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

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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