NAMIC Wiki - User contributions [en]

2013 Progress Report

2013-02-03T14:47:46Z

Ann Adams: /* Reporting Interval */

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

==Administrative Paperwork Timeline==

*3/7/2013: LOI goes to subs (Rachana)
*4/4/2013: Signed Subcontractor's Documents due back to BWH (Rachana)
*4/8/2013: Review by Radiology Administration (Trey/Jean)
*4/12/2013: Review by BWH Research Admin
*4/29/2013: Signed Facepage and budget docs due back to Katie M for page numbering (Katie)
*4/30/2013: Ship it to NIH

==Scientific Report Timeline==
*10/13/2012: wiki page setup for progress report (Ann)
*03/10/2013: all sections to be completed by owners
*03/15/2013: check NIH compliance of all publications in Pubmed (Katie)
*04/01/2013: create final report (Ann)
*04/15/2013: Update web pages with any new materials from report (Ann)
*04/15/2013: create full publications list (Katie)
*04/25/2013: final review (Tina, Ron)
*04/26/2013: final pdf created and submitted to Rachana (Katie)

==Reporting Interval==
7/1/2012 - 6/30/2013

==New Reporting Metrics for the Annual Progress Report==

*[[Media:Faculty_Information_Fields.v3.docx| Template for Reporting Faculty Metrics]]
*[[Media:NA-MIC_Personnel_Roster.xls | NA-MIC Personnel Roster]]

==Other Reporting Requirements==

*[[Media:1A_Center_Summary_Table.docx | Center Summary Table]]

==Scientific Progress Report==
*[[Media:Progress_Report_Template_National_Centers_for_Biomedical_Computing_2.1.docx | New Progress Report Template]]
*[[Media:NA-MIC_IMPACT_STATEMENT.pdf | NA-MIC IMPACT STATEMENT 2012]]
*[[Wiki_page_for_2013_Progress_Report_Assignments]]‎
*[[Wiki_page_for_2013_Preliminary_Draft]]

2013 Progress Report

2013-02-03T14:47:17Z

Ann Adams: /* Scientific Report Timeline */

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

==Administrative Paperwork Timeline==

*3/7/2013: LOI goes to subs (Rachana)
*4/4/2013: Signed Subcontractor's Documents due back to BWH (Rachana)
*4/8/2013: Review by Radiology Administration (Trey/Jean)
*4/12/2013: Review by BWH Research Admin
*4/29/2013: Signed Facepage and budget docs due back to Katie M for page numbering (Katie)
*4/30/2013: Ship it to NIH

==Scientific Report Timeline==
*10/13/2012: wiki page setup for progress report (Ann)
*03/10/2013: all sections to be completed by owners
*03/15/2013: check NIH compliance of all publications in Pubmed (Katie)
*04/01/2013: create final report (Ann)
*04/15/2013: Update web pages with any new materials from report (Ann)
*04/15/2013: create full publications list (Katie)
*04/25/2013: final review (Tina, Ron)
*04/26/2013: final pdf created and submitted to Rachana (Katie)

==Reporting Interval==

==New Reporting Metrics for the Annual Progress Report==

*[[Media:Faculty_Information_Fields.v3.docx| Template for Reporting Faculty Metrics]]
*[[Media:NA-MIC_Personnel_Roster.xls | NA-MIC Personnel Roster]]

==Other Reporting Requirements==

*[[Media:1A_Center_Summary_Table.docx | Center Summary Table]]

==Scientific Progress Report==
*[[Media:Progress_Report_Template_National_Centers_for_Biomedical_Computing_2.1.docx | New Progress Report Template]]
*[[Media:NA-MIC_IMPACT_STATEMENT.pdf | NA-MIC IMPACT STATEMENT 2012]]
*[[Wiki_page_for_2013_Progress_Report_Assignments]]‎
*[[Wiki_page_for_2013_Preliminary_Draft]]

2013 Progress Report

2013-01-09T21:38:06Z

Ann Adams: /* Other Reporting Requirements */

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

==Administrative Paperwork Timeline==

*TBA: LOI goes to subs (Sanjay/Rachana)
*TBA: Signed Subcontractor's Documents due back to BWH
*TBA: Review by Radiology Administration (Trey/Susan)
*TBA: Review by BWH RA
*TBA: Signed Facepage and budget docs due back to Katie M for page numbering (Katie)
*4/30/2013: Ship it to NIH

==Scientific Report Timeline==
*10/13/2012: wiki page setup for progress report (Ann)
*TBA: all sections to be completed by owners
*TBA: check NIH compliance of all publications in Pubmed (Katie)
*TBA: create final report (Ann)
*TBA: Update web pages with any new materials from report (Ann)
*TBA: create full publications list (Katie)
*TBA: final review (Tina, Ron)
*TBA: final pdf created and submitted to Rachana (Katie)
==New Reporting Metrics for the Annual Progress Report==

*[[Media:Faculty_Information_Fields.v3.docx| Template for Reporting Faculty Metrics]]
*[[Media:NA-MIC_Personnel_Roster.xls | NA-MIC Personnel Roster]]

==Other Reporting Requirements==

*[[Media:1A_Center_Summary_Table.docx | Center Summary Table]]

==Scientific Progress Report==
*[[Media:Progress_Report_Template_National_Centers_for_Biomedical_Computing_2.1.docx | New Progress Report Template]]
*[[Media:NA-MIC_IMPACT_STATEMENT.pdf | NA-MIC IMPACT STATEMENT 2012]]
*[[Wiki_page_for_2013_Progress_Report_Assignments]]‎
*[[Wiki_page_for_2013_Preliminary_Draft]]

2013 Progress Report

2013-01-09T21:37:38Z

Ann Adams: /* Set One Metrics */

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

==Administrative Paperwork Timeline==

*TBA: LOI goes to subs (Sanjay/Rachana)
*TBA: Signed Subcontractor's Documents due back to BWH
*TBA: Review by Radiology Administration (Trey/Susan)
*TBA: Review by BWH RA
*TBA: Signed Facepage and budget docs due back to Katie M for page numbering (Katie)
*4/30/2013: Ship it to NIH

==Scientific Report Timeline==
*10/13/2012: wiki page setup for progress report (Ann)
*TBA: all sections to be completed by owners
*TBA: check NIH compliance of all publications in Pubmed (Katie)
*TBA: create final report (Ann)
*TBA: Update web pages with any new materials from report (Ann)
*TBA: create full publications list (Katie)
*TBA: final review (Tina, Ron)
*TBA: final pdf created and submitted to Rachana (Katie)
==New Reporting Metrics for the Annual Progress Report==

*[[Media:Faculty_Information_Fields.v3.docx| Template for Reporting Faculty Metrics]]
*[[Media:NA-MIC_Personnel_Roster.xls | NA-MIC Personnel Roster]]

==Other Reporting Requirements==

*[[Media:1A_Center_Summary_Table.docx]]
==Scientific Progress Report==
*[[Media:Progress_Report_Template_National_Centers_for_Biomedical_Computing_2.1.docx | New Progress Report Template]]
*[[Media:NA-MIC_IMPACT_STATEMENT.pdf | NA-MIC IMPACT STATEMENT 2012]]
*[[Wiki_page_for_2013_Progress_Report_Assignments]]‎
*[[Wiki_page_for_2013_Preliminary_Draft]]

File:1A Center Summary Table.docx

2013-01-09T21:34:37Z

Ann Adams:

2013 Progress Report

2013-01-09T21:34:06Z

Ann Adams: /* Set One Metrics */

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

==Administrative Paperwork Timeline==

*TBA: LOI goes to subs (Sanjay/Rachana)
*TBA: Signed Subcontractor's Documents due back to BWH
*TBA: Review by Radiology Administration (Trey/Susan)
*TBA: Review by BWH RA
*TBA: Signed Facepage and budget docs due back to Katie M for page numbering (Katie)
*4/30/2013: Ship it to NIH

==Scientific Report Timeline==
*10/13/2012: wiki page setup for progress report (Ann)
*TBA: all sections to be completed by owners
*TBA: check NIH compliance of all publications in Pubmed (Katie)
*TBA: create final report (Ann)
*TBA: Update web pages with any new materials from report (Ann)
*TBA: create full publications list (Katie)
*TBA: final review (Tina, Ron)
*TBA: final pdf created and submitted to Rachana (Katie)
==New Reporting Metrics for the Annual Progress Report==

=Set One Metrics=

*[[Media:Faculty_Information_Fields.v3.docx| Template for Reporting Faculty Metrics]]
*[[Media:NA-MIC_Personnel_Roster.xls | NA-MIC Personnel Roster]]

==Scientific Progress Report==
*[[Media:Progress_Report_Template_National_Centers_for_Biomedical_Computing_2.1.docx | New Progress Report Template]]
*[[Media:NA-MIC_IMPACT_STATEMENT.pdf | NA-MIC IMPACT STATEMENT 2012]]
*[[Wiki_page_for_2013_Progress_Report_Assignments]]‎
*[[Wiki_page_for_2013_Preliminary_Draft]]

2013 Progress Report

2013-01-09T21:19:20Z

Ann Adams: /* New Reporting Metrics for the Annual Progress Report */

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

==Administrative Paperwork Timeline==

*TBA: LOI goes to subs (Sanjay/Rachana)
*TBA: Signed Subcontractor's Documents due back to BWH
*TBA: Review by Radiology Administration (Trey/Susan)
*TBA: Review by BWH RA
*TBA: Signed Facepage and budget docs due back to Katie M for page numbering (Katie)
*4/30/2013: Ship it to NIH

==Scientific Report Timeline==
*10/13/2012: wiki page setup for progress report (Ann)
*TBA: all sections to be completed by owners
*TBA: check NIH compliance of all publications in Pubmed (Katie)
*TBA: create final report (Ann)
*TBA: Update web pages with any new materials from report (Ann)
*TBA: create full publications list (Katie)
*TBA: final review (Tina, Ron)
*TBA: final pdf created and submitted to Rachana (Katie)
==New Reporting Metrics for the Annual Progress Report==

=Set One Metrics=

*[[Media:Faculty_Information_Fields.v3.docx| 1B_Template for Reporting Faculty Metrics]]
*[[Media:NA-MIC_Personnel_Roster.xls | NA-MIC Personnel Roster]]

==Scientific Progress Report==
*[[Media:Progress_Report_Template_National_Centers_for_Biomedical_Computing_2.1.docx | New Progress Report Template]]
*[[Media:NA-MIC_IMPACT_STATEMENT.pdf | NA-MIC IMPACT STATEMENT 2012]]
*[[Wiki_page_for_2013_Progress_Report_Assignments]]‎
*[[Wiki_page_for_2013_Preliminary_Draft]]

2013 Progress Report

2013-01-09T21:18:05Z

Ann Adams: /* Faculty Narratives for Annual Progress Report */

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

==Administrative Paperwork Timeline==

*TBA: LOI goes to subs (Sanjay/Rachana)
*TBA: Signed Subcontractor's Documents due back to BWH
*TBA: Review by Radiology Administration (Trey/Susan)
*TBA: Review by BWH RA
*TBA: Signed Facepage and budget docs due back to Katie M for page numbering (Katie)
*4/30/2013: Ship it to NIH

==Scientific Report Timeline==
*10/13/2012: wiki page setup for progress report (Ann)
*TBA: all sections to be completed by owners
*TBA: check NIH compliance of all publications in Pubmed (Katie)
*TBA: create final report (Ann)
*TBA: Update web pages with any new materials from report (Ann)
*TBA: create full publications list (Katie)
*TBA: final review (Tina, Ron)
*TBA: final pdf created and submitted to Rachana (Katie)
==New Reporting Metrics for the Annual Progress Report==

*[[Media:Faculty_Information_Fields.v3.docx| 1B_Template for Reporting Faculty Metrics]]
*[[Media:NA-MIC_Personnel_Roster.xls | NA-MIC Personnel Roster]]

==Scientific Progress Report==
*[[Media:Progress_Report_Template_National_Centers_for_Biomedical_Computing_2.1.docx | New Progress Report Template]]
*[[Media:NA-MIC_IMPACT_STATEMENT.pdf | NA-MIC IMPACT STATEMENT 2012]]
*[[Wiki_page_for_2013_Progress_Report_Assignments]]‎
*[[Wiki_page_for_2013_Preliminary_Draft]]

2013 Progress Report

2013-01-09T21:15:06Z

Ann Adams: /* Faculty Narratives for Annual Progress Report */

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

==Administrative Paperwork Timeline==

*TBA: LOI goes to subs (Sanjay/Rachana)
*TBA: Signed Subcontractor's Documents due back to BWH
*TBA: Review by Radiology Administration (Trey/Susan)
*TBA: Review by BWH RA
*TBA: Signed Facepage and budget docs due back to Katie M for page numbering (Katie)
*4/30/2013: Ship it to NIH

==Scientific Report Timeline==
*10/13/2012: wiki page setup for progress report (Ann)
*TBA: all sections to be completed by owners
*TBA: check NIH compliance of all publications in Pubmed (Katie)
*TBA: create final report (Ann)
*TBA: Update web pages with any new materials from report (Ann)
*TBA: create full publications list (Katie)
*TBA: final review (Tina, Ron)
*TBA: final pdf created and submitted to Rachana (Katie)
==Faculty Narratives for Annual Progress Report==

*[[Media:Faculty_Information_Fields.v3.docx| Template for Reporting Faculty Metrics]]
*[[Media:NA-MIC_Personnel_Roster.xls | NA-MIC Personnel Roster]]

==Scientific Progress Report==
*[[Media:Progress_Report_Template_National_Centers_for_Biomedical_Computing_2.1.docx | New Progress Report Template]]
*[[Media:NA-MIC_IMPACT_STATEMENT.pdf | NA-MIC IMPACT STATEMENT 2012]]
*[[Wiki_page_for_2013_Progress_Report_Assignments]]‎
*[[Wiki_page_for_2013_Preliminary_Draft]]

File:Faculty Information Fields.v3.docx

2013-01-09T21:14:43Z

Ann Adams:

2013 Progress Report

2013-01-09T21:04:12Z

Ann Adams: /* Faculty Narratives for Annual Progress Report */

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

==Administrative Paperwork Timeline==

*TBA: LOI goes to subs (Sanjay/Rachana)
*TBA: Signed Subcontractor's Documents due back to BWH
*TBA: Review by Radiology Administration (Trey/Susan)
*TBA: Review by BWH RA
*TBA: Signed Facepage and budget docs due back to Katie M for page numbering (Katie)
*4/30/2013: Ship it to NIH

==Scientific Report Timeline==
*10/13/2012: wiki page setup for progress report (Ann)
*TBA: all sections to be completed by owners
*TBA: check NIH compliance of all publications in Pubmed (Katie)
*TBA: create final report (Ann)
*TBA: Update web pages with any new materials from report (Ann)
*TBA: create full publications list (Katie)
*TBA: final review (Tina, Ron)
*TBA: final pdf created and submitted to Rachana (Katie)
==Faculty Narratives for Annual Progress Report==

*[[Media:Faculty_Information_Fields.v2.docx| Template for Reporting Faculty Metrics]]
*[[Media:NA-MIC_Personnel_Roster.xls | NA-MIC Personnel Roster]]

==Scientific Progress Report==
*[[Media:Progress_Report_Template_National_Centers_for_Biomedical_Computing_2.1.docx | New Progress Report Template]]
*[[Media:NA-MIC_IMPACT_STATEMENT.pdf | NA-MIC IMPACT STATEMENT 2012]]
*[[Wiki_page_for_2013_Progress_Report_Assignments]]‎
*[[Wiki_page_for_2013_Preliminary_Draft]]

File:Faculty Information Fields.v2.docx

2013-01-09T21:03:39Z

Ann Adams:

2013 Progress Report

2013-01-09T21:02:25Z

Ann Adams: /* Faculty Narratives for Annual Progress Report */

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

==Administrative Paperwork Timeline==

*TBA: LOI goes to subs (Sanjay/Rachana)
*TBA: Signed Subcontractor's Documents due back to BWH
*TBA: Review by Radiology Administration (Trey/Susan)
*TBA: Review by BWH RA
*TBA: Signed Facepage and budget docs due back to Katie M for page numbering (Katie)
*4/30/2013: Ship it to NIH

==Scientific Report Timeline==
*10/13/2012: wiki page setup for progress report (Ann)
*TBA: all sections to be completed by owners
*TBA: check NIH compliance of all publications in Pubmed (Katie)
*TBA: create final report (Ann)
*TBA: Update web pages with any new materials from report (Ann)
*TBA: create full publications list (Katie)
*TBA: final review (Tina, Ron)
*TBA: final pdf created and submitted to Rachana (Katie)
==Faculty Narratives for Annual Progress Report==

*[[Media:Faculty_Information_Fields.docx| Template for Reporting Faculty Metrics]]
*[[Media:NA-MIC_Personnel_Roster.xls | NA-MIC Personnel Roster]]

==Scientific Progress Report==
*[[Media:Progress_Report_Template_National_Centers_for_Biomedical_Computing_2.1.docx | New Progress Report Template]]
*[[Media:NA-MIC_IMPACT_STATEMENT.pdf | NA-MIC IMPACT STATEMENT 2012]]
*[[Wiki_page_for_2013_Progress_Report_Assignments]]‎
*[[Wiki_page_for_2013_Preliminary_Draft]]

File:Faculty Information Fields.docx

2013-01-09T21:00:50Z

Ann Adams: uploaded a new version of "File:Faculty Information Fields.docx"

2013 Progress Report

2013-01-09T20:52:55Z

Ann Adams: /* Faculty Narratives for Annual Progress Report */

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

==Administrative Paperwork Timeline==

*TBA: LOI goes to subs (Sanjay/Rachana)
*TBA: Signed Subcontractor's Documents due back to BWH
*TBA: Review by Radiology Administration (Trey/Susan)
*TBA: Review by BWH RA
*TBA: Signed Facepage and budget docs due back to Katie M for page numbering (Katie)
*4/30/2013: Ship it to NIH

==Scientific Report Timeline==
*10/13/2012: wiki page setup for progress report (Ann)
*TBA: all sections to be completed by owners
*TBA: check NIH compliance of all publications in Pubmed (Katie)
*TBA: create final report (Ann)
*TBA: Update web pages with any new materials from report (Ann)
*TBA: create full publications list (Katie)
*TBA: final review (Tina, Ron)
*TBA: final pdf created and submitted to Rachana (Katie)
==Faculty Narratives for Annual Progress Report==

*[[Media:Faculty_Information_Fields.docx | Template for Reporting Faculty Metrics]]
*[[Media:NA-MIC_Personnel_Roster.xls | NA-MIC Personnel Roster]]

==Scientific Progress Report==
*[[Media:Progress_Report_Template_National_Centers_for_Biomedical_Computing_2.1.docx | New Progress Report Template]]
*[[Media:NA-MIC_IMPACT_STATEMENT.pdf | NA-MIC IMPACT STATEMENT 2012]]
*[[Wiki_page_for_2013_Progress_Report_Assignments]]‎
*[[Wiki_page_for_2013_Preliminary_Draft]]

2013 Progress Report

2013-01-09T20:52:37Z

Ann Adams: /* Scientific Progress Report */

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

==Administrative Paperwork Timeline==

*TBA: LOI goes to subs (Sanjay/Rachana)
*TBA: Signed Subcontractor's Documents due back to BWH
*TBA: Review by Radiology Administration (Trey/Susan)
*TBA: Review by BWH RA
*TBA: Signed Facepage and budget docs due back to Katie M for page numbering (Katie)
*4/30/2013: Ship it to NIH

==Scientific Report Timeline==
*10/13/2012: wiki page setup for progress report (Ann)
*TBA: all sections to be completed by owners
*TBA: check NIH compliance of all publications in Pubmed (Katie)
*TBA: create final report (Ann)
*TBA: Update web pages with any new materials from report (Ann)
*TBA: create full publications list (Katie)
*TBA: final review (Tina, Ron)
*TBA: final pdf created and submitted to Rachana (Katie)
==Faculty Narratives for Annual Progress Report==

*[[Media:Faculty_Information_Fields.docx | Template for reporting Faculty Metrics]]
*[[Media:NA-MIC_Personnel_Roster.xls | NA-MIC Personnel Roster]]

==Scientific Progress Report==
*[[Media:Progress_Report_Template_National_Centers_for_Biomedical_Computing_2.1.docx | New Progress Report Template]]
*[[Media:NA-MIC_IMPACT_STATEMENT.pdf | NA-MIC IMPACT STATEMENT 2012]]
*[[Wiki_page_for_2013_Progress_Report_Assignments]]‎
*[[Wiki_page_for_2013_Preliminary_Draft]]

File:NA-MIC Personnel Roster.xls

2013-01-09T20:50:54Z

Ann Adams:

2013 Progress Report

2013-01-09T20:49:31Z

Ann Adams: /* Scientific Progress Report */

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

==Administrative Paperwork Timeline==

*TBA: LOI goes to subs (Sanjay/Rachana)
*TBA: Signed Subcontractor's Documents due back to BWH
*TBA: Review by Radiology Administration (Trey/Susan)
*TBA: Review by BWH RA
*TBA: Signed Facepage and budget docs due back to Katie M for page numbering (Katie)
*4/30/2013: Ship it to NIH

==Scientific Report Timeline==
*10/13/2012: wiki page setup for progress report (Ann)
*TBA: all sections to be completed by owners
*TBA: check NIH compliance of all publications in Pubmed (Katie)
*TBA: create final report (Ann)
*TBA: Update web pages with any new materials from report (Ann)
*TBA: create full publications list (Katie)
*TBA: final review (Tina, Ron)
*TBA: final pdf created and submitted to Rachana (Katie)
==Scientific Progress Report==

