Difference between revisions of "2009 Annual Scientific Report"

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=Appendix B EAB Report and Response (Kapur)=

Revision as of 16:30, 26 February 2009

Home < 2009 Annual Scientific Report

Back to 2009_Progress_Report



Contents

Guidelines for preparation

  • 2009_Progress_Report#Scientific Report Timeline - Main point is that May 15 is the date by which all sections below need to be completed. No extensions are possible.
  • DBPs - If there is work outside of the roadmap projects that you would like to report, you are welcome to create a separate section for it under "Other".
  • The outline for this report is similar to the 2008 and 2007 reports, which are provided here for reference: 2008_Annual_Scientific_Report, 2007_Annual_Scientific_Report.
  • In preparing summaries for each of the 8 topics in this report, please leverage the detailed pages for projects provided here: NA-MIC_Internal_Collaborations.
  • Publications will be mined from the SPL publications database. All core PIs need to ensure that all NA-MIC publications are in the publications database by May 15.

Introduction (Tannenbaum)

The National Alliance for Medical Imaging Computing (NA-MIC) is now in its fifth 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. This was our second year with our current DBPS of which three are centered around diseases of the brain: (a) brain lesion analysis in neuropschiatric systemic lupus erythematosus; (b) a study of cortical thickness for autism; and (c) stochastic tractography for VCFS. The and fourth is a very new direction, the prostate: brachytherapy needle positioning robot integration.

We briefly summarize the work of NAMIC during the five years of its existence. In the year one of the Center, alliances were forged amongst the cores and constituent groups in order to integrate the efforts of the cores and to define the kinds of tools needed for specific imaging applications. The second year emphasized the identification of the key research thrusts that cut across cores and were driven by the needs and requirements of the DBPs. This led to the formulation of the Center's four main themes: Diffusion Tensor Analysis, Structural Analysis, Functional MRI Analysis, and the integration of newly developed tools into the NA-MIC Tool Kit. The third year of center activity was devoted to the continuation of the collaborative efforts in order to give solutions to the various brain-oriented DBPs. The fourth year was focused on translating our work to the new DBPs.

Year five has seen progress with the work of our current DBPs. As alluded to above these include work on neuropsychiatric disorders such as Systemic Lupus Erythematosis (MIND Institute, University of New Mexico), Velocardiofacial Syndrome (Harvard), and Autism (University of North Carolina, Chapel Hill), as well as the prostate interventional work (Johns Hopkins and Queens Universities). We already have a number of publications as is indicated on our publications page, and software development is continuing as well.

In the next section (Section 3), we summarize this year’s progress on the four roadmap projects listed above: Section 3.1 stochastic tractography for Velocardiofacial Syndrome, Section 3.2 brachytherapy needle positioning for the prostate, Section 3.3 brain lesion analysis in neuropschiatric systemic lupus erythematosus, and Section 3.4 cortical thickness for autism. Next in Section 4, we describe recent work on the four infrastructure topics. These include: Diffusion Image analysis (Section 4.1), Structural analysis (Section 4.2), Functional MRI analysis (Section 4.3), and the NA-MIC Toolkit (Section 4.4). In Section 4.5, we outline some of the other key projects, in Section 4.6 some key highlights including the integration of the EM Segmentor into Slicer, and in Section 4.7 the impact of biocomputing at three different levels: within the center, within the NIH-funded research community, and externally to a national and international community. The final sections of this report, Sections 5-11, provide updated timelines on the status of the various projects of the different cores of NAMIC.

Clinical Roadmap Projects

Roadmap Project: Stochastic Tractography for VCFS (Kubicki)

Overview (Kubicki)

The goal of this project is to create an end-to-end application that would be useful in evaluating anatomical connectivity between segmented cortical regions of the brain. The ultimate goal of our program is to understand anatomical connectivity similarities and differences between genetically related schizophrenia and velocardio-facial syndrome. Thus we plan to use the "stochastic tractography" tool for the analysis of abnormalities in integrity, or connectivity, provided by arcuate fasciculus, fiber bundle involved in language processing, in schizophrenia and VCFS.

Algorithm Component (Golland)

At the core of this project is the stochastic tractography algorithm developed and implemented in collaboration between MIT and BWH. Stochastic Tractography is a Bayesian approach to estimating nerve fiber tracts from DTI images.

