Home < 2007 Scientific Report Timeline
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 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 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 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 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.
|
