Difference between revisions of "DiffusionImaging"

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__NOTOC__
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#REDIRECT [[MitkDiffusion]]
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[[File:DiffusionImaging$MITK_DIsmall.png|thumb|400px]]
 
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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 [https://phabricator.mitk.org/source/mitk/ web interface] of the Git repository
 
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* '''Download Section''' is [[#Downloads|here]]
 
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----
 
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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 [https://www.dkfz.de/en/mic/index.php Medical Image Computing] at the German Cancer Research Center (dkfz).
 
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−
 
 
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=== Features & Highlights ===
 
−
 
 
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* Support for most established image formats, such as DICOM, NIFTI, and NRRD
 
−
* Tensor and Q-ball reconstruction
 
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* Intravoxel Incoherent Motion (IVIM) analysis
 
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* Fiber tractography and fiber processing
 
−
** Global tractography [3]
 
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** Interactive (similar to [4]) deterministic and probabilistic peak, ODF and tensor streamline tractography
 
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** Machine learning based tractography [5]
 
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* Brain network statistics and visualization (connectomics)
 
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* Fiberfox: simulation of diffusion-weighted MR images [6]
 
−
* Command line tools for most functionalities
 
−
 
 
−
The MITK Diffusion application is based on the [https://www.mitk.org/wiki/ResearchPlatform 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 [https://www.mitk.org/wiki/MitkGit public git repository].
 
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−
 
 
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== Version ==
 
−
The current version is MITK Diffusion 2017.07 based on the MITK commit hash 2bda849ee86a362583ee3d2beb4baaca038bd8a5.
 
−
 
 
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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 [https://phabricator.mitk.org/maniphest/task/edit/form/21/ bugtracking] system or use the [http://mitk.org/wiki/MITK_Mailinglist MITK-users mailing list]. We are grateful for any feedback!
 
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== User manual ==
 
−
Please refer to the user manual of MITK Diffusion [http://docs.mitk.org/2017.07/org_mitk_gui_qt_diffusionimaging.html#org_mitk_gui_qt_diffusionimagingComponents 2017.07] or use the context help pages in the application (F1).
 
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−
The nightly user manual can be found [http://docs.mitk.org/nightly/org_mitk_gui_qt_diffusionimaging.html#org_mitk_gui_qt_diffusionimagingComponents here].
 
−
 
 
−
 
 
−
== 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.
 
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−
[2] Fritzsche, K., and H.-P. Meinzer. “MITK-DI A New Diffusion Imaging Component for MITK.” In Bildverarbeitung Für Die Medizin, n.d.
 
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−
[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.
 
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[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.
 
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[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.
 
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[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.
 
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−
 
 
−
== Downloads ==
 
−
Version 2017.07 ( Release date: ''17-07-2017'' )
 
−
 
 
−
 
 
−
=== Requirements ===
 
−
 
 
−
* '''For Windows users''':
 
−
** MITK Diffusion requires the Microsoft Visual C++ 2017 Redistributable to be installed on the system. The MITK Diffusion installer automatically installs this redistributable for you if not already present on the system, but it needs administrative privileges to do so. So to install the redistributable, '''''run the MITK Diffusion installer as administrator'''''.
 
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−
 
 
−
Tested systems
 
−
 
 
−
* Windows 10
 
−
* Ubuntu 16.04
 
−
 
 
−
Currently we do not provide macOS binaries.
 
−
 
 
−
 
 
−
=== Available installers for 2017.07===
 
−
{| class="wikitable" width=100% style="background-color:#ffffff;"
 
−
| Windows 7, Windows 10
 
−
| [http://mitk.org/download/releases/MITK-Diffusion-2017.07/Windows/MITK-Diffusion-2017.07-win64.exe MS Windows (64 bit) installer]
 
−
|-
 
−
| Windows 7, Windows 10
 
−
| [http://mitk.org/download/releases/MITK-Diffusion-2017.07/Windows/MITK-Diffusion-2017.07-win64.zip MS Windows (64 bit) zip archive]
 
−
|-
 
−
| Ubuntu 16.04 and newer
 
−
|  [http://mitk.org/download/releases/MITK-Diffusion-2017.07/Linux/MITK-Diffusion-2017.07-linux64.tar.gz Ubuntu (64 bit), tar.gz archive]
 