*[[Media:Faculty_Information_Fields.docx | Template for reporting Faculty Metrics]]
*[[Media:Progress_Report_Template_National_Centers_for_Biomedical_Computing_2.1.docx | New Progress Report Template]]
*[[Media:NA-MIC_IMPACT_STATEMENT.pdf | NA-MIC IMPACT STATEMENT 2012]]
*[[Wiki_page_for_2013_Progress_Report_Assignments]]‎
*[[Wiki_page_for_2013_Preliminary_Draft]]

2013 Progress Report

2013-01-09T20:49:11Z

Ann Adams: /* Scientific Progress Report */

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

==Administrative Paperwork Timeline==

*TBA: LOI goes to subs (Sanjay/Rachana)
*TBA: Signed Subcontractor's Documents due back to BWH
*TBA: Review by Radiology Administration (Trey/Susan)
*TBA: Review by BWH RA
*TBA: Signed Facepage and budget docs due back to Katie M for page numbering (Katie)
*4/30/2013: Ship it to NIH

==Scientific Report Timeline==
*10/13/2012: wiki page setup for progress report (Ann)
*TBA: all sections to be completed by owners
*TBA: check NIH compliance of all publications in Pubmed (Katie)
*TBA: create final report (Ann)
*TBA: Update web pages with any new materials from report (Ann)
*TBA: create full publications list (Katie)
*TBA: final review (Tina, Ron)
*TBA: final pdf created and submitted to Rachana (Katie)
==Scientific Progress Report==

*[[Media:Faculty_Information_Fields.docx | Template for reporting Faculty Metrics
*[[Media:Progress_Report_Template_National_Centers_for_Biomedical_Computing_2.1.docx | New Progress Report Template]]
*[[Media:NA-MIC_IMPACT_STATEMENT.pdf | NA-MIC IMPACT STATEMENT 2012]]
*[[Wiki_page_for_2013_Progress_Report_Assignments]]‎
*[[Wiki_page_for_2013_Preliminary_Draft]]

File:Faculty Information Fields.docx

2013-01-09T20:46:53Z

Ann Adams:

Wiki page for 2013 Preliminary Draft

2012-11-17T16:22:43Z

Ann Adams:

Wiki page for 2013 Preliminary Draft

2012-11-17T15:47:10Z

Ann Adams:

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

Required elements of the New Research Progress Template

1. RESEARCH AND RESOURCE METRICS

1A. Summary of Center Progress

* Brief description of overall objectives of NA-MIC

The National Alliance for Medical Image Computing (NA-MIC) is a multi-institutional, interdisciplinary community of computer scientists, software engineers, and medical investigators who share the common goal
of improving healthcare through the development of computational tools for the analysis and visualization of medical image data. The Center maintains a robust and flexible infrastructure for developing and
applying advanced imaging technologies across a range of important biomedical research disciplines. Our research and development effort is organized around the Computer Science Core, which includes independent teams for Algorithms and Engineering. The Algorithm effort responds to the challenges of the DBPs to expand the horizons of medical image analysis. As a result, the Algorithm activities are typically highly experimental, creating new approaches that are rapidly prototyped, tested, and improved. The Engineering effort supports the needs of the Algorithms effort by creating integrated software platforms that support research and eventual deployment of advanced technology. The Engineering team also develops and maintains processes used to build and sustain a large research
community. A separate Core oversees operations and maintenance of The NA-MIC Kit, an integrated set of interoperable free open source software (FOSS)
packages; developed, supported and deployed using a collaborative, agile, high quality software process. NA-MIC's current DBPs are investigating solutions to problems in patient-specific data analysis in four clinical areas: Atrial Fibrillation, Huntingdon's Disease, Adaptive Radiotherapy for Head and Neck Cancer, and Traumatic Brain Injury. NA-MIC further provides enabling technology and resources to XX collaborative research projects.

* Brief outline indicating strengths of NA-MIC as a national resource
[take from NA-MIC impact statement, August 2012]

NA-MIC takes seriously the responsibility of representing US medical imaging software development activities in the
national and international community. Through our collaborations and outreach programs, we have mobilized like-minded
scientists to contribute to open source software development for biomedical image analysis. Attracted to the concept of
sharing software development resources, leading international groups have adopted NA-MIC’s engineering framework in
lieu of undertaking the costly and redundant option of developing their own. These collaborative efforts have greatly raised
awareness of the benefits of open science, and as a result, government-funded efforts that complement NA-MIC are now
in place in Canada, Germany, Spain, France, and Italy.

* Summarize progress made in each Research and Core Project.

Algorithms. The NA-MIC Computer Science Algorithm effort responds to the challenges of the DBPs to
expand the horizons of medical image analysis. As a result, the Algorithm activities are typically highly
experimental, creating new approaches that are rapidly prototyped, tested, and improved.

Engineering. The NA-MIC Computer Science Engineering effort supports the needs of the Algorithms effort by
creating integrated software platforms that support research and eventual deployment of advanced technology.
The Engineering team also develops and maintains processes used to build and sustain a large research
community.

NA-MIC Kit. The NA-MIC Kit consists of an integrated set of interoperable free open source software (FOSS)
packages; developed, supported and deployed using a collaborative, agile, high quality software process. The
NA-MIC Kit has been constructed as a layered architecture to provide a spectrum of capabilities, ranging from
compute-intensive algorithms to easy-to-use applications. Hence users and developers can choose to engage
the NA-MIC Kit at a variety of levels, including developing extensions which can be readily deployed to the
broader biomedical imaging community.

In the following subsections we highlight the accomplishments from this reporting period for algorithms,
engineering, and NA-MIC Kit.

2.1. Algorithms
The Algorithms team develops computational methods that support patient-specific analysis of medical
images. This effort requires analysis of images that vary significantly from one patient to another, or from one
time point to another, presenting distinct challenges to existing state-of-art medical image analysis algorithms.
These technical challenges are addressed using four computational approaches: (1) Statistical models of
anatomy and pathology; (2) Geometric correspondence; (3) User interactive tools for segmentation; and (4)
Longitudinal and time-series analysis. Highlights of these efforts are described in the following sections.

'''Statistical models of anatomy and pathology.''' ''Polina Golland--Please update this section with current progress.''

A great deal of progress has been made by using modeling approaches that systematically capture the statistics of a problem domain from a collection of examples and
then use these statistics to interpret novel images. Some of the approaches include the following:

 Non-Parametric Priors for Segmentation are based on nonparametric, probabilistic models for the
automatic segmentation of medical images, given a training set of images and corresponding label
maps. The resulting inference algorithms rely on pairwise registrations between the test image and
individual training images. The training labels are then transferred to the test image and fused to
compute the final segmentation of the test subject.

 Fast Nearest-Neighbor Lookup in Large Image Databases has been found to improve segmentation
quality. Multi-atlases or nonparametric atlas-based techniques for image segmentation require
registration of a test image with a small set of very similar images from a database.

 Atlases and Registration for DTI Processing are novel methods that enhance the co-registration of DTI
data either to a prior image of the same subject or to an existing atlas with predefined fiber tracts or
regional white matter parcellation. These are applied in cases of large brain pathology (e.g., TBI).
Geometric correspondence. Establishing anatomical correspondences between pairs of patients, groups of
patients, patients and templates, and individual patients over time is important for automatic and user-assisted
image analysis. The ability to establish geometric correspondences, with and without expert guidance, in
challenging clinical circumstances is essential for the DBPs. Progress in two areas was realized this year.

 Stochastic Point Set Registration provides non-rigid point set registration algorithms that seek an optimal
set of radial basis functions to describe the registration. Preliminary results on 2D and 3D data
demonstrate the algorithms' robustness to datasets with noise and with missing information.
 Automatic Correspondences For Shape Ensembles has seen improvements in robustness of our
entropy-based correspondence system. For example, we have developed a method for particles to
interact on surfaces using geodesic distances, which improves the behavior of the system on sharp
features or convoluted shapes.

User interactive tools for segmentation. The work performed in the past year addresses important aspects
of user-interactive segmentation. The patient-specific analysis required by the DBPs has presented images of
patients with pathologies and/or injuries that sometimes defy automated approaches. We have focused our
research on three principal areas.
 Control-Based Interactive Segmentation is a novel contribution based on a modeling formulation that
represents interactive segmentation as a feedback system, enabling a principled merging of automated
methods and user input.
 Globally Optimal Segmentation is a set of methods that rely on global optimization of energy functions via
graph cuts. Results on delayed contrast MRI from the Atrial Fibrillation project are quite promising, and
this work is currently under review for publication.
 Patient-Specific Segmentation Framework for Longitudinal MR Images of Traumatic Brain Injury
addresses the need for robust, reproducible segmentations of MR images of TBI and is crucial for
quantitative analysis of recovery and treatment efficacy. Validation of this new automatic segmentation
compared to expert segmentations of acute and chronic images was provided on 3 longitudinal TBI
datasets, demonstrating that joint segmentation of 4D multi-time point data is superior to individual
segmentations.
Longitudinal and time-series analysis. An important component of patient-specific data analysis is the ability
to analyze multiple images from the same patient over time as a disease or injury progresses or responds to
treatment, or to assess neurodevelopment or neurodegeneration. Longitudinal image analysis is important for
all four DBPs in this project; we have focused in the past year on the areas described below.
 Connectivity Changes in Disease demonstrates a novel probabilistic framework to merge information
from diffusion weighted imaging tractography and resting-state functional magnetic resonance imaging
correlations to identify connectivity patterns in the brain. The method simultaneously infers the templates
of latent connectivity for each population and the differences in connectivity between the groups.
 Modeling Pathology Evolution is used in brain tumor patients to monitor the state of disease and to
evaluate therapeutic options. This work investigated a joint generative model of tumor growth and of
image observation that naturally handles multimodal and longitudinal data, important for TBI.
 Longitudinal Analysis of DTI Change Trajectories develops models that represent the growth trajectories
of individual subjects to study and understand white matter changes in neurodevelopment,
neurodegeneration, and disease progress. Application of this methodology to study early brain
development in a longitudinal neuroimaging study, including validation of reproducibility, has been
shown.
 Analysis of Longitudinal Shape Variability via Subject-Specific Growth Modeling are statistical analyses of
longitudinal imaging data which are crucial for understanding normal anatomical development as well as
disease progression. We have developed a new type of growth model parameterized by acceleration,
whereas standard methods typically control the velocity. This mimics the behavior of biological tissue;
cross validation experiments show that our method is robust to missing observations, is less sensitive to
noise, and is therefore more likely to capture the underlying biological growth.
 Longitudinal and Time Series Analysis are novel methods for longitudinal registration and time series
regression. These methods enable compact approximation of an image time-series through an initial
image and an initial momentum, resulting in dramatically simplified computations.
2.2 Engineering
The Engineering Team builds bridges between the various NA-MIC cores and ultimately to the wider
biomedical computing community. Working with the Algorithms Team, it deploys leading edge biomedical
computing tools back to the DBPs, which are then used to perform impactful health research. In addition, the
tools developed by the Engineering Team are used to train and disseminate technologies across the research
community. The Team places particular focus on developing sustainable communities through the creation of
open platforms, quality-inducing software processes, and integration to a broad variety of computational tools
and databases. The following describes some of the highlights of the past year's work.
The flagship product from the Engineering Team is the 3D Slicer application. It is the delivery platform for much
current work, and it is an enabling technology for the wider biomedical computing community. This past year
saw the release of Slicer version 4.0 (Slicer4) which represents a significant advance in capabilities and
underlying technologies. Since its release at RSNA in November, Slicer4 has been downloaded over 45,000
times, at a rate of over 100 downloads per day, from users and research groups located around the world.
Slicer4 is now a modern, stable platform built with the Qt GUI system (eliminated the previous KWWidgets
GUI), and rewritten for simplicity, enabling simpler approaches to debugging, faster startup, and more
responsive behavior.
Beyond the core Slicer4 platform, several important features were also added to the application. These
include:
 The Slicer Extension Manager is now called the "Slicer Catalog" (an App Store) and will enable the
community to create compact modules which extend the core functionality.
 Python has been adopted as the preferred scripting language, a preferred programming language in
the scientific computing community. Hence a variety of computational packages are now available to
extend Slicer capabilities at run-time.
 Slicer4 includes a DICOM listener and DICOM Query/Retrieve capabilities for integration with standard
clinical image management environments and workflows.
 Compatibility with ITK version 4 was developed and continuously maintained over the past year as
ITKv4 matured. Slicer will officially switch to ITKv4 in the coming months.
 Slicer Execution Model modules (also known as Command Line Modules) are now available as Nipype
tools, enabling local and distributed scripted execution of processing pipelines. Such methods for
distributed computing are essential to tackling the Big Data and complex algorithms that current
research is producing.
 Finally, a whole host of application improvements have been made including an improved flexible view
layout system; a revised implementation of the Expectation Maximization (EM) Segmenter; faster
hardware-accelerated volume rendering; improved markups and annotations; improved atlas and
model hierarchy support; and a streamlined and revised diffusion MRI implementation.
Community support for NA-MIC and the various NA-MIC Kit tools continues. The goals of this effort are to
transition new technologies to the wider community, to enable community members to contribute back to Slicer
and the NA-MIC Kit, and to ensure high-quality systems. Beyond some of the support activities mentioned
previously, the following are other accomplishments.
 We have begun integrating the SimpleITK module of ITKv4 into Slicer to ensure simple integration
capabilities with emerging algorithms.
 Additional open data support has been added to Slicer such as ultrasound (e.g., video) and 4D (e.g.,
gated CT) data.
 We have integrated the extension writing and the documentation generation processes. The
documentation created when an extension is written is now automatically ported to a web host for
easier access from within and outside of Slicer, ensuring that documentation resources keep up with
the rapid pace of development.
2.3 NA-MIC Kit
The NA-MIC Kit is designed to accelerate the pace of research and facilitate clinical evaluation. Along these
lines, the past year realized significant milestones toward the creation of a stable research platform, supporting
the ability to easily extend and disseminate novel additions, all in the context of a world-wide, broad research
community. Beyond the major highlights related to the Slicer4 application platform described in the previous
section, the following are a few of the highlights of the past year.
 CMake and its associated software process tools (CTest, CDash, and CPack) are used to build, test
and deploy software in a cross-platform manner. CMake continues one of the most well-known pieces
of the NA-MIC Kit, with more than 2,000 known downloads per day (as well as being included by
various Linux distributions). CMake 2.8.7 was released with NA-MIC support.
 CDash Package Manager (CDash 2.0.2) was released with support from NA-MIC. One of the most
significant contributions to CDash from NA-MIC was the package upload process. This process enables
the many Slicer testing machines to upload the executables and packages created during testing to the
main CDash server. This, in turn, allows users to download those testing packages and run additional
tests or use them in their research. This complete automation of the test-release cycle is a massive
time-saver for the Service core and has greatly reduced the time to discover and resolve bugs and to
improve the stability of Slicer.
 Significant data integration efforts were completed over the past year. XNAT was greatly improved in its
usability and interfaces. DICOM support was greatly enhanced, including the ability to embed Slicer
MRML scene files as DICOM lollipops, meaning that Slicer data exchange across the DICOM standard
is now possible. In addition, DCMTK was integrated into the NA-MIC Kit, meaning that DICOM support
and functionality was greatly increased.
 NA-MIC supports and nurtures an extensive biomedical research community. Along these lines it
develops integration tools and interfaces with other communities. CTK, supported by NA-MIC funding,
is one such community and interfaces with other open-source toolkits (e.g., MITK from the German
Cancer Research Center in Heidelberg, XIP from Siemens, GIMIAS from UPF in Spain, and OpenMAF
from U of Bologna). CTK now provides several innovative GUI and DICOM elements that specifically
save GUI space, user-time, and developer effort when building custom medical applications. The NAMIC
Kit also integrated the BRAINSFit system, a collection of programs for registering images with
mutual information based metric. BRAINSFit uses the Slicer execution model framework to define the
command line arguments and is fully integrated with Slicer using the module discovery capabilities.
 Recent developments are in the process of being integrated into the NA-MIC Kit and the Slicer
application platform.
 The Slicer Catalog allows users to install, uninstall, search, browse, and rank Slicer extensions. This
user experience is available from within Slicer and over the web, much like the Android and Apple App
Stores. Developers can contribute, update, document, and post screenshots on their modules and
receive community feedback.
 The analysis infrastructure for Diffusion Weighted MRI (DWI) IO and visualization has been generalized
to be used for other time varying acquisitions like multivolume analysis, dynamic contrast enhanced
MRI (DCE), and gated cardiac CT.
 To cover the use of Qt and newer versions of VTK (both part of the NA-MIC Kit), advanced charting and
analytics options have been demonstrated in Slicer4, and will be fleshed out in the coming year.

* Driving Biological Projects
1The Center worked synergistically with the Driving Biological
Projects (DBPs) to achieve fundamental advances in shape representation, shape analysis, groupwise
registration, diffusion estimation, segmentation and quantification, functional estimation, distortion correction,
and clustering.

* Discuss at least 3 Collaborative Research Projects (these may include collaborating R01/R21s or other projects not directly funded by the Center's NCBC grant, but using Center tools or algorithms in a substantial and enabling manner.

Collaboration 1: TBA
Collaboration 2: TBA
Collaboration 3: TBA

* Brief description of new training and outreach activities conducted during reporting interval (7/1/2012 - 6/30/2013). Provide web-links if available.

Sonia Pujol: Please update and revised. This year NA-MIC hosted XX workshops and courses at national universities and international venues, providing training and
exposure to medical researchers in 3D Slicer and other NA-MIC technologies. NA-MIC also xxxx launched the first
DTI Tractography Challenge for Neurosurgical Planning at the XXth International Conference on Medical Image
Computing and Computer Assisted Intervention (MICCAI 2011) conference in Toronto, Canada, demonstrating
its continued commitment to validation. The purpose of the validation effort is to assess the performance of
NA-MIC algorithms in a variety of settings.

* Impact of Center (i) on biomedical research and research training and outreach at our institution (BWH) and (i) broader scientific community. Institutional benefits might include, organization of special courses and meetings, attraction of students, and faculty participation. Scientific community benefits may include software released, workshops organized, collaborations established, service performed, technology developed, and technology disseminated through patents, publications, peer-reviewed citations of center collaborations by non-center investigators, and personnel trained.

Provide a Center Summary Table

Progress made by innovation and image analysis , and scientific CoresResearch CoresThe scientific development is driven by 4 DBPs. In
addition to activities that sustain the NA-MIC Kit and integrity of the Center’s software infrastructure, NA-MIC
has an impressive outreach program that delivers software, data, and innovative science to the broader biomedical community through its publications and training venues. NA-MIC also has instituted a unique validation effort where software developers and end-users participate in hands-on workshops to measure and improve medical image algorithms.

Required elements:

Finally, this year saw the release of Slicer version 4.0 and 4.1 (Slicer4) which represents a
significant advance in capabilities and underlying technologies. The software was released at RSNA 2011 in
November. As in past years, a detailed presentation of current work was made at the All Hands Meeting in Salt
Lake City, Utah, January 9-13, 2012, and can be viewed in detail on the NA-MIC Wiki [http://wiki.namic.
org/Wiki/index.php/ 2012_Winter_Project_Week].
This represents the 8th Annual Progress Report and second year of the second cycle of funding. The report
includes Highlights and Impact statements, individual progress reports from the four DBPs (Atrial Fibrillation,
Huntington’s Disease, Adaptive Radiotherapy for Head and Neck Cancer, and Traumatic Brain Injury), a
science and technology summary from the Computer Science Core (Algorithms, Engineering, and NA-MIC Kit),
and a review of Training activities, including the validation effort. The report concludes with a bibliography of 33
peer-reviewed journal articles and 21 peer-reviewed conference reports and the annual recommendations of
the External Advisory Board, which met on January 12, 2012 in Salt Lake City, coincident with Winter Project
Week.

Wiki page for 2013 Preliminary Draft

2012-10-13T16:11:54Z

Ann Adams:

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

Required elements of the New Research Progress Template

1. RESEARCH AND RESOURCE METRICS

1A. Summary of Center Progress

* Brief description of overall objectives of NA-MIC

The National Alliance for Medical Image Computing (NA-MIC) is a multi-institutional, interdisciplinary community of computer scientists, software engineers, and medical investigators who share the common goal
of improving healthcare through the development of computational tools for the analysis and visualization of medical image data. The Center maintains a robust and flexible infrastructure for developing and
applying advanced imaging technologies across a range of important biomedical research disciplines. Our research and development effort is organized around the Computer Science Core, which includes independent teams for Algorithms and Engineering. The Algorithm effort responds to the challenges of the DBPs to expand the horizons of medical image analysis. As a result, the Algorithm activities are typically highly experimental, creating new approaches that are rapidly prototyped, tested, and improved. The Engineering effort supports the needs of the Algorithms effort by creating integrated software platforms that support research and eventual deployment of advanced technology. The Engineering team also develops and maintains processes used to build and sustain a large research
community. A separate Core oversees operations and maintenance of The NA-MIC Kit, an integrated set of interoperable free open source software (FOSS)
packages; developed, supported and deployed using a collaborative, agile, high quality software process. NA-MIC's current DBPs are investigating solutions to problems in patient-specific data analysis in four clinical areas: Atrial Fibrillation, Huntingdon's Disease, Adaptive Radiotherapy for Head and Neck Cancer, and Traumatic Brain Injury. NA-MIC further provides enabling technology and resources to XX collaborative research projects.

