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

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	Partially completed - preliminary results
MIT	1.3	Validate and refine approach	Year 5	Partially completed - preliminary validation
MIT	2	Shape analysis
MIT	2.1	Methods to compute statistics of shapes	Year 4	Partially completed -software framework
MIT	3	Analysis of DTI data
MIT	3.2	Fiber statistics	Year 4	Partially completed --- tract clustering
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	Gometric 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	2.4	Plan to develop software infrastructure to integrate shape analysis tools into the pipeline for population studies.	New
MIT	4	Plans to for fMRI development including local and atlas-based priors for quantifying activation.	New
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

Core 2

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	Ongoing
UCSD	1	Testing infrastructure	Year 4	Initiated
UCSD	2	Data grid --- compatibility	Year 2	Completed
UCSD	2	Data grid --- slicer access	Year 2	In progress
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

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

Core 4

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

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

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 track
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 1-2-3	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	On track

Core 6 Timeline Notes

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