−
|-
 
−
| Ubuntu 14.04
 
−
|  [http://mitk.org/download/releases/MITK-Diffusion-2017.07/Linux/MITK-Diffusion-2017.07-Ubuntu14.04.64bit.tar.gz Ubuntu (64 bit), tar.gz archive]
 
−
|}
 
−
 
 
−
 
 
−
=== Known issues ===
 
−
The Fiberfox command line application does not read the b-value but uses a default b-value of 1000 s/mm². This bug does not affect the GUI version of Fiberfox. This bug also has no effect if the first non-zero b-value is 1000 s/mm², which is for example the case in the simulated HCP dataset (10.5281/zenodo.572345).
 
−
 
 
−
 
 
−
== Contact ==
 
−
If you have questions about the application or if you would like to give us feedback, don't hesitate to [https://www.dkfz.de/en/mic/team/people/Peter_Neher.html 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.
 
−
{| class="wikitable" width=100% style="background-color:#ffffff;"
 
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! Available Versions
 
−
! Release date
 
−
|-
 
−
| [[#Release_2014_10_02|MITK Diffusion 2014.10.02]]  
 
−
| 06 February 2014
 
−
|-
 
−
| [[#Release_2014_04|MITK Diffusion 2014.04]]
 
−
| 24 Apr 2013
 
−
|-
 
−
| [[#Release_2013_09|MITK Diffusion 2013.09]]
 
−
| 10 Okt 2013
 
−
|-
 
−
| [[#Release_2013_06|MITK Diffusion 2013.06]]
 
−
| 04 Jul 2013
 
−
|-
 
−
| [[#Release_2013_03|MITK Diffusion 2013.03]]
 
−
| 04 Apr 2013
 
−
|-
 
−
| [[#Release_2012_12|MITK Diffusion 2012.12]]
 
−
| 21 Dec 2012
 
−
|-
 
−
| [[#Release_2012_09|MITK Diffusion 2012.09]]
 
−
| 02 Oct 2012
 
−
|-
 
−
| [[#Release_2012|MITK Diffusion 2012]]
 
−
| 07 May 2012
 
−
|-
 
−
| [[#Release_2011|MITK Diffusion 2011]]
 
−
| 02 Nov 2011
 
−
|}
 
−
 
 
−
 
 
−
<span id="Release_2014_10"></span>
 
−
<div class="mw-collapsible mw-collapsed">
 
−
 
 
−
== Release 2014.10.02 ==
 
−
 
 
−
 
 
−
<div class="mw-collapsible-content">
 
−
 
 
−
== Changelog ==
 
−
'''General'''
 
−
* Based on [[MITK_ReleaseNotes_2014.10|MITK 2014.10 Release]]
 
−
 
 
−
'''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: [http://www.microsoft.com/en-us/download/details.aspx?id=14632 64 bit]
 
−
* Linux
 
−
** the [http://qt.nokia.com/downloads Qt framework], version 4.6.2 or later
 
−
 
 
−
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 ====
 
−
{| class="wikitable" width=100% style="background-color:#ffffff;"
 
−
! Windows
 
−
| Vista, Windows 7
 
−
| [https://www.mitk.org/download/releases/MITK-Diffusion-2014.10/Windows/MITK-Diffusion-2014.10.02-win64.exe MS Windows (64 bit) installer]
 
−
|-
 
−
! Linux
 
−
| Ubuntu 14.04 and newer
 
−
|  [https://www.mitk.org/download/releases/MITK-Diffusion-2014.10/Linux/MITK-Diffusion-2014.10.02-linux64.tar.gz Ubuntu (64 bit), tar.gz archive]
 
−
|-
 
−
! Mac OS X
 
−
| OS X 10.8 and newer
 
−
|  [https://www.mitk.org/download/releases/MITK-Diffusion-2014.10/MacOS/MITK-Diffusion-2014.10.02-mac64.dmg 10.8 OS X disk image]
 
