2007 Materials for NCBC Program Review

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Materials requested for NCBC Program Review

These are due to Gwen Jacobs by Friday, June 08, 2007.


Q1: A copy of two parts of your most recent progress report: the summary section and the highlights section.=

(Tina)

Summary: http://www.na-mic.org/Wiki/index.php/2007_Annual_Scientific_Report#1._Introduction

The National Alliance for Medical Imaging Computing (NA-MIC) is now in its third year. This Center is comprised of a multi-institutional, interdisciplinary team of computer scientists, software engineers, and medical investigators who have come together to develop and apply computational tools for the analysis and visualization of medical imaging data. A further purpose of the Center is to provide infrastructure and environmental support for the development of computational algorithms and open source technologies, and to oversee the training and dissemination of these tools to the medical research community. The driving biological projects (DBPs) for the first three years of the Center came from schizophrenia, although the methods and tools developed are clearly applicable to many other diseases.

In the first year of this endeavor, our main focus was to develop alliances among the many cores to increase awareness of the kinds of tools needed for specific imaging applications. Our first annual report and all-hands meeting reflected this emphasis on cores, which was necessary to bring together members of an interdisciplinary team of scientists with such diverse expertise and interests. In the second year of the center our emphasis shifted from the integration of cores to the identification of themes that cut across cores and are driven by the requirements of the DBPs. We saw this shift as a natural evolution, given that the development and application of computational tools became more closely aligned with specific clinical applications. This change in emphasis was reflected in the Center's four main themes, which included Diffusion Tensor Analysis, Structural Analysis, Functional MRI Analysis, and the integration of newly developed tools into the NA-MIC Tool Kit. In the third year of the center, collaborative efforts have continued along each of these themes among computer scientists, clinical core counterparts, and engineering partners. We are thus quite pleased with the focus on themes, and we also note that our progress has not only continued but that more projects have come to fruition with espect to publications and presentations from NA-MIC investigators, which are listed on our publications page.

Below, in the next section (Section 2) we summarize our progress over the last year using the same four central themes to organize the progress report. These four themes include: Diffusion Image analysis (Section 2.1), Structural analysis (Section 2.2), Functional MRI analysis (Section 2.3), and the NA-MIC toolkit (Section 2.4). Section 3 highlights four important accomplishments of the third year: advanced algorithm development in Shape and DTI analysis, the newly architected open source application platform, Slicer 3, and our outreach and technology transfer efforts. Section 4 summarizes the impact and value of our work to the biocomputing community at three different levels: within the center, within the NIH-funded research community, and externally to a national and international community. The final section of this report, Section 5, provides a timeline of Center activities.

In addition, the end of the first three years of the center marks a transition from the first set of DBPs that were focused entirely on Schizophrenia to a new set that span a wider range of biological problems. The new DBPs continue to include neuropsychiatric disorders such as Systemic Lupus Erythematosis (MIND Institute, University of New Mexico), Schizophrenia (Harvard), and Autism (University of North Carolina, Chapel Hill), along with a adopting a direction that is new but synergistic for NA-MIC: Prostate Interventions (Johns Hopkins University). Funding for the second round of DBPs starts in the next cycle, but the PIs were able to attend the recent All-hands meeting and start developing plans for their future research in NA-MIC.

Finally, we note that Core 3.1 (Shenton and Saykin), are in the process of applying for a Collaborative R01 to expand current research with NA-MIC, which ends on July 31, 2007. Both Drs. Shenton and Saykin have worked for three years in driving tool development for shape measures, DTI tools, and path analysis measures for fMRI as part of the driving biological project in NA-MIC, and they now plan to expand this research in a Collaborative R01 by working closely with Drs. Westin, Miller, Pieper, and Wells, to design, assess, implement, and apply tools that will enable the integration of MRI, DTI, and fMRI in individual subjects, as well as to develop an atlas of functional networks and circuits that are based on a DTI atlas (i.e., structural connectivity), which will be integrated with a network of functional connectivity that will be identified from fMRI probes of attention, memory, emotion, and semantic processing. We mention this here because this will be, to our knowledge, the first DBP to apply for further funding to continue critical work begun with NA-MIC.

Highlights: http://www.na-mic.org/Wiki/index.php/2007_Annual_Scientific_Report#3._Highlights

The third year of the NAMIC project saw continued development and dissemination of medical image analysis software. With the release of the first version of Slicer3, the transfer of this technology is accelerating. Because of NAMIC's strong ties with several large open source communities, such as ITK, VTK, and CMake, NAMIC continues to make significant impact on the nation's broader biocomputing infrastructure. The following are just a few of the many highlights from the third year of the NAMIC effort.

  • Advanced Algorithms

Core 1 continues to lead the biomedical community in DTI and shape analysis.