* Brief outline indicating strengths of NA-MIC as a national resource
[take from NA-MIC impact statement, August 2012]

NA-MIC takes seriously the responsibility of representing US medical imaging software development activities in the
national and international community. Through our collaborations and outreach programs, we have mobilized like-minded
scientists to contribute to open source software development for biomedical image analysis. Attracted to the concept of
sharing software development resources, leading international groups have adopted NA-MIC’s engineering framework in
lieu of undertaking the costly and redundant option of developing their own. These collaborative efforts have greatly raised
awareness of the benefits of open science, and as a result, government-funded efforts that complement NA-MIC are now
in place in Canada, Germany, Spain, France, and Italy.

* Summarize progress made in each Research and Core Project.

Algorithms. The NA-MIC Computer Science Algorithm effort responds to the challenges of the DBPs to
expand the horizons of medical image analysis. As a result, the Algorithm activities are typically highly
experimental, creating new approaches that are rapidly prototyped, tested, and improved.
Engineering. The NA-MIC Computer Science Engineering effort supports the needs of the Algorithms effort by
creating integrated software platforms that support research and eventual deployment of advanced technology.
The Engineering team also develops and maintains processes used to build and sustain a large research
community.
NA-MIC Kit. The NA-MIC Kit consists of an integrated set of interoperable free open source software (FOSS)
packages; developed, supported and deployed using a collaborative, agile, high quality software process. The
NA-MIC Kit has been constructed as a layered architecture to provide a spectrum of capabilities, ranging from
compute-intensive algorithms to easy-to-use applications. Hence users and developers can choose to engage
the NA-MIC Kit at a variety of levels, including developing extensions which can be readily deployed to the
broader biomedical imaging community.
In the following subsections we highlight the accomplishments from this reporting period for algorithms,
engineering, and NA-MIC Kit.
2.1. Algorithms
The Algorithms team develops computational methods that support patient-specific analysis of medical
images. This effort requires analysis of images that vary significantly from one patient to another, or from one
time point to another, presenting distinct challenges to existing state-of-art medical image analysis algorithms.
These technical challenges are addressed using four computational approaches: (1) Statistical models of
anatomy and pathology; (2) Geometric correspondence; (3) User interactive tools for segmentation; and (4)
Longitudinal and time-series analysis. Highlights of these efforts are described in the following sections.
Statistical models of anatomy and pathology. A great deal of progress has been made by using modeling
approaches that systematically capture the statistics of a problem domain from a collection of examples and
then use these statistics to interpret novel images. Some of the approaches include the following:
 Non-Parametric Priors for Segmentation are based on nonparametric, probabilistic models for the
automatic segmentation of medical images, given a training set of images and corresponding label
maps. The resulting inference algorithms rely on pairwise registrations between the test image and
individual training images. The training labels are then transferred to the test image and fused to
compute the final segmentation of the test subject.
 Fast Nearest-Neighbor Lookup in Large Image Databases has been found to improve segmentation
quality. Multi-atlases or nonparametric atlas-based techniques for image segmentation require
registration of a test image with a small set of very similar images from a database.
 Atlases and Registration for DTI Processing are novel methods that enhance the co-registration of DTI
data either to a prior image of the same subject or to an existing atlas with predefined fiber tracts or
regional white matter parcellation. These are applied in cases of large brain pathology (e.g., TBI).
Geometric correspondence. Establishing anatomical correspondences between pairs of patients, groups of
patients, patients and templates, and individual patients over time is important for automatic and user-assisted
image analysis. The ability to establish geometric correspondences, with and without expert guidance, in
challenging clinical circumstances is essential for the DBPs. Progress in two areas was realized this year.
 Stochastic Point Set Registration provides non-rigid point set registration algorithms that seek an optimal
set of radial basis functions to describe the registration. Preliminary results on 2D and 3D data
demonstrate the algorithms' robustness to datasets with noise and with missing information.
 Automatic Correspondences For Shape Ensembles has seen improvements in robustness of our
entropy-based correspondence system. For example, we have developed a method for particles to
interact on surfaces using geodesic distances, which improves the behavior of the system on sharp
features or convoluted shapes.
User interactive tools for segmentation. The work performed in the past year addresses important aspects
of user-interactive segmentation. The patient-specific analysis required by the DBPs has presented images of
patients with pathologies and/or injuries that sometimes defy automated approaches. We have focused our
research on three principal areas.
 Control-Based Interactive Segmentation is a novel contribution based on a modeling formulation that
represents interactive segmentation as a feedback system, enabling a principled merging of automated
methods and user input.
 Globally Optimal Segmentation is a set of methods that rely on global optimization of energy functions via
graph cuts. Results on delayed contrast MRI from the Atrial Fibrillation project are quite promising, and
this work is currently under review for publication.
 Patient-Specific Segmentation Framework for Longitudinal MR Images of Traumatic Brain Injury
addresses the need for robust, reproducible segmentations of MR images of TBI and is crucial for
quantitative analysis of recovery and treatment efficacy. Validation of this new automatic segmentation
compared to expert segmentations of acute and chronic images was provided on 3 longitudinal TBI
datasets, demonstrating that joint segmentation of 4D multi-time point data is superior to individual
segmentations.
Longitudinal and time-series analysis. An important component of patient-specific data analysis is the ability
to analyze multiple images from the same patient over time as a disease or injury progresses or responds to
treatment, or to assess neurodevelopment or neurodegeneration. Longitudinal image analysis is important for
all four DBPs in this project; we have focused in the past year on the areas described below.
 Connectivity Changes in Disease demonstrates a novel probabilistic framework to merge information
from diffusion weighted imaging tractography and resting-state functional magnetic resonance imaging
correlations to identify connectivity patterns in the brain. The method simultaneously infers the templates
of latent connectivity for each population and the differences in connectivity between the groups.
 Modeling Pathology Evolution is used in brain tumor patients to monitor the state of disease and to
evaluate therapeutic options. This work investigated a joint generative model of tumor growth and of
image observation that naturally handles multimodal and longitudinal data, important for TBI.
 Longitudinal Analysis of DTI Change Trajectories develops models that represent the growth trajectories
of individual subjects to study and understand white matter changes in neurodevelopment,
neurodegeneration, and disease progress. Application of this methodology to study early brain
development in a longitudinal neuroimaging study, including validation of reproducibility, has been
shown.
 Analysis of Longitudinal Shape Variability via Subject-Specific Growth Modeling are statistical analyses of
longitudinal imaging data which are crucial for understanding normal anatomical development as well as
disease progression. We have developed a new type of growth model parameterized by acceleration,
whereas standard methods typically control the velocity. This mimics the behavior of biological tissue;
cross validation experiments show that our method is robust to missing observations, is less sensitive to
noise, and is therefore more likely to capture the underlying biological growth.
 Longitudinal and Time Series Analysis are novel methods for longitudinal registration and time series
regression. These methods enable compact approximation of an image time-series through an initial
image and an initial momentum, resulting in dramatically simplified computations.
2.2 Engineering
The Engineering Team builds bridges between the various NA-MIC cores and ultimately to the wider
biomedical computing community. Working with the Algorithms Team, it deploys leading edge biomedical
computing tools back to the DBPs, which are then used to perform impactful health research. In addition, the
tools developed by the Engineering Team are used to train and disseminate technologies across the research
community. The Team places particular focus on developing sustainable communities through the creation of
open platforms, quality-inducing software processes, and integration to a broad variety of computational tools
and databases. The following describes some of the highlights of the past year's work.
The flagship product from the Engineering Team is the 3D Slicer application. It is the delivery platform for much
current work, and it is an enabling technology for the wider biomedical computing community. This past year
saw the release of Slicer version 4.0 (Slicer4) which represents a significant advance in capabilities and
underlying technologies. Since its release at RSNA in November, Slicer4 has been downloaded over 45,000
times, at a rate of over 100 downloads per day, from users and research groups located around the world.
Slicer4 is now a modern, stable platform built with the Qt GUI system (eliminated the previous KWWidgets
GUI), and rewritten for simplicity, enabling simpler approaches to debugging, faster startup, and more
responsive behavior.
Beyond the core Slicer4 platform, several important features were also added to the application. These
include:
 The Slicer Extension Manager is now called the "Slicer Catalog" (an App Store) and will enable the
community to create compact modules which extend the core functionality.
 Python has been adopted as the preferred scripting language, a preferred programming language in
the scientific computing community. Hence a variety of computational packages are now available to
extend Slicer capabilities at run-time.
 Slicer4 includes a DICOM listener and DICOM Query/Retrieve capabilities for integration with standard
clinical image management environments and workflows.
 Compatibility with ITK version 4 was developed and continuously maintained over the past year as
ITKv4 matured. Slicer will officially switch to ITKv4 in the coming months.
 Slicer Execution Model modules (also known as Command Line Modules) are now available as Nipype
tools, enabling local and distributed scripted execution of processing pipelines. Such methods for
distributed computing are essential to tackling the Big Data and complex algorithms that current
research is producing.
 Finally, a whole host of application improvements have been made including an improved flexible view
layout system; a revised implementation of the Expectation Maximization (EM) Segmenter; faster
hardware-accelerated volume rendering; improved markups and annotations; improved atlas and
model hierarchy support; and a streamlined and revised diffusion MRI implementation.
Community support for NA-MIC and the various NA-MIC Kit tools continues. The goals of this effort are to
transition new technologies to the wider community, to enable community members to contribute back to Slicer
and the NA-MIC Kit, and to ensure high-quality systems. Beyond some of the support activities mentioned
previously, the following are other accomplishments.
 We have begun integrating the SimpleITK module of ITKv4 into Slicer to ensure simple integration
capabilities with emerging algorithms.
 Additional open data support has been added to Slicer such as ultrasound (e.g., video) and 4D (e.g.,
gated CT) data.
 We have integrated the extension writing and the documentation generation processes. The
documentation created when an extension is written is now automatically ported to a web host for
easier access from within and outside of Slicer, ensuring that documentation resources keep up with
the rapid pace of development.
2.3 NA-MIC Kit
The NA-MIC Kit is designed to accelerate the pace of research and facilitate clinical evaluation. Along these
lines, the past year realized significant milestones toward the creation of a stable research platform, supporting
the ability to easily extend and disseminate novel additions, all in the context of a world-wide, broad research
community. Beyond the major highlights related to the Slicer4 application platform described in the previous
section, the following are a few of the highlights of the past year.
 CMake and its associated software process tools (CTest, CDash, and CPack) are used to build, test
and deploy software in a cross-platform manner. CMake continues one of the most well-known pieces
of the NA-MIC Kit, with more than 2,000 known downloads per day (as well as being included by
various Linux distributions). CMake 2.8.7 was released with NA-MIC support.
 CDash Package Manager (CDash 2.0.2) was released with support from NA-MIC. One of the most
significant contributions to CDash from NA-MIC was the package upload process. This process enables
the many Slicer testing machines to upload the executables and packages created during testing to the
main CDash server. This, in turn, allows users to download those testing packages and run additional
tests or use them in their research. This complete automation of the test-release cycle is a massive
time-saver for the Service core and has greatly reduced the time to discover and resolve bugs and to
improve the stability of Slicer.
 Significant data integration efforts were completed over the past year. XNAT was greatly improved in its
usability and interfaces. DICOM support was greatly enhanced, including the ability to embed Slicer
MRML scene files as DICOM lollipops, meaning that Slicer data exchange across the DICOM standard
is now possible. In addition, DCMTK was integrated into the NA-MIC Kit, meaning that DICOM support
and functionality was greatly increased.
 NA-MIC supports and nurtures an extensive biomedical research community. Along these lines it
develops integration tools and interfaces with other communities. CTK, supported by NA-MIC funding,
is one such community and interfaces with other open-source toolkits (e.g., MITK from the German
Cancer Research Center in Heidelberg, XIP from Siemens, GIMIAS from UPF in Spain, and OpenMAF
from U of Bologna). CTK now provides several innovative GUI and DICOM elements that specifically
save GUI space, user-time, and developer effort when building custom medical applications. The NAMIC
Kit also integrated the BRAINSFit system, a collection of programs for registering images with
mutual information based metric. BRAINSFit uses the Slicer execution model framework to define the
command line arguments and is fully integrated with Slicer using the module discovery capabilities.
 Recent developments are in the process of being integrated into the NA-MIC Kit and the Slicer
application platform.
 The Slicer Catalog allows users to install, uninstall, search, browse, and rank Slicer extensions. This
user experience is available from within Slicer and over the web, much like the Android and Apple App
Stores. Developers can contribute, update, document, and post screenshots on their modules and
receive community feedback.
 The analysis infrastructure for Diffusion Weighted MRI (DWI) IO and visualization has been generalized
to be used for other time varying acquisitions like multivolume analysis, dynamic contrast enhanced
MRI (DCE), and gated cardiac CT.
 To cover the use of Qt and newer versions of VTK (both part of the NA-MIC Kit), advanced charting and
analytics options have been demonstrated in Slicer4, and will be fleshed out in the coming year.

* Driving Biological Projects
1The Center worked synergistically with the Driving Biological
Projects (DBPs) to achieve fundamental advances in shape representation, shape analysis, groupwise
registration, diffusion estimation, segmentation and quantification, functional estimation, distortion correction,
and clustering.

* Discuss at least 3 Collaborative Research Projects (these may include collaborating R01/R21s or other projects not directly funded by the Center's NCBC grant, but using Center tools or algorithms in a substantial and enabling manner.

Collaboration 1: TBA
Collaboration 2: TBA
Collaboration 3: TBA

* Brief description of new training and outreach activities conducted during reporting interval (7/1/2012 - 6/30/2013). Provide web-links if available.

Sonia Pujol: Please update and revised. This year NA-MIC hosted XX workshops and courses at national universities and international venues, providing training and
exposure to medical researchers in 3D Slicer and other NA-MIC technologies. NA-MIC also xxxx launched the first
DTI Tractography Challenge for Neurosurgical Planning at the XXth International Conference on Medical Image
Computing and Computer Assisted Intervention (MICCAI 2011) conference in Toronto, Canada, demonstrating
its continued commitment to validation. The purpose of the validation effort is to assess the performance of
NA-MIC algorithms in a variety of settings.

* Impact of Center (i) on biomedical research and research training and outreach at our institution (BWH) and (i) broader scientific community. Institutional benefits might include, organization of special courses and meetings, attraction of students, and faculty participation. Scientific community benefits may include software released, workshops organized, collaborations established, service performed, technology developed, and technology disseminated through patents, publications, peer-reviewed citations of center collaborations by non-center investigators, and personnel trained.

Provide a Center Summary Table

Progress made by innovation and image analysis , and scientific CoresResearch CoresThe scientific development is driven by 4 DBPs. In
addition to activities that sustain the NA-MIC Kit and integrity of the Center’s software infrastructure, NA-MIC
has an impressive outreach program that delivers software, data, and innovative science to the broader biomedical community through its publications and training venues. NA-MIC also has instituted a unique validation effort where software developers and end-users participate in hands-on workshops to measure and improve medical image algorithms.

Required elements:

Finally, this year saw the release of Slicer version 4.0 and 4.1 (Slicer4) which represents a
significant advance in capabilities and underlying technologies. The software was released at RSNA 2011 in
November. As in past years, a detailed presentation of current work was made at the All Hands Meeting in Salt
Lake City, Utah, January 9-13, 2012, and can be viewed in detail on the NA-MIC Wiki [http://wiki.namic.
org/Wiki/index.php/ 2012_Winter_Project_Week].
This represents the 8th Annual Progress Report and second year of the second cycle of funding. The report
includes Highlights and Impact statements, individual progress reports from the four DBPs (Atrial Fibrillation,
Huntington’s Disease, Adaptive Radiotherapy for Head and Neck Cancer, and Traumatic Brain Injury), a
science and technology summary from the Computer Science Core (Algorithms, Engineering, and NA-MIC Kit),
and a review of Training activities, including the validation effort. The report concludes with a bibliography of 33
peer-reviewed journal articles and 21 peer-reviewed conference reports and the annual recommendations of
the External Advisory Board, which met on January 12, 2012 in Salt Lake City, coincident with Winter Project
Week.

Wiki page for 2013 Preliminary Draft

2012-10-13T16:11:06Z

Ann Adams:

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

Required elements of the New Research Progress Template

1. RESEARCH AND RESOURCE METRICS

1A. Summary of Center Progress

* Brief description of overall objectives of NA-MIC

The National Alliance for Medical Image Computing (NA-MIC) is a multi-institutional, interdisciplinary community of computer scientists, software engineers, and medical investigators who share the common goal
of improving healthcare through the development of computational tools for the analysis and visualization of medical image data. The Center maintains a robust and flexible infrastructure for developing and
applying advanced imaging technologies across a range of important biomedical research disciplines. Our research and development effort is organized around the Computer Science Core, which includes independent teams for Algorithms and Engineering. The Algorithm effort responds to the challenges of the DBPs to expand the horizons of medical image analysis. As a result, the Algorithm activities are typically highly experimental, creating new approaches that are rapidly prototyped, tested, and improved. The Engineering effort supports the needs of the Algorithms effort by creating integrated software platforms that support research and eventual deployment of advanced technology. The Engineering team also develops and maintains processes used to build and sustain a large research
community. A separate Core oversees operations and maintenance of The NA-MIC Kit, an integrated set of interoperable free open source software (FOSS)
packages; developed, supported and deployed using a collaborative, agile, high quality software process. NA-MIC's current DBPs are investigating solutions to problems in patient-specific data analysis in four clinical areas: Atrial Fibrillation, Huntingdon's Disease, Adaptive Radiotherapy for Head and Neck Cancer, and Traumatic Brain Injury. NA-MIC further provides enabling technology and resources to XX collaborative research projects.

* Brief outline indicating strengths of NA-MIC as a national resource
[take from NA-MIC impact statement, August 2012]

* Summarize progress made in each Research and Core Project.

