Projects:PathologyAnalysis - Revision history

Bowang: /* Literature */

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Literature

Bowang: /* Collaboration events */

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Collaboration events

Bowang: /* Collaboration events */

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Collaboration events

Bowang: /* Collaboration events */

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Collaboration events

Bowang: /* Collaboration events */

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Collaboration events

Bowang: /* Collaboration events */

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Collaboration events

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Collaboration events

Bowang: /* Literature */

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Literature

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Bowang: /* Conclusion */

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Conclusion

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 = Literature =
-[1] Bo Wang, Marcel Prastawa, Andrei Irimia, Micah C. Chambers,  Neda Sadeghi, Paul M. Vespa, John D. Van Horn, Guido Gerig, Analyzing Imaging Biomarkers for Traumatic Brain Injury Using 4D Modeling of Longitudinal MRI, In IEEE Proceedings of ISBI 2013, pp. 1392-1395. 2013.
+[1] Bo Wang, Wei Liu, Marcel Prastawa, Andrei Irimia, Paul M. Vespa, John D. Van Horn, P. Thomas Fletcher, and Guido Gerig . 4D Active Cut: An Interactive Tool for Pathological Anatomy Modeling, In Biomedical Imaging (ISBI), 2014 IEEE 11th International Symposium on, pp. 529-532. IEEE, 2014.
 [2] BoWang, Marcel Prastawa, Avishek Saha, Suyash P. Awate, Andrei Irimia, Micah C. Chambers, Paul M. Vespa, John D. Van Horn, Valerio Pascucci, and Guido Gerig., Modeling 4D Changes in Pathological Anatomy Using Domain Adaptation: Analysis of TBI Imaging Using a Tumor Database, In Multimodal Brain Image Analysis, pp. 31-39. 2013. [Best Paper Award]

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-=== (NA-MIC) Summer Project Week 2014 (June 7-11??) ===
+=== (NA-MIC) Summer Project Week 2014 (June 23-27, 2014) ===
 Bo from Utah algorithm team remotely joined the summer project week and was working on understanding the workflow of Python scripting module, and modifying the existing code for a Slicer extension. Bo also worked on the documentation of the current command line tool for interactive TBI segmentation.
 <br />[http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:TBI_Segmentation Webpage of this event]

← Older revision		Revision as of 22:39, 11 October 2014
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	=== (NA-MIC) Summer Project Week 2014 (June 7-11??) ===		=== (NA-MIC) Summer Project Week 2014 (June 7-11??) ===
		+	Bo from Utah algorithm team remotely joined the summer project week and was working on understanding the workflow of Python scripting module, and modifying the existing code for a Slicer extension. Bo also worked on the documentation of the current command line tool for interactive TBI segmentation.
		+	<br />[http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:TBI_Segmentation Webpage of this event]

	=== Software release to USC DBP Collaborators (February 13 - 14, 2014) ===		=== Software release to USC DBP Collaborators (February 13 - 14, 2014) ===

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 === (NA-MIC) Summer Project Week 2014 (June 7-11??) ===
-=== Software release to USC DBP Collaborators ===
+=== Software release to USC DBP Collaborators (February 13 - 14, 2014) ===
 === (NA-MIC) All hands meeting (AHM) and Winter Project Week 2014 (January 6-10, 2014) ===

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 === Software release to USC DBP Collaborators ===
-=== (NA-MIC) All hands meeting (AHM) and Winter Project Week 2014 (January 7-11??) ===
+=== (NA-MIC) All hands meeting (AHM) and Winter Project Week 2014 (January 6-10, 2014) ===
 === (NA-MIC) Summer Project Week 2013 (June 17-21, 2013) ===
-Utah team coordinated with UCLA regarding the release of a Slicer module to perform multimodal automatic segmentation of TBI using the methodologies developed by the Utah team.
+Utah team coordinated with UCLA regarding the release of a Slicer module to perform multimodal automatic segmentation of TBI using the methodologies developed by the Utah team. Utah team also did a progress update to the UCLA group on the current status of the matlab/C++/VTK translation of the Utah algorithm.
 <br />[http://www.na-mic.org/Wiki/index.php/Validation_and_testing_of_3D_Slicer_modules_implementing_the_Utah_segmentation_algorithm_for_traumatic_brain_injury Webpage of this event]

@@ Line 140: / Line 140: @@
 === (NA-MIC) All hands meeting (AHM) and Winter Project Week 2014 (January 7-11??) ===
-=== (NA-MIC) Summer Project Week 2013 (June 7-11??) ===
+=== (NA-MIC) Summer Project Week 2013 (June 17-21, 2013) ===
-=== UCLA DBP Collaborators visiting Utah ===
+Utah team coordinated with UCLA regarding the release of a Slicer module to perform multimodal automatic segmentation of TBI using the methodologies developed by the Utah team.
 === Telephone meeting (April 1st, 2013) ===