We first use the diffusion tensor at each voxel in the volume to construct a local probability distribution for the fiber direction around the principal direction of diffusion. We then sample the tracts between two user-selected ROIs, by simulating a random walk between the regions, based the local transition probabilities inferred from the DTI image.

The resulting collection of fibers and the associated FA values provide useful statistics on the properties of connections between the two regions. To constrain the sampling process to the relevant white matter region, we use atlas-based segmentation to label ventricles and gray matter and to exclude them from the search space. As such, this step relies heavily on the registration and segmentation functionality in Slicer.

<Note Progress in the last year>

Engineering Component (Davis)

<Note Progress in the last year>

Clinical Component (Kubicki)

<Note Progress in the last year>

Additional Information

Additional Information for this project is available here on the NA-MIC wiki.

Roadmap Project: Brachytherapy Needle Positioning Robot Integration (Fichtinger)

Overview (Fichtinger)

Numerous studies have demonstrated the efficacy of image-guided needle-based therapy and biopsy in the management of prostate cancer. The accuracy of traditional prostate interventions performed using transrectal ultrasound (TRUS) is limited by image fidelity, needle template guides, needle deflection and tissue deformation. Magnetic Resonance Imaging (MRI) is an ideal modality for guiding and monitoring such interventions due to its excellent visualization of the prostate, its sub-structure and surrounding tissues.

We have designed a comprehensive robotic assistant system that allows prostate biopsy and brachytherapy procedures to be performed entirely inside a 3T closed MRI scanner. The current system applies transrectal approach to the prostate: an endorectal coil and steerable needle guide, both tuned to 3T magnets and invariable to any particular scanner, are integrated into the MRI compatible manipulator.

Under the NAMIC initiative, the image computing, visualization, intervention planning, and kinematic planning interface is being accomplished with open source system built on the NAMIC toolkit and its components, such as Slicer3 and ITK. These are complemented by a collection of unsupervised prostate segmentation and registration methods that are of great importance to the clinical performance of the interventional system as a whole.

Algorithm Component (Tannenbaum)

<Note Progress in the last year>

Engineering Component (Hayes)

<Note Progress in the last year>


Clinical Component (Fichtinger)

<Note Progress in the last year>

Additional Information

Additional Information for this project is available here on the NA-MIC wiki.

Roadmap Project: Brain Lesion Analysis in Neuropsychiatric Systemic Lupus Erythematosus (Bockholt)

Overview (Bockholt)

The primary goal of the MIND DPB is to examine changes in white matter lesions in adults with Neuropsychiatric Systemic Lupus Erythematosus (SLE). We want to be able to characterize lesion location, size, and intensity, and would also like to examine longitudinal changes of lesions in an SLE cohort. To accomplish this goal, we will create an end-to-end application entirely within NA-MIC Kit allowing individual analysis of white matter lesions. Such a workflow will then be applied to a clinical sample in the process of being collected.

Algorithm Component (Whitaker)

The basic steps necessary for the white matter lesion analysis application entail first registration of T1, T2, and FLAIR images, second tissue classification into gray, white, csf, or lesion, thirdly clustering lesion for anatomical localization, and finally a summarization of lesion size and image intensity parameters within each unique lesion.

<Note Progress in the last year>

Engineering Component (Pieper)

<Note Progress in the last year>

Clinical Component (Bockholt)

<Note Progress in the last year>

Additional Information

Additional Information for this project is available here on the NA-MIC wiki.

Roadmap Project: Cortical Thickness for Autism(Hazlett)

Overview (Hazlett)

A primary goal of the UNC DPB is to examine changes in cortical thicknes in children with autism compared to typical controls. We want to examine group differences in both local and regional cortical thickness, and would also like to examine longitudinal changes in the cortex from ages 2-4 years. To accomplish this goal, this project will create an end-to-end application within Slicer3 allowing individual and group analysis of regional and local cortical thickness. Such a workflow will then be applied to our study data (already collected).

Algorithm Component (Styner)

The basic steps necessary for the cortical thickness application entail first tissue segmentation in order to separate white and gray matter regions, second cortical thickness measurement, thirdly cortical correspondence to compare measurements across subjects and finally a statistical analysis to locally compute group differences.

<Note Progress in the last year>

Engineering Component (Miller, Vachet)

<Note Progress in the last year>

Clinical Component (Hazlett)

<Note Progress in the last year>

Additional Information

Additional Information for this project is available here on the NA-MIC wiki.