Algorithms. The NA-MIC Computer Science Algorithm effort responds to the challenges of the DBPs to
expand the horizons of medical image analysis. As a result, the Algorithm activities are typically highly
experimental, creating new approaches that are rapidly prototyped, tested, and improved.
Engineering. The NA-MIC Computer Science Engineering effort supports the needs of the Algorithms effort by
creating integrated software platforms that support research and eventual deployment of advanced technology.
The Engineering team also develops and maintains processes used to build and sustain a large research
community.
NA-MIC Kit. The NA-MIC Kit consists of an integrated set of interoperable free open source software (FOSS)
packages; developed, supported and deployed using a collaborative, agile, high quality software process. The
NA-MIC Kit has been constructed as a layered architecture to provide a spectrum of capabilities, ranging from
compute-intensive algorithms to easy-to-use applications. Hence users and developers can choose to engage
the NA-MIC Kit at a variety of levels, including developing extensions which can be readily deployed to the
broader biomedical imaging community.
In the following subsections we highlight the accomplishments from this reporting period for algorithms,
engineering, and NA-MIC Kit.
2.1. Algorithms
The Algorithms team develops computational methods that support patient-specific analysis of medical
images. This effort requires analysis of images that vary significantly from one patient to another, or from one
time point to another, presenting distinct challenges to existing state-of-art medical image analysis algorithms.
These technical challenges are addressed using four computational approaches: (1) Statistical models of
anatomy and pathology; (2) Geometric correspondence; (3) User interactive tools for segmentation; and (4)
Longitudinal and time-series analysis. Highlights of these efforts are described in the following sections.
Statistical models of anatomy and pathology. A great deal of progress has been made by using modeling
approaches that systematically capture the statistics of a problem domain from a collection of examples and
then use these statistics to interpret novel images. Some of the approaches include the following:
 Non-Parametric Priors for Segmentation are based on nonparametric, probabilistic models for the
automatic segmentation of medical images, given a training set of images and corresponding label
maps. The resulting inference algorithms rely on pairwise registrations between the test image and
individual training images. The training labels are then transferred to the test image and fused to
compute the final segmentation of the test subject.
 Fast Nearest-Neighbor Lookup in Large Image Databases has been found to improve segmentation
quality. Multi-atlases or nonparametric atlas-based techniques for image segmentation require
registration of a test image with a small set of very similar images from a database.
 Atlases and Registration for DTI Processing are novel methods that enhance the co-registration of DTI
data either to a prior image of the same subject or to an existing atlas with predefined fiber tracts or
regional white matter parcellation. These are applied in cases of large brain pathology (e.g., TBI).
Geometric correspondence. Establishing anatomical correspondences between pairs of patients, groups of
patients, patients and templates, and individual patients over time is important for automatic and user-assisted
image analysis. The ability to establish geometric correspondences, with and without expert guidance, in
challenging clinical circumstances is essential for the DBPs. Progress in two areas was realized this year.
 Stochastic Point Set Registration provides non-rigid point set registration algorithms that seek an optimal
set of radial basis functions to describe the registration. Preliminary results on 2D and 3D data
demonstrate the algorithms' robustness to datasets with noise and with missing information.
 Automatic Correspondences For Shape Ensembles has seen improvements in robustness of our
entropy-based correspondence system. For example, we have developed a method for particles to
interact on surfaces using geodesic distances, which improves the behavior of the system on sharp
features or convoluted shapes.
User interactive tools for segmentation. The work performed in the past year addresses important aspects
of user-interactive segmentation. The patient-specific analysis required by the DBPs has presented images of
patients with pathologies and/or injuries that sometimes defy automated approaches. We have focused our
research on three principal areas.
 Control-Based Interactive Segmentation is a novel contribution based on a modeling formulation that
represents interactive segmentation as a feedback system, enabling a principled merging of automated
methods and user input.
 Globally Optimal Segmentation is a set of methods that rely on global optimization of energy functions via
graph cuts. Results on delayed contrast MRI from the Atrial Fibrillation project are quite promising, and
this work is currently under review for publication.
 Patient-Specific Segmentation Framework for Longitudinal MR Images of Traumatic Brain Injury
addresses the need for robust, reproducible segmentations of MR images of TBI and is crucial for
quantitative analysis of recovery and treatment efficacy. Validation of this new automatic segmentation
compared to expert segmentations of acute and chronic images was provided on 3 longitudinal TBI
datasets, demonstrating that joint segmentation of 4D multi-time point data is superior to individual
segmentations.
Longitudinal and time-series analysis. An important component of patient-specific data analysis is the ability
to analyze multiple images from the same patient over time as a disease or injury progresses or responds to
treatment, or to assess neurodevelopment or neurodegeneration. Longitudinal image analysis is important for
all four DBPs in this project; we have focused in the past year on the areas described below.
 Connectivity Changes in Disease demonstrates a novel probabilistic framework to merge information
from diffusion weighted imaging tractography and resting-state functional magnetic resonance imaging
correlations to identify connectivity patterns in the brain. The method simultaneously infers the templates
of latent connectivity for each population and the differences in connectivity between the groups.
 Modeling Pathology Evolution is used in brain tumor patients to monitor the state of disease and to
evaluate therapeutic options. This work investigated a joint generative model of tumor growth and of
image observation that naturally handles multimodal and longitudinal data, important for TBI.
 Longitudinal Analysis of DTI Change Trajectories develops models that represent the growth trajectories
of individual subjects to study and understand white matter changes in neurodevelopment,
neurodegeneration, and disease progress. Application of this methodology to study early brain
development in a longitudinal neuroimaging study, including validation of reproducibility, has been
shown.
 Analysis of Longitudinal Shape Variability via Subject-Specific Growth Modeling are statistical analyses of
longitudinal imaging data which are crucial for understanding normal anatomical development as well as
disease progression. We have developed a new type of growth model parameterized by acceleration,
whereas standard methods typically control the velocity. This mimics the behavior of biological tissue;
cross validation experiments show that our method is robust to missing observations, is less sensitive to
noise, and is therefore more likely to capture the underlying biological growth.
 Longitudinal and Time Series Analysis are novel methods for longitudinal registration and time series
regression. These methods enable compact approximation of an image time-series through an initial
image and an initial momentum, resulting in dramatically simplified computations.
2.2 Engineering
The Engineering Team builds bridges between the various NA-MIC cores and ultimately to the wider
biomedical computing community. Working with the Algorithms Team, it deploys leading edge biomedical
computing tools back to the DBPs, which are then used to perform impactful health research. In addition, the
tools developed by the Engineering Team are used to train and disseminate technologies across the research
community. The Team places particular focus on developing sustainable communities through the creation of
open platforms, quality-inducing software processes, and integration to a broad variety of computational tools
and databases. The following describes some of the highlights of the past year's work.
The flagship product from the Engineering Team is the 3D Slicer application. It is the delivery platform for much
current work, and it is an enabling technology for the wider biomedical computing community. This past year
saw the release of Slicer version 4.0 (Slicer4) which represents a significant advance in capabilities and
underlying technologies. Since its release at RSNA in November, Slicer4 has been downloaded over 45,000
times, at a rate of over 100 downloads per day, from users and research groups located around the world.
Slicer4 is now a modern, stable platform built with the Qt GUI system (eliminated the previous KWWidgets
GUI), and rewritten for simplicity, enabling simpler approaches to debugging, faster startup, and more
responsive behavior.
Beyond the core Slicer4 platform, several important features were also added to the application. These
include:
 The Slicer Extension Manager is now called the "Slicer Catalog" (an App Store) and will enable the
community to create compact modules which extend the core functionality.
 Python has been adopted as the preferred scripting language, a preferred programming language in
the scientific computing community. Hence a variety of computational packages are now available to
extend Slicer capabilities at run-time.
 Slicer4 includes a DICOM listener and DICOM Query/Retrieve capabilities for integration with standard
clinical image management environments and workflows.
 Compatibility with ITK version 4 was developed and continuously maintained over the past year as
ITKv4 matured. Slicer will officially switch to ITKv4 in the coming months.
 Slicer Execution Model modules (also known as Command Line Modules) are now available as Nipype
tools, enabling local and distributed scripted execution of processing pipelines. Such methods for
distributed computing are essential to tackling the Big Data and complex algorithms that current
research is producing.
 Finally, a whole host of application improvements have been made including an improved flexible view
layout system; a revised implementation of the Expectation Maximization (EM) Segmenter; faster
hardware-accelerated volume rendering; improved markups and annotations; improved atlas and
model hierarchy support; and a streamlined and revised diffusion MRI implementation.
Community support for NA-MIC and the various NA-MIC Kit tools continues. The goals of this effort are to
transition new technologies to the wider community, to enable community members to contribute back to Slicer
and the NA-MIC Kit, and to ensure high-quality systems. Beyond some of the support activities mentioned
previously, the following are other accomplishments.
 We have begun integrating the SimpleITK module of ITKv4 into Slicer to ensure simple integration
capabilities with emerging algorithms.
 Additional open data support has been added to Slicer such as ultrasound (e.g., video) and 4D (e.g.,
gated CT) data.
 We have integrated the extension writing and the documentation generation processes. The
documentation created when an extension is written is now automatically ported to a web host for
easier access from within and outside of Slicer, ensuring that documentation resources keep up with
the rapid pace of development.
2.3 NA-MIC Kit
The NA-MIC Kit is designed to accelerate the pace of research and facilitate clinical evaluation. Along these
lines, the past year realized significant milestones toward the creation of a stable research platform, supporting
the ability to easily extend and disseminate novel additions, all in the context of a world-wide, broad research
community. Beyond the major highlights related to the Slicer4 application platform described in the previous
section, the following are a few of the highlights of the past year.
 CMake and its associated software process tools (CTest, CDash, and CPack) are used to build, test
and deploy software in a cross-platform manner. CMake continues one of the most well-known pieces
of the NA-MIC Kit, with more than 2,000 known downloads per day (as well as being included by
various Linux distributions). CMake 2.8.7 was released with NA-MIC support.
 CDash Package Manager (CDash 2.0.2) was released with support from NA-MIC. One of the most
significant contributions to CDash from NA-MIC was the package upload process. This process enables
the many Slicer testing machines to upload the executables and packages created during testing to the
main CDash server. This, in turn, allows users to download those testing packages and run additional
tests or use them in their research. This complete automation of the test-release cycle is a massive
time-saver for the Service core and has greatly reduced the time to discover and resolve bugs and to
improve the stability of Slicer.
 Significant data integration efforts were completed over the past year. XNAT was greatly improved in its
usability and interfaces. DICOM support was greatly enhanced, including the ability to embed Slicer
MRML scene files as DICOM lollipops, meaning that Slicer data exchange across the DICOM standard
is now possible. In addition, DCMTK was integrated into the NA-MIC Kit, meaning that DICOM support
and functionality was greatly increased.
 NA-MIC supports and nurtures an extensive biomedical research community. Along these lines it
develops integration tools and interfaces with other communities. CTK, supported by NA-MIC funding,
is one such community and interfaces with other open-source toolkits (e.g., MITK from the German
Cancer Research Center in Heidelberg, XIP from Siemens, GIMIAS from UPF in Spain, and OpenMAF
from U of Bologna). CTK now provides several innovative GUI and DICOM elements that specifically
save GUI space, user-time, and developer effort when building custom medical applications. The NAMIC
Kit also integrated the BRAINSFit system, a collection of programs for registering images with
mutual information based metric. BRAINSFit uses the Slicer execution model framework to define the
command line arguments and is fully integrated with Slicer using the module discovery capabilities.
 Recent developments are in the process of being integrated into the NA-MIC Kit and the Slicer
application platform.
 The Slicer Catalog allows users to install, uninstall, search, browse, and rank Slicer extensions. This
user experience is available from within Slicer and over the web, much like the Android and Apple App
Stores. Developers can contribute, update, document, and post screenshots on their modules and
receive community feedback.
 The analysis infrastructure for Diffusion Weighted MRI (DWI) IO and visualization has been generalized
to be used for other time varying acquisitions like multivolume analysis, dynamic contrast enhanced
MRI (DCE), and gated cardiac CT.
 To cover the use of Qt and newer versions of VTK (both part of the NA-MIC Kit), advanced charting and
analytics options have been demonstrated in Slicer4, and will be fleshed out in the coming year.

* Driving Biological Projects
1The Center worked synergistically with the Driving Biological
Projects (DBPs) to achieve fundamental advances in shape representation, shape analysis, groupwise
registration, diffusion estimation, segmentation and quantification, functional estimation, distortion correction,
and clustering.

* Discuss at least 3 Collaborative Research Projects (these may include collaborating R01/R21s or other projects not directly funded by the Center's NCBC grant, but using Center tools or algorithms in a substantial and enabling manner.

Collaboration 1: TBA
Collaboration 2: TBA
Collaboration 3: TBA

* Brief description of new training and outreach activities conducted during reporting interval (7/1/2012 - 6/30/2013). Provide web-links if available.

Sonia Pujol: Please update and revised. This year NA-MIC hosted XX workshops and courses at national universities and international venues, providing training and
exposure to medical researchers in 3D Slicer and other NA-MIC technologies. NA-MIC also xxxx launched the first
DTI Tractography Challenge for Neurosurgical Planning at the XXth International Conference on Medical Image
Computing and Computer Assisted Intervention (MICCAI 2011) conference in Toronto, Canada, demonstrating
its continued commitment to validation. The purpose of the validation effort is to assess the performance of
NA-MIC algorithms in a variety of settings.

* Impact of Center (i) on biomedical research and research training and outreach at our institution (BWH) and (i) broader scientific community. Institutional benefits might include, organization of special courses and meetings, attraction of students, and faculty participation. Scientific community benefits may include software released, workshops organized, collaborations established, service performed, technology developed, and technology disseminated through patents, publications, peer-reviewed citations of center collaborations by non-center investigators, and personnel trained.

Provide a Center Summary Table

Progress made by innovation and image analysis , and scientific CoresResearch CoresThe scientific development is driven by 4 DBPs. In
addition to activities that sustain the NA-MIC Kit and integrity of the Center’s software infrastructure, NA-MIC
has an impressive outreach program that delivers software, data, and innovative science to the broader biomedical community through its publications and training venues. NA-MIC also has instituted a unique validation effort where software developers and end-users participate in hands-on workshops to measure and improve medical image algorithms.

Required elements:

Finally, this year saw the release of Slicer version 4.0 and 4.1 (Slicer4) which represents a
significant advance in capabilities and underlying technologies. The software was released at RSNA 2011 in
November. As in past years, a detailed presentation of current work was made at the All Hands Meeting in Salt
Lake City, Utah, January 9-13, 2012, and can be viewed in detail on the NA-MIC Wiki [http://wiki.namic.
org/Wiki/index.php/ 2012_Winter_Project_Week].
This represents the 8th Annual Progress Report and second year of the second cycle of funding. The report
includes Highlights and Impact statements, individual progress reports from the four DBPs (Atrial Fibrillation,
Huntington’s Disease, Adaptive Radiotherapy for Head and Neck Cancer, and Traumatic Brain Injury), a
science and technology summary from the Computer Science Core (Algorithms, Engineering, and NA-MIC Kit),
and a review of Training activities, including the validation effort. The report concludes with a bibliography of 33
peer-reviewed journal articles and 21 peer-reviewed conference reports and the annual recommendations of
the External Advisory Board, which met on January 12, 2012 in Salt Lake City, coincident with Winter Project
Week.

2013 Progress Report

2012-10-13T16:08:07Z

Ann Adams: /* Scientific Progress Report */

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

==Administrative Paperwork Timeline==

*TBA: LOI goes to subs (Sanjay/Rachana)
*TBA: Signed Subcontractor's Documents due back to BWH
*TBA: Review by Radiology Administration (Trey/Susan)
*TBA: Review by BWH RA
*TBA: Signed Facepage and budget docs due back to Katie M for page numbering (Katie)
*4/30/2013: Ship it to NIH

==Scientific Report Timeline==
*10/13/2012: wiki page setup for progress report (Ann)
*TBA: all sections to be completed by owners
*TBA: check NIH compliance of all publications in Pubmed (Katie)
*TBA: create final report (Ann)
*TBA: Update web pages with any new materials from report (Ann)
*TBA: create full publications list (Katie)
*TBA: final review (Tina, Ron)
*TBA: final pdf created and submitted to Rachana (Katie)
==Scientific Progress Report==

*[[Media:Progress_Report_Template_National_Centers_for_Biomedical_Computing_2.1.docx | New Progress Report Template]]
*[[Media:NA-MIC_IMPACT_STATEMENT.pdf | NA-MIC IMPACT STATEMENT 2012]]
*[[Wiki_page_for_2013_Progress_Report_Assignments]]‎
*[[Wiki_page_for_2013_Preliminary_Draft]]

2013 Progress Report

2012-10-13T16:07:17Z

Ann Adams: /* Scientific Progress Report */

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

==Administrative Paperwork Timeline==

*TBA: LOI goes to subs (Sanjay/Rachana)
*TBA: Signed Subcontractor's Documents due back to BWH
*TBA: Review by Radiology Administration (Trey/Susan)
*TBA: Review by BWH RA
*TBA: Signed Facepage and budget docs due back to Katie M for page numbering (Katie)
*4/30/2013: Ship it to NIH

==Scientific Report Timeline==
*10/13/2012: wiki page setup for progress report (Ann)
*TBA: all sections to be completed by owners
*TBA: check NIH compliance of all publications in Pubmed (Katie)
*TBA: create final report (Ann)
*TBA: Update web pages with any new materials from report (Ann)
*TBA: create full publications list (Katie)
*TBA: final review (Tina, Ron)
*TBA: final pdf created and submitted to Rachana (Katie)
==Scientific Progress Report==

*[[Media:Progress_Report_Template_National_Centers_for_Biomedical_Computing_2.1.docx | New Progress Report Template]]
*[[Media:NA-MIC_IMPACT_STATEMENT_SUMMARY.pdf | NA-MIC IMPACT STATEMENT SUMMARY 2012]]
*[[Wiki_page_for_2013_Progress_Report_Assignments]]‎
*[[Wiki_page_for_2013_Preliminary_Draft]]

File:NA-MIC IMPACT STATEMENT.pdf

2012-10-13T16:05:37Z

Ann Adams: Summary Impact Statement for NCBC August 2012

Summary Impact Statement for NCBC August 2012

Wiki page for 2013 Preliminary Draft

2012-10-13T16:00:13Z

Ann Adams:

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

Required elements of the New Research Progress Template

1. RESEARCH AND RESOURCE METRICS

1A. Summary of Center Progress

* Brief description of overall objectives of NA-MIC

The National Alliance for Medical Image Computing (NA-MIC) is a multi-institutional, interdisciplinary community of computer scientists, software engineers, and medical investigators who share the common goal
of improving healthcare through the development of computational tools for the analysis and visualization of medical image data. The Center maintains a robust and flexible infrastructure for developing and
applying advanced imaging technologies across a range of important biomedical research disciplines. Our research and development effort is organized around the Computer Science Core, which includes independent teams for Algorithms and Engineering. The NA-MIC Computer Science Algorithm effort responds to the challenges of the DBPs to expand the horizons of medical image analysis. As a result, the Algorithm activities are typically highly experimental, creating new approaches that are rapidly prototyped, tested, and improved. The Engineering effort supports the needs of the Algorithms effort by creating integrated software platforms that support research and eventual deployment of advanced technology. The Engineering team also develops and maintains processes used to build and sustain a large research
community. A separate Core oversees operations and maintenance of The NA-MIC Kit, an integrated set of interoperable free open source software (FOSS)
packages; developed, supported and deployed using a collaborative, agile, high quality software process. NA-MIC's current DBPs are investigating solutions to problems in patient-specific data analysis in four clinical areas: Atrial Fibrillation, Huntingdon's Disease, Adaptive Radiotherapy for Head and Neck Cancer, and Traumatic Brain Injury. NA-MIC further provides enabling technology and resources to XX collaborative research projects.

* Brief outline indicating strengths of NA-MIC as a national resource
[take from NA-MIC impact statement, August 2012]

* Summarize progress made in each Research and Core Project.