−
|}
 
−
</div></div>
 
−
 
 
−
<span id="Release_2014_04"></span>
 
−
<div class="mw-collapsible mw-collapsed">
 
−
== Release 2014.04 ==
 
−
 
 
−
 
 
−
<div class="mw-collapsible-content">
 
−
== Changelog ==
 
−
'''General'''
 
−
* Based on [[MITK-ReleaseNotes-2014-03|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 [https://www.mitk.org/download/releases/MITK-Diffusion-2014.03/Documentation/html/ 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: [http://www.microsoft.com/en-us/download/details.aspx?id=14632 64 bit]
 
−
* Linux
 
−
** the [http://qt.nokia.com/downloads Qt framework], version 4.6.2 or later
 
−
 
 
−
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 ===
 
−
{| class="wikitable" width=100% style="background-color:#ffffff;"
 
−
! Windows
 
−
| Vista, Windows 7
 
−
| 
 
−
| [https://www.mitk.org/download/releases/MITK-Diffusion-2014.03/Windows/MITK-Diffusion-2014.03.00-win64.exe MS Windows (64 bit) installer]
 
−
|-
 
−
! Linux
 
−
| Ubuntu 12.04 and newer
 
−
|  [https://www.mitk.org/download/releases/MITK-Diffusion-2014.03/Linux/MITK-Diffusion-2014.03.00-linux32.tar.gz Ubuntu (32 bit), tar.gz archive] 
 
−
|  [https://www.mitk.org/download/releases/MITK-Diffusion-2014.03/Linux/MITK-Diffusion-2014.03.00-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-2014.03/MacOS/MITK-Diffusion-2014.03.00-mac64.dmg 10.8 OS X disk image]
 
−
|}
 
−
</div></div>
 
−
 
 
−
<span id="Release_2013_09"></span>
 
−
<div class="mw-collapsible mw-collapsed">
 
−
== Release 2013.09 ==
 
−
 
 
−
 
 
−
<div class="mw-collapsible-content">
 
−
== Changelog ==
 
−
* Redesign of the segmentation plugin
 
−
* Based on [[MITK-ReleaseNotes-2013-09|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 [https://www.mitk.org/download/releases/MITK-Diffusion-2013.03/documentation/ 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: [http://www.microsoft.com/en-us/download/details.aspx?id=5555 32 bit] or [http://www.microsoft.com/en-us/download/details.aspx?id=14632 64 bit]
 
−
* Linux
 
−
** the [http://qt.nokia.com/downloads Qt framework], version 4.6.2 or later
 
−
 
 
−
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 ===
 
−
{| class="wikitable" width=100% style="background-color:#ffffff;"
 
−
! Windows
 
−
| Vista, Windows 7
 
−
| [http://mitk.org/download/releases/MITK-Diffusion-2013.09/Windows/MITK-Diffusion-2013.09.04-win32.exe MS Windows (32 bit) installer]
 
−
| [http://mitk.org/download/releases/MITK-Diffusion-2013.09/Windows/MITK-Diffusion-2013.09.04-win64.exe MS Windows (64 bit) installer]
 
−
|-
 
−
! Linux
 
−
| Ubuntu 12.04 and newer
 
−
|  [http://mitk.org/download/releases/MITK-Diffusion-2013.09/Linux/MITK-Diffusion-2013.09.04-linux32.tar.gz  Ubuntu (32 bit), tar.gz archive] 
 
−
|  [http://mitk.org/download/releases/MITK-Diffusion-2013.09/Linux/MITK-Diffusion-2013.09.04-linux64.tar.gz Ubuntu (64 bit), tar.gz archive]
 
−
|-
 
−
! Mac OS X
 
−
| OS X 10.6 and newer
 
−
|  [http://mitk.org/download/releases/MITK-Diffusion-2013.09/MacOS/MITK-Diffusion-2013.09.04-mac64_10.6.dmg 10.6 OS X disk image]
 
−
|  [http://mitk.org/download/releases/MITK-Diffusion-2013.09/MacOS/MITK-Diffusion-2013.09.04-mac64.dmg 10.8 OS X disk image]
 
−
|}
 
−
 
 
−
Installers for the 2013.09.00 version can be found [http://mitk.org/download/releases/MITK-Diffusion-2013.09/ here]
 
−
 
 
−
=== Testing data ===
 
−
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].
 
