2009 Winter Project Week Tractography Segmentation - Revision history

Westin: /* Key Investigators */

2009-01-05T18:23:47Z

Key Investigators

Westin: /* Key Investigators */

2009-01-05T18:22:15Z

Key Investigators

Westin: /* References */

2009-01-05T18:15:32Z

References

Westin: /* References */

2009-01-05T18:15:12Z

References

Westin: /* References */

2009-01-05T18:14:39Z

References

Westin: /* References */

2009-01-05T18:12:08Z

References

Westin at 18:05, 5 January 2009

2009-01-05T18:05:52Z

Westin at 00:09, 3 January 2009

2009-01-03T00:09:16Z

Westin: /* References */

2009-01-03T00:08:22Z

References

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References

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 Our approach models bundles as multinomial distributions over voxels and orientations. Under a hierarchical Bayesian model, Dirichlet process is used as a prior distribution to learn the number of clusters. Gibbs sampling is used for inference.
-Our plan is to integrate this approach into 3D-slicer, use 3D-slicer to do experimental evaluation (including registering multiple subjects, generating fibers and clustering fibers), and compare with approach proposed by [1] and [2], whose use the spectral clustering and the mean of closest distances.
+Our plan is to integrate this approach into 3D-slicer, use 3D-slicer to do experimental evaluation (including registering multiple subjects, generating fibers and clustering fibers), and compare with the approach proposed by [1],2], which is based on spectral clustering and the mean of closest distances.
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 Our approach models bundles as multinomial distributions over voxels and orientations. Under a hierarchical Bayesian model, Dirichlet process is used as a prior distribution to learn the number of clusters. Gibbs sampling is used for inference.
-Our plan is to integrate this approach into 3D-slicer, use 3D-slicer to do experimental evaluation (including registering multiple subjects, generating fibers and clustering fibers), and compare with approach proposed by O'Donnell and Westin, whose use the spectral clustering and the mean of closest distances.
+Our plan is to integrate this approach into 3D-slicer, use 3D-slicer to do experimental evaluation (including registering multiple subjects, generating fibers and clustering fibers), and compare with approach proposed by [1] and [2], whose use the spectral clustering and the mean of closest distances.
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 <h1>Progress</h1>
-We have the code of this approach written in C++ and matlab. In this project week, we need to figure out how to integrate our code into 3D-slicer, how to use 3D-slicer to run registration, tractography and O' Donnell's approach.
+We have the code of our new approach written in C++ and matlab. In this project week, we plan to integrate our code into 3D-slicer.  We also have a numpy-slicer module developed by Demian Wasserman that implements [2]. We plan to use this code as a template when porting our new method to numpy/slicer.
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← Older revision		Revision as of 18:15, 5 January 2009
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	[1] Brun A, Knutsson H, Park HJ, Shenton ME, Westin CF. [http://lmi.bwh.harvard.edu/papers/papers/brunMICCAI04.html Clustering fiber tracts using normalized cuts.] In Seventh International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI'04), Lecture Notes in Computer Science. Rennes - Saint Malo, France, 2004;368-375.		[1] Brun A, Knutsson H, Park HJ, Shenton ME, Westin CF. [http://lmi.bwh.harvard.edu/papers/papers/brunMICCAI04.html Clustering fiber tracts using normalized cuts.] In Seventh International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI'04), Lecture Notes in Computer Science. Rennes - Saint Malo, France, 2004;368-375.

−	[2] O'Donnell LJ, Westin CF. [http://lmi.bwh.harvard.edu/papers/papers/odonnellTMI07.html Automatic tractography segmentation using a high-dimensional white matter atlas.} IEEE Transactions on Medical Imaging 2007;26(11):1562-1575.	+	[2] O'Donnell LJ, Westin CF. [http://lmi.bwh.harvard.edu/papers/papers/odonnellTMI07.html Automatic tractography segmentation using a high-dimensional white matter atlas.] IEEE Transactions on Medical Imaging 2007;26(11):1562-1575.

← Older revision		Revision as of 18:15, 5 January 2009
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	[1] Brun A, Knutsson H, Park HJ, Shenton ME, Westin CF. [http://lmi.bwh.harvard.edu/papers/papers/brunMICCAI04.html Clustering fiber tracts using normalized cuts.] In Seventh International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI'04), Lecture Notes in Computer Science. Rennes - Saint Malo, France, 2004;368-375.		[1] Brun A, Knutsson H, Park HJ, Shenton ME, Westin CF. [http://lmi.bwh.harvard.edu/papers/papers/brunMICCAI04.html Clustering fiber tracts using normalized cuts.] In Seventh International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI'04), Lecture Notes in Computer Science. Rennes - Saint Malo, France, 2004;368-375.

