2008 Progress Report NIH QnA - Revision history

Kikinis: /* Ross Whitaker */

2008-07-31T11:17:45Z

Ross Whitaker

Kikinis: /* Ross Whitaker */

2008-07-31T11:17:14Z

Ross Whitaker

Will: /* Will Schroeder */

2008-07-30T21:08:49Z

Will Schroeder

Will: /* Will Schroeder */

2008-07-30T21:00:05Z

Will Schroeder

Will: /* Will Schroeder */

2008-07-30T20:56:32Z

Will Schroeder

Nhageman: /* UCLA Response (Arthur Toga) */

2008-07-30T19:34:55Z

UCLA Response (Arthur Toga)

Jgrethe: /* UCSD (Jeff Grethe) */

2008-07-30T18:03:26Z

UCSD (Jeff Grethe)

Hjbockholt: /* Mind Response (Jeremy Bockholt) */

2008-07-30T18:02:35Z

Mind Response (Jeremy Bockholt)

Jgrethe: /* UCSD (Jeff Grethe) */

2008-07-30T17:56:09Z

UCSD (Jeff Grethe)

RandyGollub: /* Training Core (Randy Gollub) */

2008-07-30T17:05:29Z

Training Core (Randy Gollub)

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 ====Ross Whitaker====
-Certain tasks have been removed from the Utah aims because they have been "subsumed by Core 1-2 partners", presumably MGH. Now that the plans have changed so that MGH no longer plans to do this work, this needs to be updated.
+*Certain tasks have been removed from the Utah aims because they have been "subsumed by Core 1-2 partners", presumably MGH. Now that the plans have changed so that MGH no longer plans to do this work, this needs to be updated.
 '''Reponse:''' The work for head tissue classification was based on the paper "MRI Tissue Classification with Neighborhood Statistics: A Nonparametric, Entropy-Minimizing Approach" by Tasdizen et al. in MICCAI 2005.  This was implemented in ITK and was the first tissue classification algorithm in the ITK toolkit (as far as we know).  The EM-segmenter work, which came out of MIT and Harvard, did not use learned neighborhood statistics, but used probabilistic atlases more effectively.  This is now in ITK, and is undergoing continuous improvements and updates.  It works sufficiently well that further engineering of the "Neighborhood Statistics" approach, from Utah, is probably not going to have an impact on the DBPs and is not an effective use of NAMIC resources.

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 Certain tasks have been removed from the Utah aims because they have been "subsumed by Core 1-2 partners", presumably MGH. Now that the plans have changed so that MGH no longer plans to do this work, this needs to be updated.
-The work for head tissue classification was based on the paper "MRI Tissue Classification with Neighborhood Statistics: A Nonparametric, Entropy-Minimizing Approach" by Tasdizen et al. in MICCAI 2005.  This was implemented in ITK and was the first tissue classification algorithm in the ITK toolkit (as far as we know).  The EM-segmenter work, which came out of MIT and Harvard, did not use learned neighborhood statistics, but used probabilistic atlases more effectively.  This is now in ITK, and is undergoing continuous improvements and updates.  It works sufficiently well that further engineering of the "Neighborhood Statistics" approach, from Utah, is probably not going to have an impact on the DBPs and is not an effective use of NAMIC resources.
+'''Reponse:''' The work for head tissue classification was based on the paper "MRI Tissue Classification with Neighborhood Statistics: A Nonparametric, Entropy-Minimizing Approach" by Tasdizen et al. in MICCAI 2005.  This was implemented in ITK and was the first tissue classification algorithm in the ITK toolkit (as far as we know).  The EM-segmenter work, which came out of MIT and Harvard, did not use learned neighborhood statistics, but used probabilistic atlases more effectively.  This is now in ITK, and is undergoing continuous improvements and updates.  It works sufficiently well that further engineering of the "Neighborhood Statistics" approach, from Utah, is probably not going to have an impact on the DBPs and is not an effective use of NAMIC resources.
 ====Will Schroeder====

← Older revision		Revision as of 21:08, 30 July 2008
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	'''Response:''' Yes, there is a progress. We are building a batch processing framework using BatchMake and grid computing tools. Solutions have been demonstrated; however significant work remains to integrate the Slicer modules into the framework in a user-friendly manner.		'''Response:''' Yes, there is a progress. We are building a batch processing framework using BatchMake and grid computing tools. Solutions have been demonstrated; however significant work remains to integrate the Slicer modules into the framework in a user-friendly manner.
		+
		+	As far as the timeline: Kitware still has obligations in year 5 including support and software releases. Based on our current contributions--CMake, CDash, CTest, CPack, KWWidgets, ITK, VTK, BatchMake, Slicer (support for GUI, registration, Slicer modules)--there is plenty to do. For us, improving the way these tools work together (e.g., see paragraph above), and producing solid software releases, is a significant work load, especially given reduced funding levels.