Algorithms. The NA-MIC Computer Science Algorithm effort responds to the challenges of the DBPs to
expand the horizons of medical image analysis. As a result, the Algorithm activities are typically highly
experimental, creating new approaches that are rapidly prototyped, tested, and improved.
Engineering. The NA-MIC Computer Science Engineering effort supports the needs of the Algorithms effort by
creating integrated software platforms that support research and eventual deployment of advanced technology.
The Engineering team also develops and maintains processes used to build and sustain a large research
community.
NA-MIC Kit. The NA-MIC Kit consists of an integrated set of interoperable free open source software (FOSS)
packages; developed, supported and deployed using a collaborative, agile, high quality software process. The
NA-MIC Kit has been constructed as a layered architecture to provide a spectrum of capabilities, ranging from
compute-intensive algorithms to easy-to-use applications. Hence users and developers can choose to engage
the NA-MIC Kit at a variety of levels, including developing extensions which can be readily deployed to the
broader biomedical imaging community.
In the following subsections we highlight the accomplishments from this reporting period for algorithms,
engineering, and NA-MIC Kit.
2.1. Algorithms
The Algorithms team develops computational methods that support patient-specific analysis of medical
images. This effort requires analysis of images that vary significantly from one patient to another, or from one
time point to another, presenting distinct challenges to existing state-of-art medical image analysis algorithms.
These technical challenges are addressed using four computational approaches: (1) Statistical models of
anatomy and pathology; (2) Geometric correspondence; (3) User interactive tools for segmentation; and (4)
Longitudinal and time-series analysis. Highlights of these efforts are described in the following sections.
Statistical models of anatomy and pathology. A great deal of progress has been made by using modeling
approaches that systematically capture the statistics of a problem domain from a collection of examples and
then use these statistics to interpret novel images. Some of the approaches include the following:
 Non-Parametric Priors for Segmentation are based on nonparametric, probabilistic models for the
automatic segmentation of medical images, given a training set of images and corresponding label
maps. The resulting inference algorithms rely on pairwise registrations between the test image and
individual training images. The training labels are then transferred to the test image and fused to
compute the final segmentation of the test subject.
 Fast Nearest-Neighbor Lookup in Large Image Databases has been found to improve segmentation
quality. Multi-atlases or nonparametric atlas-based techniques for image segmentation require
registration of a test image with a small set of very similar images from a database.
 Atlases and Registration for DTI Processing are novel methods that enhance the co-registration of DTI
data either to a prior image of the same subject or to an existing atlas with predefined fiber tracts or
regional white matter parcellation. These are applied in cases of large brain pathology (e.g., TBI).
Geometric correspondence. Establishing anatomical correspondences between pairs of patients, groups of
patients, patients and templates, and individual patients over time is important for automatic and user-assisted
image analysis. The ability to establish geometric correspondences, with and without expert guidance, in
challenging clinical circumstances is essential for the DBPs. Progress in two areas was realized this year.
 Stochastic Point Set Registration provides non-rigid point set registration algorithms that seek an optimal
set of radial basis functions to describe the registration. Preliminary results on 2D and 3D data
demonstrate the algorithms' robustness to datasets with noise and with missing information.
 Automatic Correspondences For Shape Ensembles has seen improvements in robustness of our
entropy-based correspondence system. For example, we have developed a method for particles to
interact on surfaces using geodesic distances, which improves the behavior of the system on sharp
features or convoluted shapes.
User interactive tools for segmentation. The work performed in the past year addresses important aspects
of user-interactive segmentation. The patient-specific analysis required by the DBPs has presented images of
patients with pathologies and/or injuries that sometimes defy automated approaches. We have focused our
research on three principal areas.
 Control-Based Interactive Segmentation is a novel contribution based on a modeling formulation that
represents interactive segmentation as a feedback system, enabling a principled merging of automated
methods and user input.
 Globally Optimal Segmentation is a set of methods that rely on global optimization of energy functions via
graph cuts. Results on delayed contrast MRI from the Atrial Fibrillation project are quite promising, and
this work is currently under review for publication.
 Patient-Specific Segmentation Framework for Longitudinal MR Images of Traumatic Brain Injury
addresses the need for robust, reproducible segmentations of MR images of TBI and is crucial for
quantitative analysis of recovery and treatment efficacy. Validation of this new automatic segmentation
compared to expert segmentations of acute and chronic images was provided on 3 longitudinal TBI
datasets, demonstrating that joint segmentation of 4D multi-time point data is superior to individual
segmentations.
Longitudinal and time-series analysis. An important component of patient-specific data analysis is the ability
to analyze multiple images from the same patient over time as a disease or injury progresses or responds to
treatment, or to assess neurodevelopment or neurodegeneration. Longitudinal image analysis is important for
all four DBPs in this project; we have focused in the past year on the areas described below.
 Connectivity Changes in Disease demonstrates a novel probabilistic framework to merge information
from diffusion weighted imaging tractography and resting-state functional magnetic resonance imaging
correlations to identify connectivity patterns in the brain. The method simultaneously infers the templates
of latent connectivity for each population and the differences in connectivity between the groups.
 Modeling Pathology Evolution is used in brain tumor patients to monitor the state of disease and to
evaluate therapeutic options. This work investigated a joint generative model of tumor growth and of
image observation that naturally handles multimodal and longitudinal data, important for TBI.
 Longitudinal Analysis of DTI Change Trajectories develops models that represent the growth trajectories
of individual subjects to study and understand white matter changes in neurodevelopment,
neurodegeneration, and disease progress. Application of this methodology to study early brain
development in a longitudinal neuroimaging study, including validation of reproducibility, has been
shown.
 Analysis of Longitudinal Shape Variability via Subject-Specific Growth Modeling are statistical analyses of
longitudinal imaging data which are crucial for understanding normal anatomical development as well as
disease progression. We have developed a new type of growth model parameterized by acceleration,
whereas standard methods typically control the velocity. This mimics the behavior of biological tissue;
cross validation experiments show that our method is robust to missing observations, is less sensitive to
noise, and is therefore more likely to capture the underlying biological growth.
 Longitudinal and Time Series Analysis are novel methods for longitudinal registration and time series
regression. These methods enable compact approximation of an image time-series through an initial
image and an initial momentum, resulting in dramatically simplified computations.
2.2 Engineering
The Engineering Team builds bridges between the various NA-MIC cores and ultimately to the wider
biomedical computing community. Working with the Algorithms Team, it deploys leading edge biomedical
computing tools back to the DBPs, which are then used to perform impactful health research. In addition, the
tools developed by the Engineering Team are used to train and disseminate technologies across the research
community. The Team places particular focus on developing sustainable communities through the creation of
open platforms, quality-inducing software processes, and integration to a broad variety of computational tools
and databases. The following describes some of the highlights of the past year's work.
The flagship product from the Engineering Team is the 3D Slicer application. It is the delivery platform for much
current work, and it is an enabling technology for the wider biomedical computing community. This past year
saw the release of Slicer version 4.0 (Slicer4) which represents a significant advance in capabilities and
underlying technologies. Since its release at RSNA in November, Slicer4 has been downloaded over 45,000
times, at a rate of over 100 downloads per day, from users and research groups located around the world.
Slicer4 is now a modern, stable platform built with the Qt GUI system (eliminated the previous KWWidgets
GUI), and rewritten for simplicity, enabling simpler approaches to debugging, faster startup, and more
responsive behavior.
Beyond the core Slicer4 platform, several important features were also added to the application. These
include:
 The Slicer Extension Manager is now called the "Slicer Catalog" (an App Store) and will enable the
community to create compact modules which extend the core functionality.
 Python has been adopted as the preferred scripting language, a preferred programming language in
the scientific computing community. Hence a variety of computational packages are now available to
extend Slicer capabilities at run-time.
 Slicer4 includes a DICOM listener and DICOM Query/Retrieve capabilities for integration with standard
clinical image management environments and workflows.
 Compatibility with ITK version 4 was developed and continuously maintained over the past year as
ITKv4 matured. Slicer will officially switch to ITKv4 in the coming months.
 Slicer Execution Model modules (also known as Command Line Modules) are now available as Nipype
tools, enabling local and distributed scripted execution of processing pipelines. Such methods for
distributed computing are essential to tackling the Big Data and complex algorithms that current
research is producing.
 Finally, a whole host of application improvements have been made including an improved flexible view
layout system; a revised implementation of the Expectation Maximization (EM) Segmenter; faster
hardware-accelerated volume rendering; improved markups and annotations; improved atlas and
model hierarchy support; and a streamlined and revised diffusion MRI implementation.
Community support for NA-MIC and the various NA-MIC Kit tools continues. The goals of this effort are to
transition new technologies to the wider community, to enable community members to contribute back to Slicer
and the NA-MIC Kit, and to ensure high-quality systems. Beyond some of the support activities mentioned
previously, the following are other accomplishments.
 We have begun integrating the SimpleITK module of ITKv4 into Slicer to ensure simple integration
capabilities with emerging algorithms.
 Additional open data support has been added to Slicer such as ultrasound (e.g., video) and 4D (e.g.,
gated CT) data.
 We have integrated the extension writing and the documentation generation processes. The
documentation created when an extension is written is now automatically ported to a web host for
easier access from within and outside of Slicer, ensuring that documentation resources keep up with
the rapid pace of development.
2.3 NA-MIC Kit
The NA-MIC Kit is designed to accelerate the pace of research and facilitate clinical evaluation. Along these
lines, the past year realized significant milestones toward the creation of a stable research platform, supporting
the ability to easily extend and disseminate novel additions, all in the context of a world-wide, broad research
community. Beyond the major highlights related to the Slicer4 application platform described in the previous
section, the following are a few of the highlights of the past year.
 CMake and its associated software process tools (CTest, CDash, and CPack) are used to build, test
and deploy software in a cross-platform manner. CMake continues one of the most well-known pieces
of the NA-MIC Kit, with more than 2,000 known downloads per day (as well as being included by
various Linux distributions). CMake 2.8.7 was released with NA-MIC support.
 CDash Package Manager (CDash 2.0.2) was released with support from NA-MIC. One of the most
significant contributions to CDash from NA-MIC was the package upload process. This process enables
the many Slicer testing machines to upload the executables and packages created during testing to the
main CDash server. This, in turn, allows users to download those testing packages and run additional
tests or use them in their research. This complete automation of the test-release cycle is a massive
time-saver for the Service core and has greatly reduced the time to discover and resolve bugs and to
improve the stability of Slicer.
 Significant data integration efforts were completed over the past year. XNAT was greatly improved in its
usability and interfaces. DICOM support was greatly enhanced, including the ability to embed Slicer
MRML scene files as DICOM lollipops, meaning that Slicer data exchange across the DICOM standard
is now possible. In addition, DCMTK was integrated into the NA-MIC Kit, meaning that DICOM support
and functionality was greatly increased.
 NA-MIC supports and nurtures an extensive biomedical research community. Along these lines it
develops integration tools and interfaces with other communities. CTK, supported by NA-MIC funding,
is one such community and interfaces with other open-source toolkits (e.g., MITK from the German
Cancer Research Center in Heidelberg, XIP from Siemens, GIMIAS from UPF in Spain, and OpenMAF
from U of Bologna). CTK now provides several innovative GUI and DICOM elements that specifically
save GUI space, user-time, and developer effort when building custom medical applications. The NAMIC
Kit also integrated the BRAINSFit system, a collection of programs for registering images with
mutual information based metric. BRAINSFit uses the Slicer execution model framework to define the
command line arguments and is fully integrated with Slicer using the module discovery capabilities.
 Recent developments are in the process of being integrated into the NA-MIC Kit and the Slicer
application platform.
 The Slicer Catalog allows users to install, uninstall, search, browse, and rank Slicer extensions. This
user experience is available from within Slicer and over the web, much like the Android and Apple App
Stores. Developers can contribute, update, document, and post screenshots on their modules and
receive community feedback.
 The analysis infrastructure for Diffusion Weighted MRI (DWI) IO and visualization has been generalized
to be used for other time varying acquisitions like multivolume analysis, dynamic contrast enhanced
MRI (DCE), and gated cardiac CT.
 To cover the use of Qt and newer versions of VTK (both part of the NA-MIC Kit), advanced charting and
analytics options have been demonstrated in Slicer4, and will be fleshed out in the coming year.

* Driving Biological Projects
1The Center worked synergistically with the Driving Biological
Projects (DBPs) to achieve fundamental advances in shape representation, shape analysis, groupwise
registration, diffusion estimation, segmentation and quantification, functional estimation, distortion correction,
and clustering.

* Discuss at least 3 Collaborative Research Projects (these may include collaborating R01/R21s or other projects not directly funded by the Center's NCBC grant, but using Center tools or algorithms in a substantial and enabling manner.

Collaboration 1: TBA
Collaboration 2: TBA
Collaboration 3: TBA

* Brief description of new training and outreach activities conducted during reporting interval (7/1/2012 - 6/30/2013). Provide web-links if available.

Sonia Pujol: Please update and revised. This year NA-MIC hosted XX workshops and courses at national universities and international venues, providing training and
exposure to medical researchers in 3D Slicer and other NA-MIC technologies. NA-MIC also xxxx launched the first
DTI Tractography Challenge for Neurosurgical Planning at the XXth International Conference on Medical Image
Computing and Computer Assisted Intervention (MICCAI 2011) conference in Toronto, Canada, demonstrating
its continued commitment to validation. The purpose of the validation effort is to assess the performance of
NA-MIC algorithms in a variety of settings.

* Impact of Center (i) on biomedical research and research training and outreach at our institution (BWH) and (i) broader scientific community. Institutional benefits might include, organization of special courses and meetings, attraction of students, and faculty participation. Scientific community benefits may include software released, workshops organized, collaborations established, service performed, technology developed, and technology disseminated through patents, publications, peer-reviewed citations of center collaborations by non-center investigators, and personnel trained.

Provide a Center Summary Table

Progress made by innovation and image analysis , and scientific CoresResearch CoresThe scientific development is driven by 4 DBPs. In
addition to activities that sustain the NA-MIC Kit and integrity of the Center’s software infrastructure, NA-MIC
has an impressive outreach program that delivers software, data, and innovative science to the broader biomedical community through its publications and training venues. NA-MIC also has instituted a unique validation effort where software developers and end-users participate in hands-on workshops to measure and improve medical image algorithms.

Required elements:

Finally, this year saw the release of Slicer version 4.0 and 4.1 (Slicer4) which represents a
significant advance in capabilities and underlying technologies. The software was released at RSNA 2011 in
November. As in past years, a detailed presentation of current work was made at the All Hands Meeting in Salt
Lake City, Utah, January 9-13, 2012, and can be viewed in detail on the NA-MIC Wiki [http://wiki.namic.
org/Wiki/index.php/ 2012_Winter_Project_Week].
This represents the 8th Annual Progress Report and second year of the second cycle of funding. The report
includes Highlights and Impact statements, individual progress reports from the four DBPs (Atrial Fibrillation,
Huntington’s Disease, Adaptive Radiotherapy for Head and Neck Cancer, and Traumatic Brain Injury), a
science and technology summary from the Computer Science Core (Algorithms, Engineering, and NA-MIC Kit),
and a review of Training activities, including the validation effort. The report concludes with a bibliography of 33
peer-reviewed journal articles and 21 peer-reviewed conference reports and the annual recommendations of
the External Advisory Board, which met on January 12, 2012 in Salt Lake City, coincident with Winter Project
Week.

Wiki page for 2013 Preliminary Draft

2012-10-13T14:22:20Z

Ann Adams: /* Summary of Center Progress */

Wiki page for 2013 Preliminary Draft

2012-10-13T13:55:22Z

Ann Adams:

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

Required elements of the New Research Progress Template

==Summary of Center Progress==

1. Brief description of overall objectives of NA-MIC

The National Alliance for Medical Image Computing (NA-MIC) is a multi-institutional, interdisciplinary
community of computer scientists, software engineers, and medical investigators who share the common goal
of improving healthcare through the development of computational tools for the analysis and visualization of
medical image data. The Center continues to maintain a robust and flexible infrastructure for developing and
applying advanced imaging technologies across a range of important biomedical research disciplines.
Research leading to innovation in medical image analysis is organized around the Computer Science Core, which includes independent teams for Algorithms and Engineering, and the NA-MIC Kit. Four DBPs drive the innovation and image analysis , and scientific CoresResearch CoresThe scientific development is driven by 4 DBPs. In
addition to activities that sustain the NA-MIC Kit and integrity of the Center’s software infrastructure, NA-MIC
has an impressive outreach program that delivers software, data, and innovative science to the broader biomedical community through its publications and training venues. NA-MIC also has instituted a unique validation effort where software developers and end-users participate in hands-on workshops to measure and improve medical image algorithms.

Required elements:

1. This year NA-MIC hosted 15 workshops and courses at national universities and international venues, providing training and
exposure to medical researchers in 3D Slicer and other NA-MIC technologies. NA-MIC also launched the first
DTI Tractography Challenge for Neurosurgical Planning at the 14th International Conference on Medical Image
Computing and Computer Assisted Intervention (MICCAI 2011) conference in Toronto, Canada, demonstrating
its continued commitment to validation. The purpose of the validation effort is to assess the performance of
NA-MIC algorithms in a variety of clinical arenas. The Center worked synergistically with the Driving Biological
Projects (DBPs) to achieve fundamental advances in shape representation, shape analysis, groupwise
registration, diffusion estimation, segmentation and quantification, functional estimation, distortion correction,
and clustering. Finally, this year saw the release of Slicer version 4.0 and 4.1 (Slicer4) which represents a
significant advance in capabilities and underlying technologies. The software was released at RSNA 2011 in
November. As in past years, a detailed presentation of current work was made at the All Hands Meeting in Salt
Lake City, Utah, January 9-13, 2012, and can be viewed in detail on the NA-MIC Wiki [http://wiki.namic.
org/Wiki/index.php/ 2012_Winter_Project_Week].
This represents the 8th Annual Progress Report and second year of the second cycle of funding. The report
includes Highlights and Impact statements, individual progress reports from the four DBPs (Atrial Fibrillation,
Huntington’s Disease, Adaptive Radiotherapy for Head and Neck Cancer, and Traumatic Brain Injury), a
science and technology summary from the Computer Science Core (Algorithms, Engineering, and NA-MIC Kit),
and a review of Training activities, including the validation effort. The report concludes with a bibliography of 33
peer-reviewed journal articles and 21 peer-reviewed conference reports and the annual recommendations of
the External Advisory Board, which met on January 12, 2012 in Salt Lake City, coincident with Winter Project
Week.

Wiki page for 2013 Preliminary Draft

2012-10-13T13:54:32Z

Ann Adams:

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

Summary of Center Progress

1. Brief description of overall objectives of NA-MIC

The National Alliance for Medical Image Computing (NA-MIC) is a multi-institutional, interdisciplinary
community of computer scientists, software engineers, and medical investigators who share the common goal
of improving healthcare through the development of computational tools for the analysis and visualization of
medical image data. The Center continues to maintain a robust and flexible infrastructure for developing and
applying advanced imaging technologies across a range of important biomedical research disciplines.
Research leading to innovation in medical image analysis is organized around the Computer Science Core, which includes independent teams for Algorithms and Engineering, and the NA-MIC Kit. Four DBPs drive the innovation and image analysis , and scientific CoresResearch CoresThe scientific development is driven by 4 DBPs. In
addition to activities that sustain the NA-MIC Kit and integrity of the Center’s software infrastructure, NA-MIC
has an impressive outreach program that delivers software, data, and innovative science to the broader biomedical community through its publications and training venues. NA-MIC also has instituted a unique validation effort where software developers and end-users participate in hands-on workshops to measure and improve medical image algorithms.

Required elements:

1. This year NA-MIC hosted 15 workshops and courses at national universities and international venues, providing training and
exposure to medical researchers in 3D Slicer and other NA-MIC technologies. NA-MIC also launched the first
DTI Tractography Challenge for Neurosurgical Planning at the 14th International Conference on Medical Image
Computing and Computer Assisted Intervention (MICCAI 2011) conference in Toronto, Canada, demonstrating
its continued commitment to validation. The purpose of the validation effort is to assess the performance of
NA-MIC algorithms in a variety of clinical arenas. The Center worked synergistically with the Driving Biological
Projects (DBPs) to achieve fundamental advances in shape representation, shape analysis, groupwise
registration, diffusion estimation, segmentation and quantification, functional estimation, distortion correction,
and clustering. Finally, this year saw the release of Slicer version 4.0 and 4.1 (Slicer4) which represents a
significant advance in capabilities and underlying technologies. The software was released at RSNA 2011 in
November. As in past years, a detailed presentation of current work was made at the All Hands Meeting in Salt
Lake City, Utah, January 9-13, 2012, and can be viewed in detail on the NA-MIC Wiki [http://wiki.namic.
org/Wiki/index.php/ 2012_Winter_Project_Week].
This represents the 8th Annual Progress Report and second year of the second cycle of funding. The report
includes Highlights and Impact statements, individual progress reports from the four DBPs (Atrial Fibrillation,
Huntington’s Disease, Adaptive Radiotherapy for Head and Neck Cancer, and Traumatic Brain Injury), a
science and technology summary from the Computer Science Core (Algorithms, Engineering, and NA-MIC Kit),
and a review of Training activities, including the validation effort. The report concludes with a bibliography of 33
peer-reviewed journal articles and 21 peer-reviewed conference reports and the annual recommendations of
the External Advisory Board, which met on January 12, 2012 in Salt Lake City, coincident with Winter Project
Week.

Wiki page for 2013 Preliminary Draft

2012-10-13T13:35:04Z

Ann Adams: Created page with 'Back to Annual_Progress_Reports The National Alliance for Medical Image Computing (NA-MIC) is a multi-institutional, interdisciplinary community of computer scientists, soft…'

Back to [[Annual_Progress_Reports]]

The National Alliance for Medical Image Computing (NA-MIC) is a multi-institutional, interdisciplinary
community of computer scientists, software engineers, and medical investigators who share the common goal
of improving healthcare through the development of computational tools for the analysis and visualization of
medical image data. The Center continues to provide robust and flexible infrastructure for developing and
applying advanced imaging technologies across a range of important biomedical research disciplines. In
addition to activities that sustain the NA-MIC Kit and integrity of the Center’s software infrastructure, NA-MIC
has continued its impressive record of reaching out to the broader biomedical community. This year NA-MIC
hosted 15 workshops and courses at national universities and international venues, providing training and
exposure to medical researchers in 3D Slicer and other NA-MIC technologies. NA-MIC also launched the first
DTI Tractography Challenge for Neurosurgical Planning at the 14th International Conference on Medical Image
Computing and Computer Assisted Intervention (MICCAI 2011) conference in Toronto, Canada, demonstrating
its continued commitment to validation. The purpose of the validation effort is to assess the performance of
NA-MIC algorithms in a variety of clinical arenas. The Center worked synergistically with the Driving Biological
Projects (DBPs) to achieve fundamental advances in shape representation, shape analysis, groupwise
registration, diffusion estimation, segmentation and quantification, functional estimation, distortion correction,
and clustering. Finally, this year saw the release of Slicer version 4.0 and 4.1 (Slicer4) which represents a
significant advance in capabilities and underlying technologies. The software was released at RSNA 2011 in
November. As in past years, a detailed presentation of current work was made at the All Hands Meeting in Salt
Lake City, Utah, January 9-13, 2012, and can be viewed in detail on the NA-MIC Wiki [http://wiki.namic.
org/Wiki/index.php/ 2012_Winter_Project_Week].
This represents the 8th Annual Progress Report and second year of the second cycle of funding. The report
includes Highlights and Impact statements, individual progress reports from the four DBPs (Atrial Fibrillation,
Huntington’s Disease, Adaptive Radiotherapy for Head and Neck Cancer, and Traumatic Brain Injury), a
science and technology summary from the Computer Science Core (Algorithms, Engineering, and NA-MIC Kit),
and a review of Training activities, including the validation effort. The report concludes with a bibliography of 33
peer-reviewed journal articles and 21 peer-reviewed conference reports and the annual recommendations of
the External Advisory Board, which met on January 12, 2012 in Salt Lake City, coincident with Winter Project
Week.

