Grundlett: Text replacement - "slicerWiki/index.php" to "wiki"

2019-11-21T16:58:55Z

Text replacement - "slicerWiki/index.php" to "wiki"

UpdateBot: Nightly -> 4.10

2018-10-19T00:47:49Z

Nightly -> 4.10

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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
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Contact: <email>slicer-users@bwh.harvard.edu</email><br>
Website: https://github.com/pnlbwh/ukftractography<br>
Website: http://slicerdmri.github.io/

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|Image:SlicerDMRIScreenshot.jpg|SlicerDMRI
|Image:NAC-logo.png|NAC
|Image:UKF 1.png|Arcuate fasciculus (AF) tract in the setting of edema [Chen et al, 2015]
|Image:UKF 2.png|Corpus callosum (CC) tract
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{{documentation/{{documentation/version}}/module-section|Module Description}}

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For additional references, please see below (References section).


{{documentation/{{documentation/version}}/module-section|Use Cases}}
By default, this module uses a tensor model (either one or two tensors). The default tensor model is a cylinder: both smaller eigenvalues are equal. The NODDI model can also be used.
* 1-Tensor tractography
* 1-Tensor tractography with free water
* 2-Tensor tractography
* 2-Tensor tractography with free water
* Neurite orientation dispersion and density imaging (NODDI)


{{documentation/{{documentation/version}}/module-section|Tutorials}}
* UKF Tractography tutorial: https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Training#UKF


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

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{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* Tractography Seeding
* Tractography ROI Seeding
* Diffusion Tensor Estimation


{{documentation/{{documentation/version}}/module-section|References}}
* Reference for 2-tensor tractography:
** Malcolm, J.G., Shenton, M.E. and Rathi, Y., 2010. [http://www.ncbi.nlm.nih.gov/pubmed/20805043 Filtered multitensor tractography. IEEE transactions on medical imaging, 29(9), pp.1664-1675].
* Reference for 1-tensor and 2-tensor + free-water:
** Baumgartner C, Michailovich O, Levitt J, Pasternak O, Bouix S, Westin C, Rathi Y. [http://cmic.cs.ucl.ac.uk/cdmri12/pdfs/o1_3.pdf A unified tractography framework for comparing diffusion models on clinical scans. In Computational Diffusion MRI Workshop of MICCAI, Nice 2012 (pp. 27-32).]
* Reference for using UKF in clinical imaging data from tumor patients with edema:
** Chen Z, Tie Y, Olubiyi O, Rigolo L, Mehrtash A, Norton I, Pasternak O, Rathi Y, Golby AJ, O'Donnell LJ. [http://www.ncbi.nlm.nih.gov/pubmed/26082890 Reconstruction of the arcuate fasciculus for surgical planning in the setting of peritumoral edema using two-tensor unscented Kalman filter tractography. NeuroImage: Clinical. 2015 Dec 31;7:815-22].
* Reference for NODDI UKF tractography:
** Reddy, C.P. and Rathi, Y., 2016. [http://www.ncbi.nlm.nih.gov/pubmed/27147956 Joint Multi-Fiber NODDI Parameter Estimation and Tractography Using the Unscented Information Filter. Frontiers in Neuroscience, 10].


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
* https://github.com/pnlbwh/ukftractography
* https://www.nitrc.org/projects/ukftractography

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-* UKF Tractography tutorial: https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Training#UKF
+* UKF Tractography tutorial: https://www.slicer.org/wiki/Documentation/Nightly/Training#UKF
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Documentation/4.10/Modules/UKFTractography - Revision history

Grundlett: Text replacement - "slicerWiki/index.php" to "wiki"

UpdateBot: Nightly -> 4.10