−
 
 
−
 
 
−
== Contact ==
 
−
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].
 
−
</div></div>
 
−
 
 
−
<span id="Release_2013_06"></span>
 
−
<div class="mw-collapsible mw-collapsed">
 
−
== Release 2013.06 ==
 
−
 
 
−
 
 
−
<div class="mw-collapsible-content">
 
−
Release date: '''04-07-2013'''
 
−
 
 
−
== Changelog ==
 
−
* Based on the [[MITK-ReleaseNotes-2013-06|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 [https://www.mitk.org/download/releases/MITK-Diffusion-2013.03/documentation/ 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: [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 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 ===
 
−
{|class="wikitable" width=100% style="background-color:#ffffff;"
 
−
! Windows
 
−
| Vista, Windows 7
 
−
| [http://mitk.org/download/releases/MITK-Diffusion-2013.06/Windows/MITK-Diffusion-2013.06.00-win32.exe MS Windows (32 bit) installer]
 
−
| [http://mitk.org/download/releases/MITK-Diffusion-2013.06/Windows/MITK-Diffusion-2013.06.00-win64.exe MS Windows (64 bit) installer]
 
−
|-
 
−
! Linux
 
−
| Ubuntu 12.04 and newer
 
−
| [http://mitk.org/download/releases/MITK-Diffusion-2013.06/Linux/MITK-Diffusion-2013.06.00-linux32.tar.gz Ubuntu (32 bit), tar.gz archive]
 
−
| [http://mitk.org/download/releases/MITK-Diffusion-2013.06/Linux/MITK-Diffusion-2013.06.00-linux64.tar.gz Ubuntu (64 bit), tar.gz archive]
 
−
|-
 
−
! Mac OS X
 
−
| OS X 10.6 and newer
 
−
|  [http://mitk.org/download/releases/MITK-Diffusion-2013.06/MacOS/MITK-Diffusion-2013.06.00-mac32-10.6.dmg 10.6 OS X disk image]
 
−
|  [http://mitk.org/download/releases/MITK-Diffusion-2013.06/MacOS/MITK-Diffusion-2013.06.00-mac64-10.8.dmg 10.8 OS X disk image]
 
−
|}
 
−
</div></div>
 
−
 
 
−
<span id="Release_2013_03"></span>
 
−
<div class="mw-collapsible mw-collapsed">
 
−
== Release 2013.03 ==
 
−
 
 
−
 
 
−
<div class="mw-collapsible-content">
 
−
Release date: '''04-04-2013'''
 
−
 
 
−
* Based on the [[MITK-ReleaseNotes-2013-03|MITK 2013.03 Release]]
 
−
 
 
−
 
 
−
=== 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: [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 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 ===
 
−
{| class="wikitable" width=100% style="background-color:#ffffff;"
 
−
! Windows
 
−
| Vista, Windows 7
 
−
| [http://mitk.org/download/releases/MITK-Diffusion-2013.03/windows/MITK-Diffusion-2013.03.00-win32.exe MS Windows (32 bit) installer]
 
−
| [http://mitk.org/download/releases/MITK-Diffusion-2013.03/windows/MITK-Diffusion-2013.03.00-win64.exe MS Windows (64 bit) installer]
 
−
|-
 
−
! Linux
 
−
| Ubuntu 11.04 and newer
 
−
| [http://mitk.org/download/releases/MITK-Diffusion-2013.03/linux/MITK-Diffusion-2013.03.00-linux32.tar.gz Ubuntu (32 bit), tar.gz archive]
 
−
| [http://mitk.org/download/releases/MITK-Diffusion-2013.03/linux/MITK-Diffusion-2013.03.00-linux64.tar.gz Ubuntu (64 bit), tar.gz archive]
 
−
|-
 
−
! Mac OS X
 
−
| OS X 10.6 and newer
 
−
| [http://mitk.org/download/releases/MITK-Diffusion-2013.03/macos/MITK-Diffusion-2013.03.00-10.6.dmg 10.6 OS X disk image]
 
−
| [http://mitk.org/download/releases/MITK-Diffusion-2013.03/macos/MITK-Diffusion-2013.03.00-10.8.dmg 10.8 OS X disk image]
 
−
|}
 
−
 
 
−
=== Documentation ===
 
−
The user manual for the MITK Diffusion 2013.03 application can be found [https://www.mitk.org/download/releases/MITK-Diffusion-2013.03/documentation/ here].
 