2013 Progress Report

2012-10-13T13:34:34Z

Ann Adams: /* Scientific Progress Report */

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

==Administrative Paperwork Timeline==

*TBA: LOI goes to subs (Sanjay/Rachana)
*TBA: Signed Subcontractor's Documents due back to BWH
*TBA: Review by Radiology Administration (Trey/Susan)
*TBA: Review by BWH RA
*TBA: Signed Facepage and budget docs due back to Katie M for page numbering (Katie)
*4/30/2013: Ship it to NIH

==Scientific Report Timeline==
*10/13/2012: wiki page setup for progress report (Ann)
*TBA: all sections to be completed by owners
*TBA: check NIH compliance of all publications in Pubmed (Katie)
*TBA: create final report (Ann)
*TBA: Update web pages with any new materials from report (Ann)
*TBA: create full publications list (Katie)
*TBA: final review (Tina, Ron)
*TBA: final pdf created and submitted to Rachana (Katie)
==Scientific Progress Report==

*[[Media:Progress_Report_Template_National_Centers_for_Biomedical_Computing_2.1.docx | New Progress Report Template]]
*[[Wiki_page_for_2013_Progress_Report_Assignments]]‎
*[[Wiki_page_for_2013_Preliminary_Draft]]

Wiki page for 2013 Progress Report Assignments

2012-10-13T13:33:16Z

Ann Adams: /* Assignments */

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

=Assignments=
Reporting Interval: 7/1/2012- 6/30/2013
{| class="wikitable sortable labelpage labelpagetable" border="1" width="100%" cellpadding="5"
|- style="background:#c2c2c2; color:black" align="left"
| style="width:20%" | Task
| style="width:20%" | Owner
| style="width:60%" | Title, comments
|-
| style="background:#ffffdd; color:black" align="center"|1. INTRODUCTION
| style="background:#c4f4af; color:black"|Ann
| style="background:#fff6a6; color:black"|Update Figure 1-1. Geo-anatomical Map of NA-MIC Collaborations, Recent changes and Center (administrative) highlights
|-
| style="background:#ffffdd; color:black" align="center"|2. [[2012_Progress_Report_HIGHLIGHTS | HIGHLIGHTS]]
| style="background:#c4f4af; color:black"|Will Schroeder, Kitware
| style="background:#b4e4d4; color:black"|2.1 Algorithms, 2.2 Engineering, 2.3 NA-MIC Kit.
| style="background:#b4e4d4; color:black"|Submitted on 4/23/2012
|-
| style="background:#ffffdd; color:black" align="center"|3. [[2012_Progress_Report_IMPACT | IMPACT AND VALUE TO BIOCOMPUTING]]
| style="background:#c4f4af; color:black"|Jim Miller, GE
| style="background:#b4e4d4; color:black"|3.1 Impact within the Center, 3.2 Impact within NIH-Funded Research, 3.3 National and International Impact
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-
| style="background:#ffffdd; color:black" align="center"|4. RESEARCH PROGRESS SUMMARIES
| style="background:#c4f4af; color:black"|
| style="background:#fff6a6; color:black"|
|-
| style="background:#ffffdd; color:black" align="center"|4.1 DRIVING BIOLOGICAL PROJECTS
| style="background:#c4f4af; color:black"|DBP PIs
| style="background:#fff6a6; color:black"|
|-
| style="background:#ffffdd; color:black" align="center"|4.1.1 [[2012_Progress_Report_DBP Atrial_Fibrillation | Atrial Fibrillation]]
| style="background:#c4f4af; color:black"|Rob MacLeod, Utah
| style="background:#b4ebd4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-
| style="background:#ffffdd; color:black" align="center"|4.1.2 [[2012_Progress_Report_DBP Huntington's Disease | Huntington's Disease]]
| style="background:#c4f4af; color:black"|Hans Johnson, Iowa
| style="background:#b4e4d4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/18/2012
|-
| style="background:#ffffdd; color:black" align="center"|4.1.3 [[2012_Progress_Report_DBP Adaptive Radiotherapy | Adaptive Radiotherapy for Head and Neck Cancer]]
| style="background:#c4f4af; color:black"|Gregory C. Sharp, MGH
| style="background:#b4e4d4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/17/2012
|-
| style="background:#ffffdd; color:black" align="center"|4.1.4 [[2012_Progress_Report_DBP_TBI | Traumatic Brain Injury]]
| style="background:#c4f4af; color:black"|Jack Van Horn, UCLA
| style="background:#b4e4d4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/2/2012
|-
| style="background:#ffffdd; color:black" align="center"|5. COMPUTER SCIENCE CORE
| style="background:#c4f4af; color:black"|Ross Whitaker
| style="background:#fff6a6; color:black"|Brief Introduction: Algorithms, Engineering, NA-MIC Kit 
|-
| style="background:#ffffdd; color:black" align="center"|5.1 Algorithms
| style="background:#c4f4af; color:black"|Polina Golland, Guido Gerig, Allen Tannenbaum, Martin Styner
| style="background:#b4e4d4; color:black"|5.1.1 Statistical Models of Anatomy and Pathology, Polina Golland A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012 
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black"|5.1.2. Geometric Correspondence, Guido Gerig A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC 
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012 
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black"|5.1.3. User Interactive Segmentation, Allen Tannenbaum A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012 
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black"|5.1.4. Longitudinal and Time Series Analysis, Martin Styner A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012 
|-
| style="background:#ffffdd; color:black" align="center"|5.2
| style="background:#c4f4af; color:black"|Will Schroeder, Steven Aylward, Steve Pieper, Jim Miller
| style="background:#b4e4d4; color:black"|5.2.1. [[2012_Progress_Report_Science_Wiki_Version_Engineering | End-user Platform, Steve Pieper]]
| style="background:#b4e4d4; color:black"|Submitted on 4/2/2012
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black" align="center"|5.2.2. [[2012_Progress_Report_Science_Wiki_Version_Engineering | Computational Platform, Jim Miller]]
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-

| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black" align="center"|5.2.3. [[2012_Progress_Report_Science_Wiki_Version_Engineering | Data Management Platform, Dan Marcus]]
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black" align="center"|5.2.4.[[2012_Progress_Report_Science_Wiki_Version_Engineering | Software Process, Stephen R. Aylward ]]
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-
| style="background:#ffffdd; color:black" align="center"|5.3 [[2012_Progress_Report_Science_Wiki_Version_Engineering | NA-MIC Kit]]
| style="background:#c4f4af; color:black"|Will Schroeder, Steven Aylward, Steve Pieper, Jim Miller
| style="background:#b4e4d4; color:black"|5.3.1. [[2012_Progress_Report_Science_Wiki_Version_Engineering | Expansion 5.3.2. Release ]]
| style="background:#b4e4d4; color:black"|Submitted on 4/21/2012
|-
| style="background:#ffffdd; color:black" align="center"|6. [[2012_Progress_Report_ARRA_Supplement| ARRA SUPPLEMENT]]
| style="background:#c4f4af; color:black"|Steve Aylward
| style="background:#b4e4d4; color:black"|6.1 Summary of Funded Activity
| style="background:#b4e4d4; color:black"|Submitted on 4/2/2012
|-
| style="background:#ffffdd; color:black" align="center"|7. [[2012_Progress_Report_Outreach| OUTREACH]]
| style="background:#c4f4af; color:black"|Sonia Pujol
| style="background:#b4e4d4; color:black"|7.1 Summary of Outreach Activities 
| style="background:#b4e4d4; color:black"|Submitted on 4/13/2012
|-
| style="background:#ffffdd; color:black" align="center"|8. NA-MIC PUBLICATIONS
| style="background:#c4f4af; color:black"|Marianna
| style="background:#fff6a6; color:black"|8.1 Papers that Acknowledge NA-MIC, 8.2. Conference Reports [[2012_Progress_Report#Dissemination|Go to All Papers List]] 
|-
| style="background:#ffffdd; color:black" align="center"|9. External Advisory Board (EAB) Report
| style="background:#c4f4af; color:black"|Bill Lorensen
| style="background:#fff6a6; color:black"|

Wiki page for 2013 Progress Report Assignments

2012-10-13T13:31:38Z

Ann Adams:

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

=Assignments=
Reporting Interval: 7/1/2012- 6/30/2013
{| class="wikitable sortable labelpage labelpagetable" border="1" width="100%" cellpadding="5"
|- style="background:#c2c2c2; color:black" align="left"
| style="width:20%" | Task
| style="width:20%" | Owner
| style="width:60%" | Title, comments
|-
| style="background:#ffffdd; color:black" align="center"|1. INTRODUCTION
| style="background:#c4f4af; color:black"|Ron
| style="background:#fff6a6; color:black"|Update Figure 1-1. Geo-anatomical Map of NA-MIC Collaborations, Recent changes and Center (administrative) highlights
|-
| style="background:#ffffdd; color:black" align="center"|2. [[2012_Progress_Report_HIGHLIGHTS | HIGHLIGHTS]]
| style="background:#c4f4af; color:black"|Will Schroeder, Kitware
| style="background:#b4e4d4; color:black"|2.1 Algorithms, 2.2 Engineering, 2.3 NA-MIC Kit.
| style="background:#b4e4d4; color:black"|Submitted on 4/23/2012
|-
| style="background:#ffffdd; color:black" align="center"|3. [[2012_Progress_Report_IMPACT | IMPACT AND VALUE TO BIOCOMPUTING]]
| style="background:#c4f4af; color:black"|Jim Miller, GE
| style="background:#b4e4d4; color:black"|3.1 Impact within the Center, 3.2 Impact within NIH-Funded Research, 3.3 National and International Impact
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-
| style="background:#ffffdd; color:black" align="center"|4. RESEARCH PROGRESS SUMMARIES
| style="background:#c4f4af; color:black"|
| style="background:#fff6a6; color:black"|
|-
| style="background:#ffffdd; color:black" align="center"|4.1 DRIVING BIOLOGICAL PROJECTS
| style="background:#c4f4af; color:black"|DBP PIs
| style="background:#fff6a6; color:black"|
|-
| style="background:#ffffdd; color:black" align="center"|4.1.1 [[2012_Progress_Report_DBP Atrial_Fibrillation | Atrial Fibrillation]]
| style="background:#c4f4af; color:black"|Rob MacLeod, Utah
| style="background:#b4ebd4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-
| style="background:#ffffdd; color:black" align="center"|4.1.2 [[2012_Progress_Report_DBP Huntington's Disease | Huntington's Disease]]
| style="background:#c4f4af; color:black"|Hans Johnson, Iowa
| style="background:#b4e4d4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/18/2012
|-
| style="background:#ffffdd; color:black" align="center"|4.1.3 [[2012_Progress_Report_DBP Adaptive Radiotherapy | Adaptive Radiotherapy for Head and Neck Cancer]]
| style="background:#c4f4af; color:black"|Gregory C. Sharp, MGH
| style="background:#b4e4d4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/17/2012
|-
| style="background:#ffffdd; color:black" align="center"|4.1.4 [[2012_Progress_Report_DBP_TBI | Traumatic Brain Injury]]
| style="background:#c4f4af; color:black"|Jack Van Horn, UCLA
| style="background:#b4e4d4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/2/2012
|-
| style="background:#ffffdd; color:black" align="center"|5. COMPUTER SCIENCE CORE
| style="background:#c4f4af; color:black"|Ross Whitaker
| style="background:#fff6a6; color:black"|Brief Introduction: Algorithms, Engineering, NA-MIC Kit 
|-
| style="background:#ffffdd; color:black" align="center"|5.1 Algorithms
| style="background:#c4f4af; color:black"|Polina Golland, Guido Gerig, Allen Tannenbaum, Martin Styner
| style="background:#b4e4d4; color:black"|5.1.1 Statistical Models of Anatomy and Pathology, Polina Golland A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012 
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black"|5.1.2. Geometric Correspondence, Guido Gerig A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC 
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012 
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black"|5.1.3. User Interactive Segmentation, Allen Tannenbaum A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012 
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black"|5.1.4. Longitudinal and Time Series Analysis, Martin Styner A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012 
|-
| style="background:#ffffdd; color:black" align="center"|5.2
| style="background:#c4f4af; color:black"|Will Schroeder, Steven Aylward, Steve Pieper, Jim Miller
| style="background:#b4e4d4; color:black"|5.2.1. [[2012_Progress_Report_Science_Wiki_Version_Engineering | End-user Platform, Steve Pieper]]
| style="background:#b4e4d4; color:black"|Submitted on 4/2/2012
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black" align="center"|5.2.2. [[2012_Progress_Report_Science_Wiki_Version_Engineering | Computational Platform, Jim Miller]]
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-

| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black" align="center"|5.2.3. [[2012_Progress_Report_Science_Wiki_Version_Engineering | Data Management Platform, Dan Marcus]]
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black" align="center"|5.2.4.[[2012_Progress_Report_Science_Wiki_Version_Engineering | Software Process, Stephen R. Aylward ]]
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-
| style="background:#ffffdd; color:black" align="center"|5.3 [[2012_Progress_Report_Science_Wiki_Version_Engineering | NA-MIC Kit]]
| style="background:#c4f4af; color:black"|Will Schroeder, Steven Aylward, Steve Pieper, Jim Miller
| style="background:#b4e4d4; color:black"|5.3.1. [[2012_Progress_Report_Science_Wiki_Version_Engineering | Expansion 5.3.2. Release ]]
| style="background:#b4e4d4; color:black"|Submitted on 4/21/2012
|-
| style="background:#ffffdd; color:black" align="center"|6. [[2012_Progress_Report_ARRA_Supplement| ARRA SUPPLEMENT]]
| style="background:#c4f4af; color:black"|Steve Aylward
| style="background:#b4e4d4; color:black"|6.1 Summary of Funded Activity
| style="background:#b4e4d4; color:black"|Submitted on 4/2/2012
|-
| style="background:#ffffdd; color:black" align="center"|7. [[2012_Progress_Report_Outreach| OUTREACH]]
| style="background:#c4f4af; color:black"|Sonia Pujol
| style="background:#b4e4d4; color:black"|7.1 Summary of Outreach Activities 
| style="background:#b4e4d4; color:black"|Submitted on 4/13/2012
|-
| style="background:#ffffdd; color:black" align="center"|8. NA-MIC PUBLICATIONS
| style="background:#c4f4af; color:black"|Marianna
| style="background:#fff6a6; color:black"|8.1 Papers that Acknowledge NA-MIC, 8.2. Conference Reports [[2012_Progress_Report#Dissemination|Go to All Papers List]] 
|-
| style="background:#ffffdd; color:black" align="center"|9. External Advisory Board (EAB) Report
| style="background:#c4f4af; color:black"|Bill Lorensen
| style="background:#fff6a6; color:black"|

Wiki page for 2013 Progress Report Assignments

2012-10-13T13:31:00Z

Ann Adams:

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]
Back to [[2013_Progress_Report_Assignments]]

=Assignments=
Reporting Interval: 7/1/2012- 6/30/2013
{| class="wikitable sortable labelpage labelpagetable" border="1" width="100%" cellpadding="5"
|- style="background:#c2c2c2; color:black" align="left"
| style="width:20%" | Task
| style="width:20%" | Owner
| style="width:60%" | Title, comments
|-
| style="background:#ffffdd; color:black" align="center"|1. INTRODUCTION
| style="background:#c4f4af; color:black"|Ron
| style="background:#fff6a6; color:black"|Update Figure 1-1. Geo-anatomical Map of NA-MIC Collaborations, Recent changes and Center (administrative) highlights
|-
| style="background:#ffffdd; color:black" align="center"|2. [[2012_Progress_Report_HIGHLIGHTS | HIGHLIGHTS]]
| style="background:#c4f4af; color:black"|Will Schroeder, Kitware
| style="background:#b4e4d4; color:black"|2.1 Algorithms, 2.2 Engineering, 2.3 NA-MIC Kit.
| style="background:#b4e4d4; color:black"|Submitted on 4/23/2012
|-
| style="background:#ffffdd; color:black" align="center"|3. [[2012_Progress_Report_IMPACT | IMPACT AND VALUE TO BIOCOMPUTING]]
| style="background:#c4f4af; color:black"|Jim Miller, GE
| style="background:#b4e4d4; color:black"|3.1 Impact within the Center, 3.2 Impact within NIH-Funded Research, 3.3 National and International Impact
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-
| style="background:#ffffdd; color:black" align="center"|4. RESEARCH PROGRESS SUMMARIES
| style="background:#c4f4af; color:black"|
| style="background:#fff6a6; color:black"|
|-
| style="background:#ffffdd; color:black" align="center"|4.1 DRIVING BIOLOGICAL PROJECTS
| style="background:#c4f4af; color:black"|DBP PIs
| style="background:#fff6a6; color:black"|
|-
| style="background:#ffffdd; color:black" align="center"|4.1.1 [[2012_Progress_Report_DBP Atrial_Fibrillation | Atrial Fibrillation]]
| style="background:#c4f4af; color:black"|Rob MacLeod, Utah
| style="background:#b4ebd4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-
| style="background:#ffffdd; color:black" align="center"|4.1.2 [[2012_Progress_Report_DBP Huntington's Disease | Huntington's Disease]]
| style="background:#c4f4af; color:black"|Hans Johnson, Iowa
| style="background:#b4e4d4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/18/2012
|-
| style="background:#ffffdd; color:black" align="center"|4.1.3 [[2012_Progress_Report_DBP Adaptive Radiotherapy | Adaptive Radiotherapy for Head and Neck Cancer]]
| style="background:#c4f4af; color:black"|Gregory C. Sharp, MGH
| style="background:#b4e4d4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/17/2012
|-
| style="background:#ffffdd; color:black" align="center"|4.1.4 [[2012_Progress_Report_DBP_TBI | Traumatic Brain Injury]]
| style="background:#c4f4af; color:black"|Jack Van Horn, UCLA
| style="background:#b4e4d4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/2/2012
|-
| style="background:#ffffdd; color:black" align="center"|5. COMPUTER SCIENCE CORE
| style="background:#c4f4af; color:black"|Ross Whitaker
| style="background:#fff6a6; color:black"|Brief Introduction: Algorithms, Engineering, NA-MIC Kit 
|-
| style="background:#ffffdd; color:black" align="center"|5.1 Algorithms
| style="background:#c4f4af; color:black"|Polina Golland, Guido Gerig, Allen Tannenbaum, Martin Styner
| style="background:#b4e4d4; color:black"|5.1.1 Statistical Models of Anatomy and Pathology, Polina Golland A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012 
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black"|5.1.2. Geometric Correspondence, Guido Gerig A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC 
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012 
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black"|5.1.3. User Interactive Segmentation, Allen Tannenbaum A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012 
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black"|5.1.4. Longitudinal and Time Series Analysis, Martin Styner A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012 
|-
| style="background:#ffffdd; color:black" align="center"|5.2
| style="background:#c4f4af; color:black"|Will Schroeder, Steven Aylward, Steve Pieper, Jim Miller
| style="background:#b4e4d4; color:black"|5.2.1. [[2012_Progress_Report_Science_Wiki_Version_Engineering | End-user Platform, Steve Pieper]]
| style="background:#b4e4d4; color:black"|Submitted on 4/2/2012
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black" align="center"|5.2.2. [[2012_Progress_Report_Science_Wiki_Version_Engineering | Computational Platform, Jim Miller]]
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-

| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black" align="center"|5.2.3. [[2012_Progress_Report_Science_Wiki_Version_Engineering | Data Management Platform, Dan Marcus]]
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black" align="center"|5.2.4.[[2012_Progress_Report_Science_Wiki_Version_Engineering | Software Process, Stephen R. Aylward ]]
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-
| style="background:#ffffdd; color:black" align="center"|5.3 [[2012_Progress_Report_Science_Wiki_Version_Engineering | NA-MIC Kit]]
| style="background:#c4f4af; color:black"|Will Schroeder, Steven Aylward, Steve Pieper, Jim Miller
| style="background:#b4e4d4; color:black"|5.3.1. [[2012_Progress_Report_Science_Wiki_Version_Engineering | Expansion 5.3.2. Release ]]
| style="background:#b4e4d4; color:black"|Submitted on 4/21/2012
|-
| style="background:#ffffdd; color:black" align="center"|6. [[2012_Progress_Report_ARRA_Supplement| ARRA SUPPLEMENT]]
| style="background:#c4f4af; color:black"|Steve Aylward
| style="background:#b4e4d4; color:black"|6.1 Summary of Funded Activity
| style="background:#b4e4d4; color:black"|Submitted on 4/2/2012
|-
| style="background:#ffffdd; color:black" align="center"|7. [[2012_Progress_Report_Outreach| OUTREACH]]
| style="background:#c4f4af; color:black"|Sonia Pujol
| style="background:#b4e4d4; color:black"|7.1 Summary of Outreach Activities 
| style="background:#b4e4d4; color:black"|Submitted on 4/13/2012
|-
| style="background:#ffffdd; color:black" align="center"|8. NA-MIC PUBLICATIONS
| style="background:#c4f4af; color:black"|Marianna
| style="background:#fff6a6; color:black"|8.1 Papers that Acknowledge NA-MIC, 8.2. Conference Reports [[2012_Progress_Report#Dissemination|Go to All Papers List]] 
|-
| style="background:#ffffdd; color:black" align="center"|9. External Advisory Board (EAB) Report
| style="background:#c4f4af; color:black"|Bill Lorensen
| style="background:#fff6a6; color:black"|

Wiki page for 2013 Progress Report Assignments

2012-10-13T13:29:16Z

Ann Adams: /* Assignments: Short version */

=Assignments=
Reporting Interval: 7/1/2012- 6/30/2013
{| class="wikitable sortable labelpage labelpagetable" border="1" width="100%" cellpadding="5"
|- style="background:#c2c2c2; color:black" align="left"
| style="width:20%" | Task
| style="width:20%" | Owner
| style="width:60%" | Title, comments
|-
| style="background:#ffffdd; color:black" align="center"|1. INTRODUCTION
| style="background:#c4f4af; color:black"|Ron
| style="background:#fff6a6; color:black"|Update Figure 1-1. Geo-anatomical Map of NA-MIC Collaborations, Recent changes and Center (administrative) highlights
|-
| style="background:#ffffdd; color:black" align="center"|2. [[2012_Progress_Report_HIGHLIGHTS | HIGHLIGHTS]]
| style="background:#c4f4af; color:black"|Will Schroeder, Kitware
| style="background:#b4e4d4; color:black"|2.1 Algorithms, 2.2 Engineering, 2.3 NA-MIC Kit.
| style="background:#b4e4d4; color:black"|Submitted on 4/23/2012
|-
| style="background:#ffffdd; color:black" align="center"|3. [[2012_Progress_Report_IMPACT | IMPACT AND VALUE TO BIOCOMPUTING]]
| style="background:#c4f4af; color:black"|Jim Miller, GE
| style="background:#b4e4d4; color:black"|3.1 Impact within the Center, 3.2 Impact within NIH-Funded Research, 3.3 National and International Impact
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-
| style="background:#ffffdd; color:black" align="center"|4. RESEARCH PROGRESS SUMMARIES
| style="background:#c4f4af; color:black"|
| style="background:#fff6a6; color:black"|
|-
| style="background:#ffffdd; color:black" align="center"|4.1 DRIVING BIOLOGICAL PROJECTS
| style="background:#c4f4af; color:black"|DBP PIs
| style="background:#fff6a6; color:black"|
|-
| style="background:#ffffdd; color:black" align="center"|4.1.1 [[2012_Progress_Report_DBP Atrial_Fibrillation | Atrial Fibrillation]]
| style="background:#c4f4af; color:black"|Rob MacLeod, Utah
| style="background:#b4ebd4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-
| style="background:#ffffdd; color:black" align="center"|4.1.2 [[2012_Progress_Report_DBP Huntington's Disease | Huntington's Disease]]
| style="background:#c4f4af; color:black"|Hans Johnson, Iowa
| style="background:#b4e4d4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/18/2012
|-
| style="background:#ffffdd; color:black" align="center"|4.1.3 [[2012_Progress_Report_DBP Adaptive Radiotherapy | Adaptive Radiotherapy for Head and Neck Cancer]]
| style="background:#c4f4af; color:black"|Gregory C. Sharp, MGH
| style="background:#b4e4d4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/17/2012
|-
| style="background:#ffffdd; color:black" align="center"|4.1.4 [[2012_Progress_Report_DBP_TBI | Traumatic Brain Injury]]
| style="background:#c4f4af; color:black"|Jack Van Horn, UCLA
| style="background:#b4e4d4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/2/2012
|-
| style="background:#ffffdd; color:black" align="center"|5. COMPUTER SCIENCE CORE
| style="background:#c4f4af; color:black"|Ross Whitaker
| style="background:#fff6a6; color:black"|Brief Introduction: Algorithms, Engineering, NA-MIC Kit 
|-
| style="background:#ffffdd; color:black" align="center"|5.1 Algorithms
| style="background:#c4f4af; color:black"|Polina Golland, Guido Gerig, Allen Tannenbaum, Martin Styner
| style="background:#b4e4d4; color:black"|5.1.1 Statistical Models of Anatomy and Pathology, Polina Golland A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012 
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black"|5.1.2. Geometric Correspondence, Guido Gerig A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC 
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012 
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black"|5.1.3. User Interactive Segmentation, Allen Tannenbaum A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012 
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black"|5.1.4. Longitudinal and Time Series Analysis, Martin Styner A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012 
|-
| style="background:#ffffdd; color:black" align="center"|5.2
| style="background:#c4f4af; color:black"|Will Schroeder, Steven Aylward, Steve Pieper, Jim Miller
| style="background:#b4e4d4; color:black"|5.2.1. [[2012_Progress_Report_Science_Wiki_Version_Engineering | End-user Platform, Steve Pieper]]
| style="background:#b4e4d4; color:black"|Submitted on 4/2/2012
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black" align="center"|5.2.2. [[2012_Progress_Report_Science_Wiki_Version_Engineering | Computational Platform, Jim Miller]]
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-

| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black" align="center"|5.2.3. [[2012_Progress_Report_Science_Wiki_Version_Engineering | Data Management Platform, Dan Marcus]]
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black" align="center"|5.2.4.[[2012_Progress_Report_Science_Wiki_Version_Engineering | Software Process, Stephen R. Aylward ]]
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-
| style="background:#ffffdd; color:black" align="center"|5.3 [[2012_Progress_Report_Science_Wiki_Version_Engineering | NA-MIC Kit]]
| style="background:#c4f4af; color:black"|Will Schroeder, Steven Aylward, Steve Pieper, Jim Miller
| style="background:#b4e4d4; color:black"|5.3.1. [[2012_Progress_Report_Science_Wiki_Version_Engineering | Expansion 5.3.2. Release ]]
| style="background:#b4e4d4; color:black"|Submitted on 4/21/2012
|-
| style="background:#ffffdd; color:black" align="center"|6. [[2012_Progress_Report_ARRA_Supplement| ARRA SUPPLEMENT]]
| style="background:#c4f4af; color:black"|Steve Aylward
| style="background:#b4e4d4; color:black"|6.1 Summary of Funded Activity
| style="background:#b4e4d4; color:black"|Submitted on 4/2/2012
|-
| style="background:#ffffdd; color:black" align="center"|7. [[2012_Progress_Report_Outreach| OUTREACH]]
| style="background:#c4f4af; color:black"|Sonia Pujol
| style="background:#b4e4d4; color:black"|7.1 Summary of Outreach Activities 
| style="background:#b4e4d4; color:black"|Submitted on 4/13/2012
|-
| style="background:#ffffdd; color:black" align="center"|8. NA-MIC PUBLICATIONS
| style="background:#c4f4af; color:black"|Marianna
| style="background:#fff6a6; color:black"|8.1 Papers that Acknowledge NA-MIC, 8.2. Conference Reports [[2012_Progress_Report#Dissemination|Go to All Papers List]] 
|-
| style="background:#ffffdd; color:black" align="center"|9. External Advisory Board (EAB) Report
| style="background:#c4f4af; color:black"|Bill Lorensen
| style="background:#fff6a6; color:black"|

Wiki page for 2013 Progress Report Assignments

2012-10-13T13:29:03Z

Ann Adams: /* Assignments: Short version */

=Assignments: Short version=
Reporting Interval: 7/1/2012- 6/30/2013
{| class="wikitable sortable labelpage labelpagetable" border="1" width="100%" cellpadding="5"
|- style="background:#c2c2c2; color:black" align="left"
| style="width:20%" | Task
| style="width:20%" | Owner
| style="width:60%" | Title, comments
|-
| style="background:#ffffdd; color:black" align="center"|1. INTRODUCTION
| style="background:#c4f4af; color:black"|Ron
| style="background:#fff6a6; color:black"|Update Figure 1-1. Geo-anatomical Map of NA-MIC Collaborations, Recent changes and Center (administrative) highlights
|-
| style="background:#ffffdd; color:black" align="center"|2. [[2012_Progress_Report_HIGHLIGHTS | HIGHLIGHTS]]
| style="background:#c4f4af; color:black"|Will Schroeder, Kitware
| style="background:#b4e4d4; color:black"|2.1 Algorithms, 2.2 Engineering, 2.3 NA-MIC Kit.
| style="background:#b4e4d4; color:black"|Submitted on 4/23/2012
|-
| style="background:#ffffdd; color:black" align="center"|3. [[2012_Progress_Report_IMPACT | IMPACT AND VALUE TO BIOCOMPUTING]]
| style="background:#c4f4af; color:black"|Jim Miller, GE
| style="background:#b4e4d4; color:black"|3.1 Impact within the Center, 3.2 Impact within NIH-Funded Research, 3.3 National and International Impact
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-
| style="background:#ffffdd; color:black" align="center"|4. RESEARCH PROGRESS SUMMARIES
| style="background:#c4f4af; color:black"|
| style="background:#fff6a6; color:black"|
|-
| style="background:#ffffdd; color:black" align="center"|4.1 DRIVING BIOLOGICAL PROJECTS
| style="background:#c4f4af; color:black"|DBP PIs
| style="background:#fff6a6; color:black"|
|-
| style="background:#ffffdd; color:black" align="center"|4.1.1 [[2012_Progress_Report_DBP Atrial_Fibrillation | Atrial Fibrillation]]
| style="background:#c4f4af; color:black"|Rob MacLeod, Utah
| style="background:#b4ebd4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-
| style="background:#ffffdd; color:black" align="center"|4.1.2 [[2012_Progress_Report_DBP Huntington's Disease | Huntington's Disease]]
| style="background:#c4f4af; color:black"|Hans Johnson, Iowa
| style="background:#b4e4d4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/18/2012
|-
| style="background:#ffffdd; color:black" align="center"|4.1.3 [[2012_Progress_Report_DBP Adaptive Radiotherapy | Adaptive Radiotherapy for Head and Neck Cancer]]
| style="background:#c4f4af; color:black"|Gregory C. Sharp, MGH
| style="background:#b4e4d4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/17/2012
|-
| style="background:#ffffdd; color:black" align="center"|4.1.4 [[2012_Progress_Report_DBP_TBI | Traumatic Brain Injury]]
| style="background:#c4f4af; color:black"|Jack Van Horn, UCLA
| style="background:#b4e4d4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/2/2012
|-
| style="background:#ffffdd; color:black" align="center"|5. COMPUTER SCIENCE CORE
| style="background:#c4f4af; color:black"|Ross Whitaker
| style="background:#fff6a6; color:black"|Brief Introduction: Algorithms, Engineering, NA-MIC Kit 
|-
| style="background:#ffffdd; color:black" align="center"|5.1 Algorithms
| style="background:#c4f4af; color:black"|Polina Golland, Guido Gerig, Allen Tannenbaum, Martin Styner
| style="background:#b4e4d4; color:black"|5.1.1 Statistical Models of Anatomy and Pathology, Polina Golland A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012 
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black"|5.1.2. Geometric Correspondence, Guido Gerig A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC 
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012 
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black"|5.1.3. User Interactive Segmentation, Allen Tannenbaum A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012 
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black"|5.1.4. Longitudinal and Time Series Analysis, Martin Styner A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012 
|-
| style="background:#ffffdd; color:black" align="center"|5.2
| style="background:#c4f4af; color:black"|Will Schroeder, Steven Aylward, Steve Pieper, Jim Miller
| style="background:#b4e4d4; color:black"|5.2.1. [[2012_Progress_Report_Science_Wiki_Version_Engineering | End-user Platform, Steve Pieper]]
| style="background:#b4e4d4; color:black"|Submitted on 4/2/2012
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black" align="center"|5.2.2. [[2012_Progress_Report_Science_Wiki_Version_Engineering | Computational Platform, Jim Miller]]
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-

| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black" align="center"|5.2.3. [[2012_Progress_Report_Science_Wiki_Version_Engineering | Data Management Platform, Dan Marcus]]
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black" align="center"|5.2.4.[[2012_Progress_Report_Science_Wiki_Version_Engineering | Software Process, Stephen R. Aylward ]]
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-
| style="background:#ffffdd; color:black" align="center"|5.3 [[2012_Progress_Report_Science_Wiki_Version_Engineering | NA-MIC Kit]]
| style="background:#c4f4af; color:black"|Will Schroeder, Steven Aylward, Steve Pieper, Jim Miller
| style="background:#b4e4d4; color:black"|5.3.1. [[2012_Progress_Report_Science_Wiki_Version_Engineering | Expansion 5.3.2. Release ]]
| style="background:#b4e4d4; color:black"|Submitted on 4/21/2012
|-
| style="background:#ffffdd; color:black" align="center"|6. [[2012_Progress_Report_ARRA_Supplement| ARRA SUPPLEMENT]]
| style="background:#c4f4af; color:black"|Steve Aylward
| style="background:#b4e4d4; color:black"|6.1 Summary of Funded Activity
| style="background:#b4e4d4; color:black"|Submitted on 4/2/2012
|-
| style="background:#ffffdd; color:black" align="center"|7. [[2012_Progress_Report_Outreach| OUTREACH]]
| style="background:#c4f4af; color:black"|Sonia Pujol
| style="background:#b4e4d4; color:black"|7.1 Summary of Outreach Activities 
| style="background:#b4e4d4; color:black"|Submitted on 4/13/2012
|-
| style="background:#ffffdd; color:black" align="center"|8. NA-MIC PUBLICATIONS
| style="background:#c4f4af; color:black"|Marianna
| style="background:#fff6a6; color:black"|8.1 Papers that Acknowledge NA-MIC, 8.2. Conference Reports [[2012_Progress_Report#Dissemination|Go to All Papers List]] 
|-
| style="background:#ffffdd; color:black" align="center"|9. External Advisory Board (EAB) Report
| style="background:#c4f4af; color:black"|Bill Lorensen
| style="background:#fff6a6; color:black"|

Wiki page for 2013 Progress Report Assignments

2012-10-13T13:28:24Z

Ann Adams: Created page with '=Assignments: Short version= Reporting Interval: 7/1/2011- 6/30/2012 {| class="wikitable sortable labelpage labelpagetable" border="1" width="100%" cellpadding="5" |- style="bac…'

=Assignments: Short version=
Reporting Interval: 7/1/2011- 6/30/2012
{| class="wikitable sortable labelpage labelpagetable" border="1" width="100%" cellpadding="5"
|- style="background:#c2c2c2; color:black" align="left"
| style="width:20%" | Task
| style="width:20%" | Owner
| style="width:60%" | Title, comments
|-
| style="background:#ffffdd; color:black" align="center"|1. INTRODUCTION
| style="background:#c4f4af; color:black"|Ron
| style="background:#fff6a6; color:black"|Update Figure 1-1. Geo-anatomical Map of NA-MIC Collaborations, Recent changes and Center (administrative) highlights
|-
| style="background:#ffffdd; color:black" align="center"|2. [[2012_Progress_Report_HIGHLIGHTS | HIGHLIGHTS]]
| style="background:#c4f4af; color:black"|Will Schroeder, Kitware
| style="background:#b4e4d4; color:black"|2.1 Algorithms, 2.2 Engineering, 2.3 NA-MIC Kit.
| style="background:#b4e4d4; color:black"|Submitted on 4/23/2012
|-
| style="background:#ffffdd; color:black" align="center"|3. [[2012_Progress_Report_IMPACT | IMPACT AND VALUE TO BIOCOMPUTING]]
| style="background:#c4f4af; color:black"|Jim Miller, GE
| style="background:#b4e4d4; color:black"|3.1 Impact within the Center, 3.2 Impact within NIH-Funded Research, 3.3 National and International Impact
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-
| style="background:#ffffdd; color:black" align="center"|4. RESEARCH PROGRESS SUMMARIES
| style="background:#c4f4af; color:black"|
| style="background:#fff6a6; color:black"|
|-
| style="background:#ffffdd; color:black" align="center"|4.1 DRIVING BIOLOGICAL PROJECTS
| style="background:#c4f4af; color:black"|DBP PIs
| style="background:#fff6a6; color:black"|
|-
| style="background:#ffffdd; color:black" align="center"|4.1.1 [[2012_Progress_Report_DBP Atrial_Fibrillation | Atrial Fibrillation]]
| style="background:#c4f4af; color:black"|Rob MacLeod, Utah
| style="background:#b4ebd4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-
| style="background:#ffffdd; color:black" align="center"|4.1.2 [[2012_Progress_Report_DBP Huntington's Disease | Huntington's Disease]]
| style="background:#c4f4af; color:black"|Hans Johnson, Iowa
| style="background:#b4e4d4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/18/2012
|-
| style="background:#ffffdd; color:black" align="center"|4.1.3 [[2012_Progress_Report_DBP Adaptive Radiotherapy | Adaptive Radiotherapy for Head and Neck Cancer]]
| style="background:#c4f4af; color:black"|Gregory C. Sharp, MGH
| style="background:#b4e4d4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/17/2012
|-
| style="background:#ffffdd; color:black" align="center"|4.1.4 [[2012_Progress_Report_DBP_TBI | Traumatic Brain Injury]]
| style="background:#c4f4af; color:black"|Jack Van Horn, UCLA
| style="background:#b4e4d4; color:black"|A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/2/2012
|-
| style="background:#ffffdd; color:black" align="center"|5. COMPUTER SCIENCE CORE
| style="background:#c4f4af; color:black"|Ross Whitaker
| style="background:#fff6a6; color:black"|Brief Introduction: Algorithms, Engineering, NA-MIC Kit 
|-
| style="background:#ffffdd; color:black" align="center"|5.1 Algorithms
| style="background:#c4f4af; color:black"|Polina Golland, Guido Gerig, Allen Tannenbaum, Martin Styner
| style="background:#b4e4d4; color:black"|5.1.1 Statistical Models of Anatomy and Pathology, Polina Golland A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012 
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black"|5.1.2. Geometric Correspondence, Guido Gerig A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC 
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012 
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black"|5.1.3. User Interactive Segmentation, Allen Tannenbaum A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012 
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black"|5.1.4. Longitudinal and Time Series Analysis, Martin Styner A. Introduction, B. Research Progress Report, C. Plans for the Coming Year, D. Papers that Acknowledge NA-MIC
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012 
|-
| style="background:#ffffdd; color:black" align="center"|5.2
| style="background:#c4f4af; color:black"|Will Schroeder, Steven Aylward, Steve Pieper, Jim Miller
| style="background:#b4e4d4; color:black"|5.2.1. [[2012_Progress_Report_Science_Wiki_Version_Engineering | End-user Platform, Steve Pieper]]
| style="background:#b4e4d4; color:black"|Submitted on 4/2/2012
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black" align="center"|5.2.2. [[2012_Progress_Report_Science_Wiki_Version_Engineering | Computational Platform, Jim Miller]]
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-

| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black" align="center"|5.2.3. [[2012_Progress_Report_Science_Wiki_Version_Engineering | Data Management Platform, Dan Marcus]]
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-
| style="background:#ffffdd; color:black" align="center"|
| style="background:#c4f4af; color:black"|
| style="background:#b4e4d4; color:black" align="center"|5.2.4.[[2012_Progress_Report_Science_Wiki_Version_Engineering | Software Process, Stephen R. Aylward ]]
| style="background:#b4e4d4; color:black"|Submitted on 4/20/2012
|-
| style="background:#ffffdd; color:black" align="center"|5.3 [[2012_Progress_Report_Science_Wiki_Version_Engineering | NA-MIC Kit]]
| style="background:#c4f4af; color:black"|Will Schroeder, Steven Aylward, Steve Pieper, Jim Miller
| style="background:#b4e4d4; color:black"|5.3.1. [[2012_Progress_Report_Science_Wiki_Version_Engineering | Expansion 5.3.2. Release ]]
| style="background:#b4e4d4; color:black"|Submitted on 4/21/2012
|-
| style="background:#ffffdd; color:black" align="center"|6. [[2012_Progress_Report_ARRA_Supplement| ARRA SUPPLEMENT]]
| style="background:#c4f4af; color:black"|Steve Aylward
| style="background:#b4e4d4; color:black"|6.1 Summary of Funded Activity
| style="background:#b4e4d4; color:black"|Submitted on 4/2/2012
|-
| style="background:#ffffdd; color:black" align="center"|7. [[2012_Progress_Report_Outreach| OUTREACH]]
| style="background:#c4f4af; color:black"|Sonia Pujol
| style="background:#b4e4d4; color:black"|7.1 Summary of Outreach Activities 
| style="background:#b4e4d4; color:black"|Submitted on 4/13/2012
|-
| style="background:#ffffdd; color:black" align="center"|8. NA-MIC PUBLICATIONS
| style="background:#c4f4af; color:black"|Marianna
| style="background:#fff6a6; color:black"|8.1 Papers that Acknowledge NA-MIC, 8.2. Conference Reports [[2012_Progress_Report#Dissemination|Go to All Papers List]] 
|-
| style="background:#ffffdd; color:black" align="center"|9. External Advisory Board (EAB) Report
| style="background:#c4f4af; color:black"|Bill Lorensen
| style="background:#fff6a6; color:black"|

2013 Progress Report

2012-10-13T13:23:23Z

Ann Adams:

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

==Administrative Paperwork Timeline==

*TBA: LOI goes to subs (Sanjay/Rachana)
*TBA: Signed Subcontractor's Documents due back to BWH
*TBA: Review by Radiology Administration (Trey/Susan)
*TBA: Review by BWH RA
*TBA: Signed Facepage and budget docs due back to Katie M for page numbering (Katie)
*4/30/2013: Ship it to NIH

==Scientific Report Timeline==
*10/13/2012: wiki page setup for progress report (Ann)
*TBA: all sections to be completed by owners
*TBA: check NIH compliance of all publications in Pubmed (Katie)
*TBA: create final report (Ann)
*TBA: Update web pages with any new materials from report (Ann)
*TBA: create full publications list (Katie)
*TBA: final review (Tina, Ron)
*TBA: final pdf created and submitted to Rachana (Katie)
==Scientific Progress Report==

*[[Media:Progress_Report_Template_National_Centers_for_Biomedical_Computing_2.1.docx | New Progress Report Template]]
*[[Wiki_page_for_2013_Progress_Report_Assignments]]‎

2013 Progress Report

2012-10-13T13:18:55Z

Ann Adams: /* Scientific Progress Report */

==Scientific Progress Report==

*[[Media:Progress_Report_Template_National_Centers_for_Biomedical_Computing_2.1.docx | New Progress Report Template]]‎

2013 Progress Report

2012-10-13T13:18:36Z

Ann Adams:

===Scientific Progress Report===

*[[Media:Progress_Report_Template_National_Centers_for_Biomedical_Computing_2.1.docx | New Progress Report Template]]‎

2013 Progress Report

2012-10-13T13:18:17Z

Ann Adams: /* Scientific Progress Report */

NAMIC Annual Reports

2012-10-13T13:17:43Z

Ann Adams: /* 2013 Progress Report */

== Introduction to NAMIC Progress Reports ==

This page documents all Progress Reports prepared for NA-MIC. This includes the annual progress reports as well as intermediate reports and milestones submitted in response to requests by NIH.

==[[2013_Progress_Report|2013 Progress Report]]==

This is the 2013 Progress Report and all related materials.

==[[2012_Progress_Report|2012 Progress Report]]==
This is the 2012 Progress Report and all related materials.

== [[2011_Progress_Report|2011 Progress Report]] ==
This is the 2011 Progress Report and all related materials.

== 2010 Progress Report ==
This was the competitive renewal year, so a summary progress report was submitted with the renewal application.

== [[2009_Progress_Report|2009 Progress Report]] ==
This is the 2009 Progress Report and all related materials.

== [[2008_Progress_Report|2008 Progress Report]] ==
This is the 2008 Progress Report and all related materials.

== [[2007_Progress_Report|2007 Progress Report]] ==
This is the 2007 Progress Report and all related materials.

== [[2006_Progress_Report|2006 Progress Report]] ==

This is the 2006 Progress Report and all related materials as well as followup questions and answers.

== [[2005_Progress_Report|2005 Progress Report]] ==

2013 Progress Report

2012-10-13T12:57:46Z

Ann Adams:

===Scientific Progress Report===

*[[Media:Progress_Report_Template_National_Centers_for_Biomedical_Computing_2.1.docx | New Progress Report Template]]‎

NAMIC Annual Reports

2012-10-13T12:57:03Z

Ann Adams: /* 2013 Progress Report */

== Introduction to NAMIC Progress Reports ==

This page documents all Progress Reports prepared for NA-MIC. This includes the annual progress reports as well as intermediate reports and milestones submitted in response to requests by NIH.

==[[2013_Progress_Report|2013 Progress Report]]==

This is the 2013 Progress Report and all related materials.

Scientific Progress Report

==[[2012_Progress_Report|2012 Progress Report]]==
This is the 2012 Progress Report and all related materials.

== [[2011_Progress_Report|2011 Progress Report]] ==
This is the 2011 Progress Report and all related materials.

== 2010 Progress Report ==
This was the competitive renewal year, so a summary progress report was submitted with the renewal application.

== [[2009_Progress_Report|2009 Progress Report]] ==
This is the 2009 Progress Report and all related materials.

== [[2008_Progress_Report|2008 Progress Report]] ==
This is the 2008 Progress Report and all related materials.

== [[2007_Progress_Report|2007 Progress Report]] ==
This is the 2007 Progress Report and all related materials.

