): 1460–70. doi:10.1002/mrm.25045.


Downloads

Version 2017.07 ( Release date: 17-07-2017 )


Requirements

  • the Qt framework, version 5.9.1 or later
  • For Linux users: The environment variable QT_PLUGIN_PATH has to be set to point to the Qt 5 plugins directory. When not set, the attempt to run the application terminates with following error message: This application failed to start because it could not find or load the Qt platform plugin "xcb".

Tested systems

  • Windows 10
  • Ubuntu 16.04 and newer

Currently we do not provide macOS binaries.


Available installers for 2017.07

Windows Windows 7, Windows 10 MS Windows (64 bit) installer
Windows Windows 7, Windows 10 MS Windows (64 bit) zip archive
Linux Ubuntu 16.04 and newer Ubuntu (64 bit), tar.gz archive


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 2014.10.02 06 February 2014
MITK Diffusion 2014.04 24 Apr 2013
MITK Diffusion 2013.09 10 Okt 2013
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 2014.10.02

Changelog

General

Diffusion

  • Refactored the dicom diffusion loading
    • You are now able to split Siemens mosaic images
    • Support of GE and Philips data
  • Reworked the MITK Diffusion GUI to be based around the View Navigator
    • By putting less focus on perspectives it should be easier for users to find functionality they need and customize their experience to their needs
  • Updated and refactored all mini apps
  • Provide a mini app interface in the application itself
  • A heavy focus was put on bugfixes and improving the user experience and stability of MITK Diffusion
  • Added a view for creating random parcellations for connectomics
  • Switched the diffusion readers/writers to the microservice based concept

Downloads

Version 2014.10 ( Release date: 01-12-2014 )


Requirements

Additional system specific requirements:

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

Tested systems

  • Windows 7
  • Ubuntu 14.04 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

2014.10.02

Windows Vista, Windows 7 MS Windows (64 bit) installer
Linux Ubuntu 14.04 and newer Ubuntu (64 bit), tar.gz archive
Mac OS X OS X 10.8 and newer 10.8 OS X disk image

Release 2014.04

Changelog

General

  • Based on MITK 2014.03 Release
  • VTK was upgraded to version 6.1
  • ITK was upgraded to version 4.5.1
  • and many others

Diffusion

  • QBall Multishell Rekonstruction: error handling improved
  • Preprocessing-Functionality: Create single q-shell data out of multi q-shell data, using different radial signal fit methods like ADC averaging, kurtosis fitting or bi-exponential fitting.
  • Filters for the denoising of dwi data were added
  • Fiberfox:
    • Improved four-compartment signal modeling using a voxel-wise defined volume fraction for the fourth compartment instead of a fixed value for all voxels.
    • Many small bug-fixes.

Additional the minimum required version for

  • CMake is now version 2.8.9
  • and for Qt version 4.7


User manual

Please refer to the user manual of MITK Diffusion 2014.03 or use the context help pages in the application.


Known issues as of 2014.03

  • bug 14655 Dicom import sometimes fails to detect b0 images
  • bug 14490 Diffusion installer is not independent of the build-machine
  • bug 14719 Maximum Intensity Projection is only possible for 21 slices
  • bug 16234 DWI Registration do not support 2D images Error/Warning
  • bug 14828 QBall Reconstruction - Images should get meaningful names
  • bug 16154 Preprocessing manual does not explain all options
  • bug 16160 IVIM view output images automatically close hierarchy

Downloads

Version 2014.03 ( Release date: 24-04-2014 )


Requirements

Additional system specific requirements:

  • Windows
    • If you have problems running the Windows application, please install the Microsoft Redistributable Packages for VS 2010: 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 (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 10.8 OS X disk image

Release 2013.09

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.


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.

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)
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