Documentation/Nightly/Modules/UKFTractography - Revision history

Grundlett: Text replacement - "https?:\/\/(?:www|wiki)\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) " to "https://www.slicer.org/wiki/$1 "

2019-11-27T13:19:44Z

Text replacement - "https?:\/\/(?:www|wiki)\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) " to "https://www.slicer.org/wiki/$1 "

Inorton at 17:41, 22 June 2018

2018-06-22T17:41:27Z

Lauren at 15:29, 8 October 2016

2016-10-08T15:29:00Z

Inorton: Add reference paper links.

2016-08-05T19:25:46Z

Add reference paper links.

Lauren at 18:57, 5 August 2016

2016-08-05T18:57:13Z

Lauren at 18:55, 5 August 2016

2016-08-05T18:55:17Z

Lauren at 18:53, 5 August 2016

2016-08-05T18:53:53Z

Lauren at 18:33, 5 August 2016

2016-08-05T18:33:05Z

Lauren at 18:32, 5 August 2016

2016-08-05T18:32:16Z

Lauren at 18:31, 5 August 2016

2016-08-05T18:31:02Z

@@ Line 50: / Line 50: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Tutorials}}
-* 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 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Panels and their use}}

@@ Line 50: / Line 50: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Tutorials}}
-* UKF Tractography tutorial: https://www.slicer.org/slicerWiki/index.php/Documentation/4.5/Training#UKF
+* UKF Tractography tutorial: https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Training#UKF
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← Older revision		Revision as of 15:29, 8 October 2016
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	{{documentation/{{documentation/version}}/module-description}}		{{documentation/{{documentation/version}}/module-description}}

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

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@@ Line 66: / Line 66: @@
 {{documentation/{{documentation/version}}/module-section|References}}
 * Reference for 2-tensor tractography:
-** Malcolm, J.G., Shenton, M.E. and Rathi, Y., 2010. Filtered multitensor tractography. IEEE transactions on medical imaging, 29(9), pp.1664-1675.
+** 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. A unified tractography framework for comparing diffusion models on clinical scans. In Computational Diffusion MRI Workshop of MICCAI, Nice 2012 (pp. 27-32).
+** 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. 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.
+** 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. Joint Multi-Fiber NODDI Parameter Estimation and Tractography Using the Unscented Information Filter. Frontiers in neuroscience, 10.
+** 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].

@@ Line 71: / Line 71: @@
 * 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. 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:

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 {{documentation/{{documentation/version}}/module-section|Information for Developers}}
 * https://github.com/pnlbwh/ukftractography
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@@ Line 55: / Line 55: @@
 {{documentation/{{documentation/version}}/module-parametersdescription}}
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Similar Modules}}
-N/A
+* Tractography Seeding
+* Tractography ROI Seeding
+* Diffusion Tensor Estimation
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|References}}
-Reference for 2-tensor tractography:
+* Reference for 2-tensor tractography: Malcolm, J.G., Shenton, M.E. and Rathi, Y., 2010. Filtered multitensor tractography. IEEE transactions on medical imaging, 29(9), pp.1664-1675.
-* http://pnl.bwh.harvard.edu/pub/papers_html/MalcolmIEEETransMed10.html
+* Reference for 1-tensor and 2-tensor + free-water: Baumgartner C, Michailovich O, Levitt J, Pasternak O, Bouix S, Westin C, Rathi Y. A unified tractography framework for comparing diffusion models on clinical scans. InComputational 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. 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.