== [[2006_Progress_Report|2006 Progress Report]] ==

This is the 2006 Progress Report and all related materials as well as followup questions and answers.

== [[2005_Progress_Report|2005 Progress Report]] ==

2013 Progress Report

2012-10-13T12:56:15Z

Ann Adams:

*[[Media:Progress_Report_Template_National_Centers_for_Biomedical_Computing_2.1.docx | New Progress Report Template]]‎

File:Progress Report Template National Centers for Biomedical Computing 2.1.docx

2012-10-13T12:55:16Z

Ann Adams:

2012 Progress Report

2012-10-13T12:51:09Z

Ann Adams: /* Scientific Progress Report */

Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]

==Administrative Paperwork Timeline==

*3/14: LOI goes to subs (Sanjay/Rachana)
*4/06: Signed Subcontractor's Documents due back to BWH
*4/09: Review by Radiology Administration (Trey/Susan)
*4/13: Review by BWH RA
*4/27: Signed Facepage and budget docs due back to Katie M for page numbering (Katie)
*4/30: Ship it to NIH

==Scientific Report Timeline==
*4/1: wiki page setup for progress report (Ann)
*4/16: all sections to be completed by owners
*4/16: check NIH compliance of all publications in Pubmed (Katie)
*4/20: create final report (Ann)
*4/23: Update web pages with any new materials from report (Ann)
*4/20: create full publications list (Katie)
*4/22: final review (Tina, Ron)
*4/23: final pdf created and submitted to Rachana (Katie)

==Scientific Progress Report==

*[[media:Final_NA-MIC_APR_04.27.12_km.pdf | 2012 Scientific Progress Report]]

*[[media:2012 NA-MIC Progress Report Response (1).doc | 2012 Supplemental Response]]

==Dissemination==
Compiled from the SPL PubDB using search filter for EB005149.

http://www.na-mic.org/publications/pages/display?search=EB005149
===Publications===
#Choi H., Kubicki M., Whitford T.J., Alvarado J.L., Terry D.P., Niznikiewicz M., McCarley R.W., Kwon J.S., Shenton M.E. Diffusion Tensor Imaging of Anterior Commissural Fibers in Patients with Schizophrenia. Schizophr Res. 2011 Aug;130(1-3):78-85. PMID: 21561738. '''Keywords: Schizophrenia, Diffusion tensor imaging, Anterior commissure, White matter tractography, Fractional anisotropy, Trace''' 
#Cohen-Adad J., Benner T., Greve D., Kinkel R.P., Radding A., Fischl B., Rosen B.R., Mainero C. In vivo Evidence of Disseminated Subpial T2* Signal Changes in Multiple Sclerosis at 7 T: A Surface-based Analysis. Neuroimage. 2011 Jul 1;57(1):55-62. PMID: 21511042. '''Keywords: Multiple sclerosis, Surface-based analysis, Subpial pathology, Ultra-high field MRI, T2-weighted''' 
#Fedorov A., Li X., Pohl K.M., Bouix S., Styner M., Addicott M., Wyatt C., Daunais J.B., Wells III W.M., Kikinis R. Atlas-Guided Segmentation of Vervet Monkey Brain MRI. Open Neuroimag J. 2011; 5:186–197. PMID: 22253661. PMCID: PMC3256578. '''Keywords: Vervet monkey, brain MRI, brain morphology, image segmentation, image registration, open source software, 3D Slicer''' 
#Gadde S., Aucoin N., Grethe J.S., Keator D.B., Marcus D.S., Pieper S. XCEDE: An Extensible Schema for Biomedical Data. Neuroinformatics. 2012 Jan;10(1):19-32. PMID: 21479735. '''Keywords: XML, Schema, database, Biomedical technology''' 
#Gao Y., Corn B., Schifter D., Tannenbaum A. Multiscale 3D shape Representation and Segmentation with Applications to Hippocampal/Caudate Extraction from Brain MRI. Med Image Anal. 2012 Feb;16(2):374-85. PMID: 22119491. PMCID: PMC3267872. '''Keywords: Multiscale shape representation, Shape-based segmentation''' 
#Geng X., Gouttard S., Sharma A., Gu H., Styner M., Lind W., Gerig G., Gilmore J.H.. Quantitative Tract-Based White Matter Development from Birth to Age Two Years. Neuroimage. 2012 March 28. '''Keywords: white matter maturation, axonal myelination, early brain development, diffusion properties, DTI atlas, fiber tracking, functional regression analysis''' 
#Glasser M.F., Van Essen D.C. Mapping Human Cortical Areas in vivo Based on Myelin Content as Revealed by T1- and T2-weighted MRI. J Neurosci. 2011 Aug 10;31(32):11597-616. PMID: 21832190. PMCID: PMC3167149. 
#Hartley C.A., Fischl B., Phelps E.A. Brain Structure Correlates of Individual Differences in the Acquisition and Inhibition of Conditioned Fear. Cereb Cortex. 2011 Sep;21(9):1954-62. PMID: 21263037. PMCID: PMC3155599. 
#Irimia A., Chambers M.C., Alger J.R., Filippou M., Prastawa M.W., Wang B., Hovda D., Gerig G., Toga A.W., Kikinis R., Vespa P.M., Van Horn J.D. Comparison of Acute and Chronic Traumatic Brain Injury using Semi-automatic Multimodal Segmentation of MR Volumes. J Neurotrauma. 2011 Nov;28(11):2287-306. PMID: 21787171. '''Keywords: magnetic resonance imaging, segmentation, TBI, visualization''' 
#Irimia A., Chambers M.C., Torgerson C.M., Filippou M., Hovda D.A., Alger J.R., Gerig G., Toga A.W., Vespa P.M., Kikinis R., Van Horn J.D. Patient-tailored Connectomics Visualization for the Assessment of White Matter Atrophy in Traumatic Brain Injury. Front. Neur. 3:10. doi: 10.3389/fneur.2012.00010. '''Keywords: connectomics, traumatic brain injury, atrophy, rehabilitation, DTI''' 
#Irimia A., Van Horn J.D., Halgren E. Source Cancellation Profiles of Electroencephalography and Magnetoencephalography. Neuroimage. 2012 Feb 1;59(3):2464-74. PMID: 21959078. PMCID: PMC3254784. '''Keywords: Electroencephalography, Magnetoencephalography, Cancellation, Neuroimaging, Modeling''' 
#Irimia A., Chambers M.C., Torgerson C.M., Horn J.D.V. Circular Representation of Human Cortical Networks for Subject and Population-level Connectomic Visualization. Neuroimage. 2012 Apr 2;60(2):1340-51. PMID: 22305988. '''Keywords: Connectomics , DTI, MRI, Neuroimaging, Cortical network''' 
#Kim I., Tannenbaum A., Tannenbaum R. Anisotropic Conductivity of Magnetic Carbon Nanotubes Embedded in Epoxy Matrices. Carbon 2011; 49:54–61. 
#Koven N.S., Roth R.M., Garlinghouse M.A., Flashman L.A., Saykin A.J. Regional Gray Matter Correlates of Perceived Emotional Intelligence. Soc Cogn Affect Neurosci. 2011 Oct;6(5):582-90. PMID: 20934987. PMCID: PMC3190210. 
#Kremen W.S., Panizzon M.S., Neale M.C., Fennema-Notestine C., Prom-Wormley E., Eyler L.T., Stevens A., Franz C.E., Lyons M.J., Grant M.D., Jak A.J., Jernigan T.L., Xian H., Fischl B., Thermenos H.W., Seidman L.J., Tsuang M.T., Dale A.M. Heritability of Brain Ventricle Volume: Converging Evidence from Inconsistent Results. Neurobiol Aging. 2012 Jan;33(1):1-8. PMID: 20363053. PMCID: PMC3221930. '''Keywords: Aging, Alzheimer's Disease, Endophenotype, Genetics, Lateral ventricles, Mild cognitive impairment, Structural MRI, Twins''' 
#Lashkari D., Sridharan R., Vul E., Hsieh P-J., Kanwisher N., Golland P. Search for Patterns of Functional Specificity in the Brain: A Nonparametric Hierarchical Bayesian Model for Group fMRI Data. Neuroimage. 2012 Jan 16;59(2):1348-68. PMID: 21884803. '''Keywords: fMRI, Clustering, High level vision, Category selectivity''' 
#Lee J., Lankton S., Tannenbaum A. Object Tracking and Target Reacquisition Based on 3-D Range Data for Moving Vehicles. IEEE Trans Image Process. 2011 Oct;20(10):2912-24. PMID: 21486717. 
#Looi J.C.L., Macfarlane M.D., Walterfang M., Styner M., Velakoulis D., Lätt J., Van Westen D., Nilsson C. Morphometric Analysis of Subcortical Structures in Progressive Supranuclear Palsy: In vivo Evidence of Neostriatal and Mesencephalic Atrophy. Psychiatry Res. 2011 Nov 30;194(2):163-75. PMID: 21899988. PMCID: PMC3204393. '''Keywords: Neostriatum, Caudate, Putamen, Mesencephalon, Magnetic resonance imaging''' 
#Lyall A.E., Woolson S., Wolfe H.M., Goldman B.D., Reznick J.S., Hamer R.M., Lin W., Styner M., Gerig G., Gilmore J.H. Prenatal Isolated Mild Ventriculomegaly is Associated with Persistent Ventricle Enlargement at Ages 1 and 2. Early Hum Dev. 2012 Mar 21. PMID: 22445211. '''Keywords: Magnetic resonance imaging, Ultrasound, Gray matter, White matter, Cognitive development''' 
#Maltbie E., Bhatt K., Paniagua B., Smith R.G., Graves M.M., Mosconi M.W., Peterson S., White S., Blocher J., El-Sayed M., Hazlett H.C., Styner M.A. Asymmetric Bias in User Guided Segmentations of Brain Structures. Neuroimage. 2012 Jan 16;59(2):1315-23. PMID: 21889995. PMCID: PMC3230681. '''Keywords: Manual segmentation, Subcortical structures neuroimaging, Asymmetry analysis, Rater bias''' 
#McGann C., Kholmovski E., Blauer J., Vijayakumar S., Haslam T., Cates J., DiBella E., Burgon N., Wilson B., Alexander A., Prastawa M., Daccarett M., Vergara G., Akoum N., Parker D., MacLeod R., Marrouche N. Dark Regions of No-reflow on Late Gadolinium Enhancement Magnetic Resonance Imaging Result in Scar Formation after Atrial Fibrillation Ablation. J Am Coll Cardiol. 2011 Jul 5;58(2):177-85. PMID: 21718914. '''Keywords: Ablation, Atrium, Fibrosis, Magnetic Resonance Imaging''' 
#Melonakos E.D., Shenton M.E., Rathi Y., Terry D.P., Bouix S., Kubicki M. Voxel-based Morphometry (VBM) Studies in Schizophrenia-Can White Matter Changes Be Reliably Detected with VBM?. Psychiatry Res. 2011 Aug 30;193(2):65-70. PMID: 21684124. '''Keywords: Diffusion tensor imaging, Meta-analysis, Chronic schizophrenia, First-episode schizophrenia, Fractional anisotropy''' 
#Nakhmani A., Tannenbaum A. Self-Crossing Detection and Location for Parametric Active Contours. IEEE Trans Image Process. 2012 Feb 23. PMID: 22374361. 
#Paniagua B., Cevidanes L., Walker D., Zhu H., Guo R., Styner M. Clinical Application of SPHARM-PDM to Quantify Temporomandibular Joint Osteoarthritis. Comput Med Imaging Graph. 2011 Jul;35(5):345-52. PMID: 21185694. PMCID: PMC3083466. '''Keywords: projects:ShapeAnalysisFrameworkUsingSPHARMPDM, TMJ-OA, SPHARM-PDM, Bone tissue reabsorption simulation, Bone tissue reabsorption measurement''' 
#Paniagua B., Cevidanes L., Zhu H., Styner M. Outcome Quantification using SPHARM-PDM Toolbox in Orthognathic Surgery. Int J Comput Assist Radiol Surg. 2011 Sep;6(5):617-26. PMID: 21161693. PMCID: PMC3088776. '''Keywords: Projects:ShapeAnalysisFrameworkUsingSPHARMPDM, Orthognathic surgery, Surgical outcome, SPHARM-PDM, Statistical shape analysis''' 
#Rosenberger G., Nestor P.G., Oh J.S., Levitt J.J., Kindleman G., Bouix S., Fitzsimmons J., Niznikiewicz M., Westin C-F., Kikinis R., McCarley R.W., Shenton M.E., Kubicki M. Anterior Limb of the Internal Capsule in Schizophrenia: a Diffusion Tensor Tractography Study. Brain Imaging Behav. 2012 Mar 14. PMID: 22415192. '''Keywords: Schizophrenia, Disconnection, MRI, Cognitive neuropsychology''' 
#Sandhu R., Dambreville S., Yezzi A., Tannenbaum A. A Non-Rigid Kernel Based Framework for 2D3D Pose Estimation and 2D Image Segmentation. IEEE Trans Pattern Anal Mach Intell. 2011 Jun;33(6):1098-115. PMID: 20733218. '''Keywords: Statistical Learning, Image Segmentation, 3D Pose Estimation, kernel PCA''' 
#Schaer M., Cuadra M.B., Schmansky N., Fischl B., Thiran J-P., Eliez S. How to Measure Cortical Folding from MR Images: a Step-by-step Tutorial to Compute Local Gyrification Index. J Vis Exp. 2012 Jan 2;(59):e3417. PMID: 22230945. 
#Shusharina N., Sharp G. Analytic Regularization for Landmark-based Image Registration. Phys Med Biol. 2012 Mar 21;57(6):1477-98. PMID: 22390947. 
#Venkataraman A., Rathi Y., Kubicki M., Westin C-F., Golland P. Joint Modeling of Anatomical and Functional Connectivity for Population Studies. IEEE Trans Med Imaging. 2012 Feb;31(2):164-82. PMID: 21878411. 
#Voineskos A.N., Rajji T.K., Lobaugh N.J., Miranda D., Shenton M.E., Kennedy J.L., Pollock B.G., Mulsant B.H. Age-related Decline in White Matter Tract Integrity and Cognitive Performance: A DTI Tractography and Structural Equation Modeling Study. Neurobiol Aging. 2012 Jan;33(1):21-34. PMID: 20363050. PMCID: PMC2945445. '''Keywords: Aging, Anisotropy, Cognition, Diffusion tensor imaging, White matter''' 
#Whitford T.J., Savadjiev P., Kubicki M., O'Donnell L.J., Terry D.P., Bouix S., Westin C-F., Schneiderman J.S., Bobrow L., Rausch A.C., Niznikiewicz M., Nestor P.G., Pantelis C., Wood S.J., McCarley R.W., Shenton M.E. Fiber Geometry in the Corpus Callosum in Schizophrenia: Evidence for Transcallosal Misconnection. Schizophr Res. 2011 Oct;132(1):69-74. PMID: 21831601. PMCID: PMC3172336. '''Keywords: Callosal, Diffusion-Tensor Imaging, Neurodevelopment, Morphometry, White-matter, Genu''' 
#Zhu H., Kong L., Li R., Styner M., Gerig G., Lin W., Gilmore J.H. FADTTS: Functional Analysis of Diffusion Tensor Tract Statistics. Neuroimage. 2011 Jun 1;56(3):1412-25. PMID: 21335092. PMCID: PMC3085665. '''Keywords: Confidence band, Diffusion tensor imaging, Fiber bundle, Global test statistic, Varying coefficient model'''

===Conference Papers===
#Dalca A., Danagoulian G., Kikinis R., Schmidt E., Golland P. Segmentation of Nerve Bundles and Ganglia in Spine MRI Using Particle Filters. Int Conf Med Image Comput Comput Assist Interv. 2011;14(Pt 3):537-45. PMID: 22003741. PMCID: PMC3232745. '''Keywords: nerve bundles, tracking, segmentation, particle filter, Projects:NerveSegmentation''' 
#Datar M., Gur Y., Paniagua B., Styner M., Whitaker R. Geometric Correspondence for Ensembles of Nonregular Shapes. Int Conf Med Image Comput Comput Assist Interv. 2011;14(Pt 2):368-75. PMID: 21995050. 
#Depa M., Holmvang G., Schmidt E.J., Golland P., Sabuncu M.R. Towards Efficient Label Fusion by Pre-Alignment of Training Data. Int Conf Med Image Comput Comput Assist Interv. 2011;14(WS):38-46. Workshop on Multi-Atlas Labeling and Statistical Fusion. '''Keywords: Image Segmentation, Groupwise Registration, Label Fusion, Projects:NonparametricSegmentation, Projects:CardiacAblation''' 
#Durrleman S., Prastawa M., Gerig G., Joshi S. Optimal Data-driven Sparse Parameterization of Diffeomorphisms for Population Analysis. Inf Process Med Imaging. 2011;22:123-34. PMID: 21761651. 
#Fishbaugh J., Durrleman S., Piven J., Gerig G. A Framework for Longitudinal Data Analysis via Shape Regression. Proceedings of SPIE 2012;8314, 83143K 
#Fishbaugh J., Durrleman S., Gerig G. Estimation of Smooth Growth Trajectories with Controlled Acceleration from Time Series Shape Data. Int Conf Med Image Comput Comput Assist Interv. 2011;14(Pt 2):401-8. PMID: 21995054. 
#Gouttard S., Goodlett C.B., Kubicki M., Gerig G. Measures for Validation of DTI Tractography. Proceedings of SPIE 2012;8314, 83140J 
#Hao X., Whitaker R.T., Fletcher P.T. Adaptive Riemannian Metrics for Improved Geodesic Tracking of White Matter. Inf Process Med Imaging. 2011;22:13-24. PMID: 21761642. PMCID: PMC3250233. 
#Karasev P., Kolesov I., Chudy K., Tannenbaum A., Muller G., Xerogeanes J. Interactive MRI Segmentation with Controlled Active Vision. IEEE Conference on Decision and Control Dec. 2011; 
#Langs G., Lashkari D., Sweet A., Tie Y., Rigolo L., Golby A.J., Golland P. Learning an Atlas of a Cognitive Process in its Functional Geometry. Inf Process Med Imaging. 2011;22:135-46. PMID: 21761652. PMCID: PMC3222689. '''Keywords: Functional connectivity atlases and tumors, Projects:ConnectivityAtlas''' 
#Menze B.H., Van Leemput K., Honkela A., Konukoglu E., Weber M-A., Ayache N., Golland P. A Generative Approach for Image-based Modeling of Tumor Growth. Inf Process Med Imaging. 2011;22:735-47. PMID: 21761700. PMCID: PMC3237122. '''Keywords: Projects:TumorModeling''' 
#Nho K., Shen L., Kim S., Swaminathan S., Risacher S.L., Saykin A.J. The Effect of Reference Panels and Software Tools on Genotype Imputation. AMIA Annu Symp Proc. 2011;2011:1013-1018. PMID: 22195161. PMCID: PMC3243280. 
#Niethammer M., Hart G.L., Pace D.F., Vespa P.M., Irimia A., Van Horn J.D., Aylward S.R. Geometric Metamorphosis. Int Conf Med Image Comput Comput Assist Interv. 2011;14(Pt 2):639-46. PMID: 21995083. 
#Pace D.F., Niethammer M., Aylward S.R. Sliding Geometries in Deformable Image Registration. Int Conf Med Image Comput Comput Assist Interv. 2011;14(WS):141-148. Workshop on Abdominal Imaging. 
#Peroni M., Golland P., Sharp G.C., Baroni G. Ranking of Stopping Criteria for Log Domain Diffeomorphic Demons Application in Clinical Radiation Therapy. Conf Proc IEEE Eng Med Biol Soc. 2011;2011:4884-7. PMID: 22255433. 
#Prastawa M., Awate S.P., Gerig G. Building Spatiotemporal Anatomical Models using Joint 4-D Segmentation, Registration, and Subject-Specific Atlas Estimation. IEEE Workshop on Mathematical Methods in Biomedical Image Analysis 2012; p. 49-56. 
#Seshamani S., Chintalapani G., Taylor R. Iterative Refinement of Point Correspondences for 3D Statistical Shape Models. Int Conf Med Image Comput Comput Assist Interv. 2011;14(Pt 2):417-25. PMID: 21995056. 
#Tokuda J., Hata N. OpenIGTLink Protocol Version 2. Int Conf Med Image Comput Comput Assist Interv. 2011;14(WS). Workshop on Systems & Architecture for Computer Assisted Intervention. '''Keywords: OpenIGTLink''' 
#Wang B., Prastawa M., Irimia A., Chambers M.C., Vespa P.M., Van Horn J.D., Gerig G. A Patient-specific Segmentation Framework for Longitudinal MR Images of Traumatic Brain Injury. Proceedings of SPIE 2012;8314, 831402. '''Keywords: Image segmentation, Atlas formation, Longitudinal analysis''' 
#Wassermann D., Rathi Y., Bouix S., Kubicki M., Kikinis R., Shenton M.E., Westin C-F. White Matter Bundle Registration and Population Analysis Based on Gaussian Processes. Inf Process Med Imaging. 2011;22:320-32. PMID: 21761667. PMCID: PMC3140022. '''Keywords: Diffusion MRI, White Matter Fiber Tracts, Gaussian Processes, Registration''' 
#Zhu P., Awate S.P., Gerber S., Whitaker R. Fast Shape-based Nearest-neighbor Search for Brain MRIs using Hierarchical Feature Matching. Int Conf Med Image Comput Comput Assist Interv. 2011;14(Pt 2):484-91. PMID: 21995064.

File:2012 NA-MIC Progress Report Response (1).doc

2012-10-13T12:49:00Z

Ann Adams: