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Ann Adams at 16:22, 17 November 2012

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Ann Adams: /* Summary of Center Progress */

2012-10-13T14:22:20Z

Summary of Center Progress

Ann Adams at 13:55, 13 October 2012

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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…'

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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…'

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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.

@@ Line 31: / Line 31: @@
 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
@@ Line 41: / Line 43: @@
 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.
 .1. Algorithms
 The Algorithms team develops computational methods that support patient-specific analysis of medical
@@ Line 50: / Line 54: @@
 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
+'''Statistical models of anatomy and pathology.''' ''Polina Golland--Please update this section with current progress.''
 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
@@ Line 58: / Line 65: @@
 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
@@ Line 68: / Line 77: @@
 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
@@ Line 75: / Line 85: @@
 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

@@ Line 17: / Line 17: @@
 * 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.

@@ Line 11: / Line 11: @@
 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
+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.

@@ Line 3: / Line 3: @@
 Required elements of the New Research Progress Template
-==Summary of Center Progress==
+.  RESEARCH AND RESOURCE METRICS
-.  Brief description of overall objectives of NA-MIC
+A. Summary of Center Progress
-The National Alliance for Medical Image Computing (NA-MIC) is a multi-institutional, interdisciplinary
+*  Brief description of overall objectives of NA-MIC
 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
+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
-medical image data. The Center continues to maintain a robust and flexible infrastructure for developing and
+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.
+applying advanced imaging technologies across a range of important biomedical research disciplines. The NA-MIC research and development effort is organized around the Computer Science Core, which includes independent teams for Algorithms and Engineering. A separate core is responsible for the operation and maintenance of the NA-MIC Kit, an interoperable suite of software tools that enables Center technologies. NA-MIC's research effort is currently driven by 4 DBPs, which are finding solutions to problems in patient-specific data analysis.  Center resesarch and technology is being further developed through XX collaborative research projects.
-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.
@@ Line 18: / Line 50: @@
 Required elements:
-.  This year NA-MIC hosted 15 workshops and courses at national universities and international venues, providing training and
+  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

@@ Line 1: / Line 1: @@
    Back to [[NAMIC_Annual_Reports|NAMIC_Annual_Reports]]
-Summary of Center Progress
+Required elements of the New Research Progress Template
 .  Brief description of overall objectives of NA-MIC