2009 Annual Scientific Report
Back to 2009_Progress_Report
Contents
- 1 Guidelines for preparation
- 2 Introduction (Tannenbaum)
- 3 Clinical Roadmap Projects
- 3.1 Roadmap Project: Stochastic Tractography for VCFS (Kubicki)
- 3.2 Roadmap Project: Brachytherapy Needle Positioning Robot Integration (Fichtinger)
- 3.3 Roadmap Project: Brain Lesion Analysis in Neuropsychiatric Systemic Lupus Erythematosus (Bockholt)
- 3.4 Roadmap Project: Cortical Thickness for Autism(Hazlett)
- 4 Four Infrastructure Topics
- 5 Highlights(Schroeder)
- 6 Impact and Value to Biocomputing (Miller)
- 7 Timeline (Ross)
- 8 Appendix A Publications (Kapur, Melonakos)
- 9 Appendix B EAB Report and Response (Kapur)
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:
- MIT: Polina Golland, Danial Lashkari, Bryce Kim
- 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 (Kapur, Melonakos)
The attached list is mined from the SPL Publications Database. Media:NA-MICPeerReviewedPapers2007.doc
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.