  • NAMIC published an open source framework for shape analysis, including providing access to the open source software repository. Shape analysis has become of increasing relevance to the neuroimaging community due to its potential to precisely locate morphological changes between healthy and pathological structures. The software has been downloaded many times since the first online publication in October 2006, and is now used by several prestigious image analysis groups.
  • The spherical based wavelet shape analysis package has been contributed into ITK, and in the next few months the multiscale segmentation work will be incorporated as well.
  • The NAMIC community has implemented a very fast method for the optimal transport approach to elastic image registration which is currently being added to ITK.
  • The conformal flattening algorithm has been implemented as an ITK filter and is in the NAMIC Sandbox in preparation for formal acceptance into the NAMIC Kit.
  • Technology Deployment Platform: Slicer3

Core 2 in conjunction with Algorithms (Core 1) and DBP (Core 3) are creating new tools to accelerate the transition of technology to the biomedical imaging community.

  • One of the year's major achievements was the release of the first viable version of Slicer3 application, which evolved from concept to a full-featured application. The second beta version of Slicer3 was released in April 2007. The application provides a full range of functionality for loading, viewing, editing, and saving models, volumes, transforms, fiducials and other common medical data types. Slicer3 also includes a powerful execution model that enables Core 1 developers (and other in the NAMIC community) to easily deploy algorithms to Core 2 and other biocomputing clients.
  • Slicer3's execution model supports plug-in modules. These modules can be run stand alone or integrated into the Slicer3 framework. When integrated, the GUI to the module can be automatically generated from an associated XML file describing input parameters to the module. A variety of modules were created, ranging from simple image processing algorithms, to complex, multi-step segmentation procedures.
  • To stress test Slicer3's architecture and demonstrate its capabilities, the EM Segment module (http://wiki.na-mic.org/Wiki/index.php/Slicer3:EM) was created and added to Slicer's library of modules. EM Segment is an automatic segmentation algorithm for medical images and represents a collaborative effort between the NAMIC engineering, algorithms, and biological problem cores. The EM Segment module enables users to quickly configure the algorithm to a variety of imaging protocols as well as anatomical structures through a wizard-style, workflow interface. The workflow tools have been integrated into the NAMIC Kit, and are now available to all other modules built on the Slicer3 framework.
  • Outreach and Technology Transfer

Cores 4-5-6 continue to support, train and dissemniate to the NAMIC community, and the broader biomedical computing community.

  • NAMIC continues to practice the best of collaborative science through its bi-annual Project Week events. These events, which gather key representatives from Cores 1-7 and external collaborators, are organized to gather experts from a variety of domains to address current research problems. This year's first Project Week was held in January and hosted by the University of Utah. It saw several significant accomplishments including the first beta release of the next generation Slicer3 computing platform. The second Project Week is scheduled for June in Boston, MA.
  • Twelve NAMIC-supported papers were published in high-quality peer reviewed conference proceedings (four papers in MICCAI alone). Another paper on the NAMIC software process was published in IEEE Software. All three DTI papers presented at MICCAI last year were NAMIC associated.
  • Several workshops through the year were held at various institutions. This includes the DTI workshop at UNC, the MICCAI Open Source Workshop, and the NA-MIC Training Workshop at the Harvard Center for Neurodegeneration and Repair.

Q2

A brief statement - (one page, max) addressing each of the questions listed below. These are the questions that we have been asked to address in our report. Our goal in asking for this information is to be able to produce a report that reviews the program as a whole. Your view, from the vantage point of the center you direct, is critical to our work. In addition, your answers will provide us with more information that we can use in our discussion with program staff on June 11th. We know that some of this information can be found on your websites, so in those cases a link to the information would be most helpful.

Q2.1 To what extent does the vision and direction of the NCBC initiative promote biomedical computing?

(Eric/Polina)

Q2.2 In what ways has the NCBC initiative advanced biomedical computing?

(Tina)

Answer:http://www.na-mic.org/Wiki/index.php/2007_Annual_Scientific_Report#4._Impact_and_Value_to_Biocomputing

Q2.3 Are the NCBCs interfacing appropriately? (recommended by RICC)

(Will Schroeder)

Q2.4. What new collaborations have been formed through the NCBC initiative?

(Jim Miller)

Q2.5. What new training opportunities have the centers provided?

(Randy Gollub)

Q2.6. What changes could make the program more effective in the future?

(Steve Pieper)

Q2.7. What lessons have been learned from the NCBC initiative that can guide future NIH efforts in biomedical computing?

(Martha Shenton)

Q3:A list of publications and/or software tools produced by the Center. If this information is provided in your progress report or is available on your website, a link will be sufficient. We are especially interested in your assessment of the maturity of your software tools and the impact they are having on the scientific community.=

(Will Schroeder, Allen Tannenbaum)

A3:

Logistics

When completed, the information should be sent to:

Gwen Jacobs, PhD

Professor of Neuroscience

Asst. CIO and Director of Academic Computing

1 Lewis Hall

Montana State University

Bozeman, MT 59717

406-994-7334 - phone

406-994-7077 - FAX

gwen@cns.montana.edu <mailto:gwen@cns.montana.edu>

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