Four Infrastructure Topics

Diffusion Image Analysis (Gerig)

<Note Progress in the last year>

Key Investigators

<Need to update the list below>

  • BWH: Marek Kubicki, Martha Shenton, Marc Niethammer, Sylvain Bouix, Jennifer Fitzsimmons, Katarina Quintis, Doug Markant, Kate Smith, Carl-Fredrik Westin, Gordon Kindlmann
  • MIT: Lauren O'Donnell, Polina Golland, Tri Ngo
  • UCI: James Fallon
  • Utah I: Tom Fletcher, Ross Whitaker, Ran Tao, Yongsheng Pan
  • Utah II: Casey Goodlett, Sylvain Gouttard, Guido Gerig
  • GA Tech: John Melonakos, Vandana Mohan, Shawn Lankton, Allen Tannenbaum
  • GE: Xiaodong Tao, Jim Miller
  • Isomics: Steve Pieper
  • Kitware: Luis Ibanez

Additional Information

Additional Information for this topic is available here on the NA-MIC wiki.

Structural Analysis(Tannenbaum)

Progress

Under Structural Analysis, the main topics of research for NAMIC are structural segmentation, registration techniques and shape analysis. These topics are correlated and research in one often finds application in another. For example, shape analysis can yield useful priors for segmentation, or segmentation and registration can provide structural correspondences for use in shape analysis and so on.

An overview of selected progress highlights under these broad topics follows.

<Note Progress in the last year>

Key Investigators

Needs to be updated:

  • MIT: Polina Golland, Kilian Pohl, Sandy Wells, Eric Grimson, Mert R. Sabuncu
  • UNC: Martin Styner, Ipek Oguz, Xavier Barbero
  • Utah: Ross Whitaker, Guido Gerig, Suyash Awate, Tolga Tasdizen, Tom Fletcher, Joshua Cates, Miriah Meyer
  • GaTech: Allen Tannenbaum, John Melonakos, Vandana Mohan, Tauseef ur Rehman, Shawn Lankton, Samuel Dambreville, Yi Gao, Romeil Sandhu, Xavier Le Faucheur, James Malcolm
  • Isomics: Steve Pieper
  • GE: Bill Lorensen, Jim Miller
  • Kitware: Luis Ibanez, Karthik Krishnan
  • UCLA: Arthur Toga, Michael J. Pan, Jagadeeswaran Rajendiran
  • BWH: Sylvain Bouix, Motoaki Nakamura, Min-Seong Koo, Martha Shenton, Marc Niethammer, Jim Levitt, Yogesh Rathi, Marek Kubicki, Steven Haker

Additional Information

Additional Information for this topic is available here on the NA-MIC wiki.

fMRI Analysis (Golland)

Progress

One of the major goals in analysis of fMRI data is the detection of functionally homogeneous networks in the brain.

<note progress here>

Key Investigators

Need to update this list:

  1. MIT: Polina Golland, Danial Lashkari, Bryce Kim
  2. Harvard/BWH: Sylvain Bouix, Martha Shenton, Marek Kubicki

Additional Information

Additional Information for this topic is available here on the NA-MIC wiki.

NA-MIC Kit Theme (Schroeder)

Progress

The NAMIC-Kit consists of a framework of advanced computational components, as well as the support infrastructure for testing, documenting, and deploying leading edge medical imaging algorithms and software tools. The framework has been carefully constructed to provide low-level access to libraries and modules for advanced users, plus high-level application access that non-computer professionals can use to address a variety of problems in biomedical computing. In this fifth year of the NA-MIC projects <summary of progress>

Software Releases

The NAMIC-Kit can be represented as a pyramid of capabilities, with the base consisting of toolkits and libraries, and the apex standing in for the Slicer3 user application. In between, Slicer modules are stand-alone executables that can be integrated directly into the Slicer3 application, including GUI integration, while work-flows are groups of modules that are integrated together to manifest sophisticated segmentation, registration and biomedical computing algorithms. In a coordinated NAMIC effort, major releases of these many components were realized over the past year. This includes, but is not limited to:

Slicer3 and the Software Framework

One of the major achievements of the past year has been...