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 = Literature =
-[2] Bo Wang, Marcel Prastawa, Suyash P. Awate, Andrei Irimia, Micah C. Chambers, Paul M. Vespa, John D. Van Horn, Guido Gerig, Segmentation of Serial MRI of TBI patients using Personalized Atlas Construction and Topological Change Estimation, In Proceedings of IEEE ISBI 2012, pp. 1152--1155. 2012.
+[1] Bo Wang, Marcel Prastawa, Andrei Irimia, Micah C. Chambers,  Neda Sadeghi, Paul M. Vespa, John D. Van Horn, Guido Gerig, Analyzing Imaging Biomarkers for Traumatic Brain Injury Using 4D Modeling of Longitudinal MRI, In IEEE Proceedings of ISBI 2013, pp. 1392-1395. 2013.
-[3] Bo Wang, Marcel Prastawa, Andrei Irimia, Micah C. Chambers, Paul M. Vespa, John D. Van Horn, and Guido Gerig, A Patient-Specific Segmentation Framework for Longitudinal MR Images of Traumatic Brain Injury, Proc. SPIE 8314, 831402 (2012).
+[2] BoWang, Marcel Prastawa, Avishek Saha, Suyash P. Awate, Andrei Irimia, Micah C. Chambers, Paul M. Vespa, John D. Van Horn, Valerio Pascucci, and Guido Gerig., Modeling 4D Changes in Pathological Anatomy Using Domain Adaptation: Analysis of TBI Imaging Using a Tumor Database, In Multimodal Brain Image Analysis, pp. 31-39. 2013. [Best Paper Award]
-[4] Marcel Prastawa, Elizabeth Bullitt, Guido Gerig, Simulation of brain tumors in MR images, Medical Image Analysis 13 (2009), pp. 297-311, PMID: 19119055
+[3] Bo Wang, Marcel Prastawa, Andrei Irimia, Micah C. Chambers,  Neda Sadeghi, Paul M. Vespa, John D. Van Horn, Guido Gerig, Analyzing Imaging Biomarkers for Traumatic Brain Injury Using 4D Modeling of Longitudinal MRI, In IEEE Proceedings of ISBI 2013, pp. 1392-1395. 2013.
-[5] Marcel Prastawa and Guido Gerig, Brain Lesion Segmentation through Physical Model Estimation, International Symposium on Visual Computing ISVC 2008, LNCS, Vol. 5358, pp. 562--571.
+[4] Bo Wang, Marcel Prastawa, Suyash P. Awate, Andrei Irimia, Micah C. Chambers, Paul M. Vespa, John D. Van Horn, Guido Gerig, Segmentation of Serial MRI of TBI patients using Personalized Atlas Construction and Topological Change Estimation, In Proceedings of IEEE ISBI 2012, pp. 1152--1155. 2012.
-[6] Marcel Prastawa, John H. Gilmore, Weili Lin, Guido Gerig, Automatic Segmentation of MR Images of the Developing Newborn Brain, Medical Image Analysis (MedIA). Vol 9, October 2005, pages 457-466
+[5] Bo Wang, Marcel Prastawa, Andrei Irimia, Micah C. Chambers, Paul M. Vespa, John D. Van Horn, and Guido Gerig, A Patient-Specific Segmentation Framework for Longitudinal MR Images of Traumatic Brain Injury, Proc. SPIE 8314, 831402 (2012).
 =Key Investigators=

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 = Collaboration events =
 === Telephone meeting (April 1st, 2013) ===
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 This is the first NA-MIC meeting between UCLA group and Utah group. During the project week, a lot of discussions have been done between the collaborators (UCLA and Utah groups) of this project. We worked together and answered each other's questions. Marcel introduced the purpose of all parameters of ABC and how these parameters would affect the final results. We discussed the possible user interaction we would use in the next step for better segmentation. Moreover, we knew more about the requirements of neurosurgeons and clinicians. Andrei pointed out the result of one subject was not good enough. Bo checked his results and redid the processing, and found the reason of the problem. <br />[http://www.na-mic.org/Wiki/index.php/2011_Winter_Project_Week:Extension_of_ABC_to_detect_pathology_categories Webpage of this event]
 = Literature =

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 === Conclusion ===
-In this work, we will develop new methodologies and tools for user-guided segmentation of cerebral lesions in multi-modal brain MRI. Driving application is TBI imaging research as conducted by the NA-MIC DBP partner UCLA. Components to be included will be robust clustering as presented in [6], initialization of multi-modal intensity patterns via prior knowledge [6], and evaluation of generative models as presented in [4] and [5]. Developments will also include efficient user-guidance for localization and characterization of subject-specific lesion patterns, and tools to provide quantitative measurements and indices of spatial extent of pathologies currently used in clinical assessment. We will evaluate extension of the commonly used indices derived from 2D images to 3D shape features.
+In this work, we will develop new methodologies and tools for user-guided segmentation of cerebral lesions in multi-modal brain MRI. Driving application is TBI imaging research as conducted by the NA-MIC DBP partner UCLA. Components to be included will be robust clustering as presented in [8], initialization of multi-modal intensity patterns via prior knowledge [6], and evaluation of generative models as presented in [6] and [7]. Developments will also include efficient user-guidance for localization and characterization of subject-specific lesion patterns, and tools to provide quantitative measurements and indices of spatial extent of pathologies currently used in clinical assessment. We will evaluate extension of the commonly used indices derived from 2D images to 3D shape features.
 = Collaboration events =