−	[2] [http://lmi.bwh.harvard.edu/papers/papers/odonnellTMI07.html ~~O'Donnell LJ, Westin CF.~~ Automatic tractography segmentation using a high-dimensional white matter atlas. IEEE Transactions on Medical Imaging 2007;26(11):1562-1575.]	+	[2] O'Donnell LJ, Westin CF. [http://lmi.bwh.harvard.edu/papers/papers/odonnellTMI07.html Automatic tractography segmentation using a high-dimensional white matter atlas.} IEEE Transactions on Medical Imaging 2007;26(11):1562-1575.

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 ===References===
-[1] [http://lmi.bwh.harvard.edu/papers/papers/brunMICCAI04.html Brun A, Knutsson H, Park HJ, Shenton ME, Westin CF. Clustering fiber tracts using normalized cuts. In Seventh International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI'04), Lecture Notes in Computer Science. Rennes - Saint Malo, France, 2004;368-375.]
+[1] Brun A, Knutsson H, Park HJ, Shenton ME, Westin CF. [http://lmi.bwh.harvard.edu/papers/papers/brunMICCAI04.html Clustering fiber tracts using normalized cuts.] In Seventh International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI'04), Lecture Notes in Computer Science. Rennes - Saint Malo, France, 2004;368-375.
 [2] [http://lmi.bwh.harvard.edu/papers/papers/odonnellTMI07.html O'Donnell LJ, Westin CF. Automatic tractography segmentation using a high-dimensional white matter atlas. IEEE Transactions on Medical Imaging 2007;26(11):1562-1575.]

← Older revision		Revision as of 18:12, 5 January 2009
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	===References===		===References===
−	O'Donnell LJ, Westin CF. Automatic tractography segmentation using a high-dimensional white matter atlas. IEEE Transactions on Medical Imaging 2007;26(11):1562-1575.	+	[1] [http://lmi.bwh.harvard.edu/papers/papers/brunMICCAI04.html Brun A, Knutsson H, Park HJ, Shenton ME, Westin CF. Clustering fiber tracts using normalized cuts. In Seventh International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI'04), Lecture Notes in Computer Science. Rennes - Saint Malo, France, 2004;368-375.]
		+
		+	[2] [http://lmi.bwh.harvard.edu/papers/papers/odonnellTMI07.html O'Donnell LJ, Westin CF. Automatic tractography segmentation using a high-dimensional white matter atlas. IEEE Transactions on Medical Imaging 2007;26(11):1562-1575.]

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 ===Key Investigators===

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	===References===		===References===
−	* [1] G. Kindlmann, D. B. Ennis, R. T. Whitaker and C-F Westin. "Diffusion tensor analysis with invariant gradients and rotation tangents. IEEE TMI, Vol. 26, No. 11, pp. 1483-1499, 2007.	+	O'Donnell LJ, Westin CF. Automatic tractography segmentation using a high-dimensional white matter atlas. IEEE Transactions on Medical Imaging 2007;26(11):1562-1575.
−	* [2] P. Savadjiev, S. W. Zucker and K. Siddiqi. On the Differential Geometry of 3D Flow Patterns: Generalized Helicoids and Diffusion MRI Analysis. Proc. ICCV 2007.
−	O'Donnell~~, L. J.~~, Westin~~, C. F~~., Automatic ~~Tractography Segmentation Using~~ a ~~High~~-~~Dimensional White Matter Atlas~~. IEEE ~~Trans.~~ on Medical Imaging~~, Vol.~~ 26, 1562-1575.

← Older revision		Revision as of 00:07, 3 January 2009
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	* [1] G. Kindlmann, D. B. Ennis, R. T. Whitaker and C-F Westin. "Diffusion tensor analysis with invariant gradients and rotation tangents. IEEE TMI, Vol. 26, No. 11, pp. 1483-1499, 2007.		* [1] G. Kindlmann, D. B. Ennis, R. T. Whitaker and C-F Westin. "Diffusion tensor analysis with invariant gradients and rotation tangents. IEEE TMI, Vol. 26, No. 11, pp. 1483-1499, 2007.
	* [2] P. Savadjiev, S. W. Zucker and K. Siddiqi. On the Differential Geometry of 3D Flow Patterns: Generalized Helicoids and Diffusion MRI Analysis. Proc. ICCV 2007.		* [2] P. Savadjiev, S. W. Zucker and K. Siddiqi. On the Differential Geometry of 3D Flow Patterns: Generalized Helicoids and Diffusion MRI Analysis. Proc. ICCV 2007.
		+	O'Donnell, L. J., Westin, C. F., Automatic Tractography Segmentation Using a High-Dimensional White Matter Atlas. IEEE Trans. on Medical Imaging, Vol. 26, 1562-1575.