Software Process

One of the challenges facing developers has been the requirement to implement, test and deploy software systems across multiple computing platforms. NAMIC continues to push the state of the art with further development of the CMake, CTest, and CPack tools for cross-platform development, testing, and packaging, respectively...

Key Investigators

THis list needs to be updated:

  • Kitware - Will Schroeder (Core 2 PI), Sebastien Barre, Luis Ibanez, Bill Hoffman
  • GE - Jim Miller, Xiaodong Tao
  • Isomics - Steve Pieper

Additional Information

Additional Information for this topic is available here on the NA-MIC wiki.


Highlights(Schroeder)

Advanced Algorithms

NAMIC-Kit

Outreach and Technology Transfer

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

  • The Slicer community held several workshops and tutorials. In xxx a satellite event was held for the international Organization for Human Brain Mapping at the annual meeting in xxx. The xx workshop on xx hosted xx participants representing xx countries from around the world, xx states within the US and xxdifferent laboratories including xx NIH institutes. In addition, <note how many slicer tutorials were held and where etc>
  • Project Week continues to be a successful NAMIC venue. These semi-annual events are held in Boston in June, and January in Salt Lake City. These events are well attended with approximately 100 participants, of which about a third are outside collaborators. At the last Project Week in Salt Lake City, approximately xx projects were realized.
  • NAMIC continues to participate in conferences and other technical venues. For example, NAMIC hosted xxx


Impact and Value to Biocomputing (Miller)

NA-MIC impacts Biocomputing through a variety of mechanisms. First, NA-MIC produces scientific results, methodologies, workflows, algorithms, imaging platforms, and software engineering tools and paradigms in an open enviroment that contributes directly to the body of knowledge available to the field. Second, NA-MIC science and technology enables the entire medical imaging community to build on NA-MIC results, methods, and techniques, to concentrate on the new science instead of developing supporting infrastructure, to leverage NA-MIC scientists and engineers to adapt NA-MIC technology to new problem domains, and to leverage NA-MIC infrastructure to distribute their own technology to a larger community.

Impact within the Center

Impact within NIH Funded Research

National and International Impact

Timeline (Ross)

<The table needs to be updated>


This section of the report gives the milestones for years 1 through 5 that are associated with the timelines in the original proposal. We have organized the milestones by core. For each milestone we have indicated the proposed year of completion and a very brief description of the current status. In some cases the milestones include ongoing work, and we have try to indicate that in the status. We have also included tables that list any significant changes to the proposed timelines. On the wiki page, we have links to the notes from the various PIs that give more details on their progress and the status of the milestones.

These tables demonstrate that the project is, on the whole, proceeding according to the originally planned schedule.


Core 1: Algorithms

Timelines and Milestones

Group Aim Milestone Proposed time of completion Status
MIT 1 Shape-based segmentation
MIT 1.1 Methods to learn shape representations Year 2 Completed
MIT 1.2 Shape in atlas-driven segmentation Year 4 Completed
MIT 1.3 Validate and refine approach Year 5 In Progress
MIT 2 Shape analysis
MIT 2.1 Methods to compute statistics of shapes Year 4 Completed
MIT 2.3 Validation of shape methods on application data Year 5 Completed, refinements ongoing
MIT 3 Analysis of DTI data
MIT 3.1 Fiber geometry Year 3 Completed
MIT 3.2 Fiber statistics Year 5 Completed, new developments ongoing
MIT 3.3 Validation on real data Year 5 Completed, refinements ongoing
Utah 1 Processing of DTI data
Utah 1.1 Filtering of DTI Year 2 Completed
Utah 1.2 Quantitative analysis of DTI Year 3 Completed, refinements ongoing
Utah 1.3 Segmentation of cortex/WM Year 3 Completed partially, modified below
Utah 1.4 Segmentation analysis of white matter tracts Year 3 Completed, applications ongoing
Utah 1.5 Joint analysis of DTI and functional data Year 5 Initiated
Utah 2 Nonparametric Shape Analysis Year 5 Completed
Utah 2.1 Framework in place Year 3 Complete
Utah 2.2 Demonstration on shape of neuranatomy (from Core 3) Year 4 Complete
Utah 2.3 Development for multiobject complexes Year 4 Complete
Utah 2.4 Demonstration of NP shape representations on clinical hypotheses from Core 3 Year 5 Complete, publications in progress
Utah 2.6 Integration into NAMIC-kit Year 5 Incomplete (initiated)
Utah 2.7 Shape regression Year 5 Incomplete
UNC 1 Statistical shape analysis
UNC 1.1 Comparative anal. of shape anal. schemes Year 2 Completed
UNC 1.3 Statistical shape analysis incl. patient variable Year 5 Complete, refinements ongoing
UNC 2 Structural analysis of DW-MRI
UNC 2.1 DTI tractography tools Year 4 Completed
UNC 2.2 Geometric characterization of fiber tracts Year 5 Completed
UNC 2.3 Quant. anal. of diffusion along fiber tracts Year 5 Completed.
GaTech 1.1 ITK Implementation of PDEs Year 2 Completed
GaTech 1.1 Applications to Core 3 data Year 4 Completed
GaTech 1.2 New statistic models Year 4 Completed
GaTech 1.2 Shape anaylsis Year 4 Completed, refinements ongoing
GaTech 2.0 Integration in to Slicer Year 4-5 Preliminary results and ongoing
MGH 1 Registration
MGH 1.1 Collect DTI/QBALL data Year 2 Completed
MGH 1.2 Develop registration method Year 2 Completed
MGH 1.3 Test/optimize registration method Year 3 In Progress
MGH 1.4 Apply registration on core 3 data Year 5 In Queue
MGH 2 Group DTI Statistics
MGH 2.1 Develop group statistic method Year 2 Partially Complete
MGH 2.2 Apply on core 3 data Year 5 In Queue
MGH 3 Diffusion Segmentation
MGH 3.1 Collect DTI/QBALL data Year 2 Completed
MGH 3.2 Develop/optimize segmentation algorithm Year 3 Modified
MGH 3.3 Integrate w/ tractography Year 4 Modified
MGH 3.4 Apply on core 3 data Year 5 Modified
MGH 4 Group Morphometry Statistics
MGH 4.1 Develop/optimize statistics algorithms Year 3 Modified
MGH 4.2 Develop GUI for Linux Year 3 Modified
MGH 4.3 Slicer integration Year 3 Modified
MGH 4.4 Compile application on Windows Year 4 Modified
MGH 5 XNAT Desktop Years 4-5
MGH 5.1 Establish requirements for desktop version of XNAT Years 4-5 Complete
MGH 5.2 Develop implementation plan for prototype Years 4-5 Complete
MGH 5.3 Implement prototype version Years 4-5 Incomplete (in progress)
MGH 5.4 Implement alpha version Year 5 Incomplete
MGH 6 XNAT Central Years 4-5
MGH 6.1 Deploy XNAT Central, a public access XNAT host Years 4-5 Complete
MGH 6.2 Coordinate with NAMIC sites to upload project data Years 4-5 Incomplete (ongoing)
MGH 6.3 Continue developing XNAT Central based on feedback from NAMIC sites Years 4-5 Incomplete (ongoing)
MGH 7 NAMIC Kit integration Years 4-5
MGH 7.1 Implement web services to exchange data with Slicer, Batchmake, and other client applications Years 4-5 Incomplete (ongoing)
MGH 7.2 Add XNAT Desktop to standard NAMIC kit distribution Year 5 Incomplete

Timeline Modifications

Group Aim Milestone Modification
MIT 2.2 Methods to compare shape statistics Removed, the effort refocused on registration necessary for population studies
MIT 2.4 Software infrastructure to integrate shape analysis tools into the pipeline for population studies. New, morphed into collaboration with XNAT to provide more general population analysis tools. Partially completed.
MIT 4 fMRI analysis including local and atlas-based priors for quantifying activation. New, partially completed. Refinements in progress. Clinical study with Core 1 is in progress.
Utah 2.2 (removed) Feature-based brain image registration. Shift emphasis to shape-based analysis/registration
Utah 2.1 (removed) Cortical filtering and feature detection Effort is subsumed by other Core 1 partners (e.g. see MGH/Freesurfer)
Utah 1.3 (removed) Segmentation of cortex/WM Effort is subsumed by other Core 1-2 partners (e.g. see EM-Segmenter)
Utah 3.0 (removed) Fast implmentations of PDEs Real-time filtering is demphasized in favor of shape/DTI analysis
Utah 1.5 (added) Joint analysis of DTI and functional data Opportunities/needs within various collaborations
Utah 2.1-2.3 (added, in place of cortical analysis) Shape analysis Nonparametric shape analysis added to address needs of core 3.
Utah 2.7 Shape regression Extension/completion of framework. Opportunities/needs within various collaborations.
UNC 1.2 Develop medially-based shape representation Remove
UNC 1.4 Develop generic cortical correspondence framework (Years 3-5) New
UNC 2.4 DTI Atlas Building (Years 2--4) New
GaTech 2.1 FA analysis New
MGH 4.1 - 4.4 Group Morphometry Statistics Added and then removed, based on personnel changes
MGH 5-7 XNAT Added to support remote image database capabilities

Core 1 Timeline Notes

Core 2: Engineering

Core 2 Timelines and Milestones

Group Aim Milestone Proposed time of completion Status
GE 1 Define software architecture
GE 1 Object design Yr 1 Completed
GE 1 Identify patterns Yr 3 Patterns for processing scalar and vector images, models, fiducials complete. Patterns for diffusion weighted completed, fMRI ongoing.
GE 1 Create frameworks Yr 3 Frameworks for processing scalar and vector images, models, fiducials complete. Frameworks for diffusion weighted completed, fMRI ongoing.
GE 2 Software engineering process
GE 2 Extreme programming Yr 1-5 On schedule, ongoing
GE 2 Process automatiion Yr 3 On schedule, ongoing
GE 2 Refactoring Yr 3 Complete
GE 3 Automated quality system
GE 3 DART deployment Yr 2 Complete
GE 3 Persistent testing system Yr 5 Incomplete
GE 3 Automatic defect detection Yr 5 Incomplete
Kitware 1 Cross-platform development
Kitware 1 Deploy environment (CMake, CTest) Yr 1 Complete
Kitware 1 DART Integration and testing Yr 1 Complete
Kitware 1 Documentation tools Yr 2 Complete
Kitware 2 Integration tools
Kitware 2 File Formats/IO facilities Yr 2 Complete
Kitware 2 CableSWIG deployment Yr 3 Complete (integration ongoing)
Kitware 2 Establish XML schema Yr 4 Complete, refinements ongoing
Kitware 3 Technology delivery
Kitware 3 Deploy applications Yr 1 Complete (ongoing)
Kitware 3 Establish plug-in repository Yr 2 Incomplete
Kitware 3 Cpack Yr 4-5 Incomplete
Isomics 1 NAMIC builds of slicer Years 2--5 Complete
Isomics 1 Schizophrenia and DBP intefaces Year 3---5 Completed (refinements ongoing)
Isomics 2 ITK Integration tools Year 1---3 Completed
Isomics 2 Experiment Control Interfaces Year 2---5 Migration from LONI to BatchMake Underway
Isomics 2 fMRI/DTI algorithm support Year 2---5 Completed DTI, fMRI Ongoing
Isomics 2 New DBP algorithm support Year 2---5 Ongoing
Isomics 3 Compatible build process Year 1---3 Completed
Isomics 3 Dart Integration Year 1---2 Completed (upgrades ongoing)
Isomics 3 Test scripts for new code Year 2---5 Ongoing
UCSD 1 Grid computing---base Year 1 Completed
UCSD 1 Grid enabled algorithms Year 3 First version (GWiz alpha) available - initial integration with Slicer3 and execution model.
UCSD 1 Testing infrastructure Year 4 Initiated
UCSD 2 Data grid --- compatibility Year 2 Completed
UCSD 2 Data grid --- slicer access Year 2 Completed for version 2.6. In progress for Slicer3
UCSD 3 Data mediation --- deploy Year 1 Incomplete (modfication below)
UCLA 1 Debabeler functionality Year 1 Continued Progress
UCLA 2 SLIPIE Interpretation (Layer 1) Year 1--Year2 In Progress
UCLA 3 SLIPIE Interpretation (Layer 2) Year 1--Year2 On Schedule
UCLA 3 Developing ITK Modules Year2 In Progress
UCLA 4 Integrating SRB (GSI-enabled) Year2 Completed
UCLA 5 Integrating IDA Year2 Completed
UCLA 5 Integrating External Visualization Applications Year2 Completed

Core 2 Timeline Modifications

Group Aim Milestone Modification
Isomics 3 Data mediation Delayed pending integration of databases into NAMIC infractructure

Core 2 Timeline Notes

Core 3: Driving Biological Problems

The Core 3 projects submitted R01 style proposals, as specified in the RFA, and did not submit timelines.

Core 4: Service

Core 4 Timelines and Milestones

Group Aim Milestone Proposed time of completion Status
Kitware 1 Implement Development Farms
Kitware 1 Deploy platforms Yrs 1 Complete
Kitware 1 Communications Yrs 1 Complete, ongoing
Kitware 2 Establish software process
Kitware 2 Secure developer database Yr 1 Complete, ongoing
Kitware 2 Collect guidelines Yr 1 Complete
Kitware 2 Manage software submission process Yr 1 Complete
Kitware 2 Configure process tools Yr 1 Complete
Kitware 2 Survey community Yr 1 Complete
Kitware 3 Deploy NAMIC Tools
Kitware 3 Toolkits Yr 1 Complete
Kitware 3 Integration tools Yr 1 Complete
Kitware 3 Applications Yr 1 Complete
Kitware 3 Integrate new computing resources Yr 1 Complete
Kitware 4 Provide support
Kitware 4 Esablish support infrastructure Yrs 1--5 On schedule, ongoing
Kitware 4 NAMIC support Yr 1 Complete
Kitware 5 Manage NAMIC Software Releases Yrs 1--5 On schedule, ongoing

Core 4 Timeline Modifications

Group Aim Milestone Modification
Kitware 2-5 Various Refined/modified the sub aims

Core 4 Timeline Notes

Core 5: Training

Core 5 Timelines and Milestones

Group Aim Milestone Proposed time of completion Status
Harvard 1 Formal Training Guidllines
Harvard 1 Functional neuroanatomy Yr 1 Complete
Harvard 1 Clinical correlations Yr 1 Complete
Harvard 2 Mentoring
Harvard 2 Programming workshops Yrs 1-5 On schedule, ongoing
Harvard 2 One-on-one mentoring, Cores 1, 2, 3 Yrs 1-5 On schedule, ongoing
Harvard 3 Collaborative work environment
Harvard 3 Wiki Yrs 1 Complete
Harvard 3 Mailing lists Yrs 1 Complete
Harvard 3 Regular telephone conferences Yrs 1-5 On schedule, ongoing
Harvard 4 Educational component for tools
Harvard 4 Slicer training modules Yr 2-5 Slicer 2.x tutorials complete, Two Slicer 3 tutorials complete, translation of 2.x tutorials to 3 is ongoing and on schedule
Harvard 5 Demonstrations and hands-on training
Harvard 5 Various workshops and conferences Yrs 1--5 On schedule, ongoing

Core 5 Timeline Modifications

None.

Core 5 Timeline Notes

Core 6: Dissemination

Core 6 Timelines and Milestones

Group Aim Milestone Proposed time of completion Status
Isomics 1 Create a collaboration metholdology for NA-MIC
Isomics 1.1 develop a selection process Yr 1 Complete
Isomics 1.2 guidelines to govern the collaborations Yr 1-2 Complete
Isomics 1.3 Provide on-site training Yr 1-5 Complete for current tools (ongoing for tool refinement)
Isomics 1.4 develop a web site infrastructure Yr 1 Complete
Isomics 2 Facilitate communication between NA-MIC developers and wider research community
Isomics 2.1 develop materials describing NAMIC technology Yr 1-5 On Schedule
Isomics 2.2 participate in scientific meetings Yr 2-5 On Schedule
Isomics 2.3 Document interactions with external researchers Yr 2-5 On Schedule
Isomics 2.4 Coordinate publication strategies Yr 3-5 On Schedule
Isomics 3 Develop a publicly accessible internet resource of data, software, documentation, and publication of new discoveries
Isomics 3.1 On-line repository of NAMIC related publications and presentations Yr 1-5 On Schedule
Isomics 3.2 On-line repository of NAMIC tutorial and training material Yr 1-5 On Schedule
Isomics 3.3 Index and a searchable database Yr 1-2 Done
Isomics 3.4 Automated feedback systems that track software downloads Yr 3 Done

Core 6 Timeline Modifications

None.

Core 6 Timeline Notes

Appendix A Publications (Katie)

A list should be mined from the publications database and attached here in MS word format.

Appendix B EAB Report and Response (Kapur)

EAB Report

This will be added on Wednesday, May 28th.

Response to EAB Report

This will be added on Thursday, May 29th.