2007 Scientific Report Timeline

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Introduction

This section of the report gives the milestones for years 1 through 3 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 In progress
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 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 partially, ongoing
Utah 1.3 Segmentation of cortex/WM Year 3 Completed partially, ongoing
Utah 1.4 Segmentation analysis of white matter tracts Year 3 Algorithms complete/published, refining and applying to Core 3 data.
Utah 2 Nonparametric Shape Analysis Year 5 Incomplete, ongoing.
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 comlexes Year 4 Complete
Utah 2.4 Demonstration of NP shape representations on clinical hypotheses from Core 3 Year 5 Incomplete, ongoing
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 Incomplete, 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 Preliminary results and 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 In Progress
MGH 3.3 Integrate w/ tractography Year 4 In Progress
MGH 3.4 Apply on core 3 data Year 5 In Queue
MGH 4 Group Morphometry Statistics
MGH 4.1 Develop/optimize statistics algorithms Year 3 Complete
MGH 4.2 Develop GUI for Linux Year 3 Partially Complete
MGH 4.3 Slicer integration Year 3 In Queue
MGH 4.4 Compile application on Windows Year 4 In Queue

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, partially completed
MIT 4 fMRI analysis including local and atlas-based priors for quantifying activation. New, partially completed
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 3.0 (removed) Fast implmentations of PDEs Real-time filtering is demphasized in favor of shape/DTI analysis
Utah 2.1-2.3 (added, in place of cortical analysis) Shape analysis Nonparametric shape analysis added to address needs of core 3.
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 added Group morphometry statistics New

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 imageryand fMRI ongoing.
GE 1 Create frameworks Yr 3 Frameworks for processing scalar and vector images, models, fiducials complete. Frameworks for diffusion weighted imageryand 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 (ongoing)
Kitware 2 CableSWIG deployment Yr 3 Complete (integration ongoing)
Kitware 2 Establish XML schema Yr 4 Incomplete
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 Partially completed, 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 Many complete for Slicer 2.x, Slicer 3 ongoing
Harvard 5 Demonstrations and hands-on training
Harvard 5 Various workshops and conferences Yrs 1--5 On schedule, ongoing (see also link)

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 Done
Isomics 1.2 guidelines to govern the collaborations Yr 1-2 Done
Isomics 1.3 Provide on-site training Yr 1-5 On Schedule
Isomics 1.4 develop a web site infrastructure Yr 1 Done
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

Group Aim Milestone Modification
Isomics 3.1 On-line repository of NAMIC related publications and presentations Duration of this extended to the full grant cycle.

Core 6 Timeline Notes