−
</div></div>
 
−
 
 
−
<span id="Release_2012_12"></span>
 
−
<div class="mw-collapsible mw-collapsed">
 
−
== Release 2012.12 ==
 
−
 
 
−
 
 
−
<div class="mw-collapsible-content">
 
−
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 ===
 
−
{| class="wikitable" width=100% style="background-color:#ffffff;"
 
−
! 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
 
−
| 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]
 
−
| 
 
−
|-
 
−
! Mac OS X
 
−
| OS X 10.6 and newer
 
−
| [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)]
 
−
|}
 
−
</div></div>
 
−
 
 
−
<span id="Release_2012_09"></span>
 
−
<div class="mw-collapsible mw-collapsed">
 
−
== Release 2012.09 ==
 
−
 
 
−
 
 
−
<div class="mw-collapsible-content">
 
−
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 ===
 
−
{| class="wikitable" width=100% style="background-color:#ffffff;"
 
−
! 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)]
 
−
|}
 
−
</div></div>
 
−
 
 
−
<div class="mw-collapsible mw-collapsed">
 
−
<span id="Release_2012"></span>
 
−
== Release 2012 ==
 
−
 
 
−
 
 
−
<div class="mw-collapsible-content">
 
−
Release date : '''07 May 2012'''
 
−
 
 
−
 
 
−
== Changelog ==
 
−
A list of the major changes from the 2011 to the 2012 release of MITK Diffusion.
 
−
 
 
−
{| class="wikitable" width=100% style="background-color:#ffffff;"
 
−
|rowspan="2" style="text-align:center;vertical-align:middle;" |'''Connectomics'''
 
−
|Added global clustering computation
 
−
|-
 
−
|Added generator for synthetic networks
 
−
|-
 
−
|rowspan="4" style="text-align:center;vertical-align:middle;"|'''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
 
−
|-
 
−
|rowspan="3" style="text-align:center; vertical-align:middle;"|'''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
 
−
|-
 
−
|style="text-align:center; vertical-align:middle;"|'''Stochastic Tracking'''
 
−
|gui completely refactored
 
−
|-
 
−
|rowspan="3" style="text-align:center;vertical-align:middle;"|'''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
 
−
|-
 
−
|rowspan="3" style="text-align:center;vertical-align:middle;"|'''ODF Details'''
 
−
|refactored gui
 
−
|-
 
−
|tensor data is displayed
 
−
|-
 
−
|normalization of the ODFs is applied correctly
 
−
|-
 
−
|style="text-align:center; vertical-align:middle;"|'''Partial volume analysis'''
 
−
| Export of clustering result as image is now possible
 
−
|-
 
−
|rowspan="2" style="text-align:center; vertical-align:middle;"|'''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
 
−
|-
 
−
|style="text-align:center; vertical-align:middle;"|'''Q-Ball Reconstruction'''
 
−
| removed erroneous numerical reconstruction method
 
−
|-
 
−
|style="text-align:center; vertical-align:middle;"|'''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: [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 ===
 
−
{| class="wikitable" width=100% style="background-color:#ffffff;"
 
−
! 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)]
 
−
|}
 
−
</div></div>
 
−
<span id="Release_2011"></span>
 
−
<div class="mw-collapsible mw-collapsed">
 
−
== Release 2011 ==
 
−
 
 
−
 
 
−
<div class="mw-collapsible-content">
 
−
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.
 
−
{| class="wikitable" width=100% style="background-color:#ffffff;"
 
−
! 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" <style="text-align:center">|[https://www.mitk.org/download/releases/MITK-Diffusion-2011/MITK-Diffusion-2011_OSX.dmg OS X disk image (.dmg)]
 
−
|}
 
−
 
 
−
</div></div>
 

Latest revision as of 12:35, 24 August 2018

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