	====Tina Kapur====		====Tina Kapur====

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 *Based on the timeline, Kitware has completed its tasks . Some new tasks are listed in the statement of work and should be entered into the timeline.
-'''Response:'''
+'''Response:''' Yes, there is a progress. We are building a batch processing framework using BatchMake and grid computing tools. Solutions have been demonstrated; however significant work remains to integrate the Slicer modules into the framework in a user-friendly manner.
 ====Tina Kapur====

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 *Has there been progress in the migration from LONI to batchmake? It is not yet listed as complete in the Isomics timeline.
 *Based on the timeline, Kitware has completed its tasks . Some new tasks are listed in the statement of work and should be entered into the timeline.
 ====Tina Kapur====

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 **Timeline information is out of date. It has not been updated to reflect the changes in the statement of work that was agreed upon in August 2007.
 ==UCLA Response ('''Arthur Toga''')==
 *Q1: A paper citing the NAMIC grant that describes our fluid mechanic DTI tractography method has been accepted to IEEE TMI.  It will become available in the NAMIC publications database shortly.
 *Q2: We have updated the timeline based on the most recent NIH statement of work.

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 The report includes no specific information on progress at UCSD in developing and supporting grid computing for NA-MIC.
-'''Response:''' The submitted progress report contains a detailed description of specific information on progress at UCSD in developing and supporting grid computing for NA-MIC, beginning on page 155. The report detailed the progress in the development of a package (GWE) that bridges the gap between biomedical researchers and tools such as Slicer and the Grid (i.e. grid middleware such as Condor, PBS, Torque used to schedule applications on a variety of individual cluster resources).  Nearly 3 pages are spent on the architecture that was developed and an additional 3 pages were devoted to describing how GWE enables access to distributed computational resources through Slicer.  In addition, work continues with further integration of new features in GWE and its integration with Slicer, such as the Chain Module Engine (work that was described as current work in the report) that was a project during the NA-MIC summer project week (http://wiki.na-mic.org/Wiki/index.php/Slicer3:JavaBasedChainCLMsEngine).  In addition, the summer project week also had a dedicated dissemination event and project that featured GWE and details progress on running Slicer3 modules on the SPL cluster in addition to the UCSD cluster (http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:Batch_Processing).  The results of this project detail specific NA-MIC use cases that were enabled by GWE including: 175 cases processed with BSplineDeformableRegistration on the SPL cluster using GWE; 2275 cases processed with BSplineDeformableRegistration on the BIRN cluster using GWE; 16 cases processed with FreeSurfer on the BIRN cluster using GWE.  The project also specified current and future work that continues to enable more processing on distributed resources via GWE and the integration of GWE and BatchMake.
+'''Response:''' The submitted progress report contains a detailed description of specific information on progress at UCSD in developing and supporting grid computing for NA-MIC, beginning on page 155. The report detailed the progress in the development of a package (GWE) that bridges the gap between biomedical researchers and tools such as Slicer and the Grid (i.e. grid middleware such as Condor, PBS, Torque used to schedule applications on a variety of individual cluster resources).  Nearly 3 pages are spent on the architecture that was developed and an additional 3 pages were devoted to describing how GWE enables access to distributed computational resources through Slicer.  In addition, work continues with further integration of new features in GWE and its integration with Slicer, such as the Chain Module Engine (work that was described as current work in the report) that was a project during the NA-MIC summer project week (http://wiki.na-mic.org/Wiki/index.php/Slicer3:JavaBasedChainCLMsEngine).  In addition, the summer project week also had a special GWE session (http://www.na-mic.org/Wiki/index.php/Project_Week_2008_Special_topic_breakout:_GWE) and project that featured GWE and details progress on running Slicer3 modules on the SPL cluster in addition to the UCSD cluster (http://www.na-mic.org/Wiki/index.php/2008_Summer_Project_Week:Batch_Processing).  The results of this project detail specific NA-MIC use cases that were enabled by GWE including: 175 cases processed with BSplineDeformableRegistration on the SPL cluster using GWE; 2275 cases processed with BSplineDeformableRegistration on the BIRN cluster using GWE; 16 cases processed with FreeSurfer on the BIRN cluster using GWE.  The project also specified current and future work that continues to enable more processing on distributed resources via GWE and the integration of GWE and BatchMake.
 ===Training Core ('''Randy Gollub''')===

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 **Has manual segmentation (which is serving as the gold standard for this project) been shown to have low inter-observer variability?
 ===Mind Response ('''Jeremy Bockholt''')===
 ==Structural Image Analysis==

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 ===UCSD ('''Jeff Grethe''')===
 The report includes no specific information on progress at UCSD in developing and supporting grid computing for NA-MIC.
 ===Training Core ('''Randy Gollub''')===
 Please tell us a bit more about the training core's program to provide one-on-one mentoring (it's mentioned in the timeline , but there's no information on the Wiki). How is it structured? Who can be mentored? How does one arrange for mentorship?<br>