Andy: Update from Wiki

2006-12-18T13:25:17Z

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NAMIC Core 1 Plans March 2005

This document is intended to serve as an outline of plans for NAMIC Core 1. This includes:

* Goals of Core 1
* Interactions with Core 3
* Plans for integration of tools into the toolkit (including interactions directly with Core 2)
* Scientific agendas as executed at Core 1 sites

== Goals: ==

* What have we learned about the pathophysiology of schizophrenia?
** How did or will NAMIC tools provide valuable leverage in asking and answering questions about schizophrenia?
* What is the vision of the NAMIC software solution?
** How do the needs of the end-users get factored into design of software toolkit?
** How do the interests of the algorithms developers get matched to those needs?

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== Timeline: ==

To focus the development of relevant tools for the Core 3 collaborators, it is critical that essential information be gathered and coordinated, and that teams of investigators be coordinated for focused interaction. The list below is a proposed set of needs, and associated timetable for addressing them.

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=== Requirements dashboard ===

The goal of this stage is to assemble a coherent collection of requirements needs for software in the toolkit, especially as it supports Core 3 activities. Note that there probably needs to be some decision making process to cull out Core 3 requests that are not feasible/reasonable either for technical reasons or for time constraint reasons.

* Date Action Responsibility
* April 1 Management Core convenes requirements dashboard working group.
* April 15 Specifications for requirements dashboard due.
* May 1 Phase 1 dashboard release.
* May 15 Requirements dashboard Core feedback due.
* June 1 Phase 2 dashboard release.
* June 1 Requirements entered.
* June 30 Quantitative process review.
* July 10 Lessons learned. Process improvement recommendations.

=== Requirements elicitation/extraction ===

A more detailed cut at this plan, focused on getting requirements is listed below:

* April 15 Management Core defines small cross-functional teams for requirements extraction.
* May 1 Cross-functional teams TCON with Core 3 team members for software profile and requirements elicitation/extraction.
* June 1 Requirements dashboard entries due.
* June 1 Cores 1 and 3 feedback on functional requirements specification.
* June 30 Tool integration Round 2 (below).
* June 30 Quantitative process review.
* June 30 Requirements satisfaction read-out.
* July 10 Lessons learned. Process improvement.

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== Requirements elicitation/gathering: ==

* Cross-functional team (Cores 1,2,4,6,…) meet with Core 3 investigators to profile current tools and elicit functional requirements for NAMIC solutions.
* Profile existing software solutions at Core 3 sites.

# What software tools do you use and why?
# What is your vision of the ideal software solution?
# Do you use FSL, SPM2, SPM99, AFNI, BrainVoyager, VoxBo, MedX, …?
# What do you like and dislike about these software tools?
# What are their strengths and weaknesses?
# On a scale of 1-10, how would you rate these tools?

* Elicit functional requirements.

# What do you need? Why is that important for your research?
# Using a scale of 1-10, can you prioritize these in terms of anticipated difficulty and scientific impact?
# What questions will you be able to ask with these tools that you can’t ask now?
# If you had to identify 3 scientific concepts that all team members should be familiar with, what would these be, e.g., statistical mapping, the localization problem, … ?
# On a scale of 1-10, how well is the current software process serving your needs? How can we improve the process?
# Do you think we ‘get it’?

== Requirements management: ==

* Define requirements management framework

# Define quantitative metrics for functional requirements satisfaction.
# Define channels for continual input from Core 3.
# Functional requirements entered into requirements management dashboard.
# Specific individuals from Cores 1, 2, 4, 6, … designated as requirements champions to advocate for requirements at design meetings.

== Lessons learned: ==

* What lessons can we learn from the mixed successes of other large collaborative scientific software projections?

# “Get it”: Embrace software processes/philosophy which will allow the Core 1 investigators to say that we understand their needs and challenges.
# Get religion about requirements.
# Distinction between functional and non-functional requirements.
# Align personal goals/wants early.
# Monitor the ground.
# Regular use cases.
# Build investigator focus into software processes.
# Priority on scientific/clinical output.

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== Software definition: ==

We need to develop a coherent vision of what the NAMIC software system will be, and how to effectively deliver it to our current Core 3 collaborators, as well as to future collaborators.

* Define NAMIC solution

# What are the software needs?
# What is the NAMIC solution?
# What are the strengths and weaknesses of the NAMIC solution relative to existing solutions?
# Is there a framework for interoperability with existing software solutions at Core 1 and 3 sites?
# Integration of new methods into the toolkit (Slicer, ITK)
# Build adoption for NAMIC solutions at Core 3 sites. Profile and address barriers to adoption.
# Collaboration with Core 3 to use new tools to investigate clinical questions

== Toolkit integration: ==

We need to assemble a rough schedule of expected tools. Initially this comes from Core 1 interests, clearly as we work on requirements from the Core 3 side, we will need to modify this. However, this provides a starting point for capturing current algorithm development plans.

== Expected Tools and Working Groups ==

* MIT

# Shape-guided level sets for segmentation (already exists in ITK)
# DTI analysis tools (already exists in Slicer)
# Shape-based MRF segmentation (expected by July 1, Kilian Pohl is already working on incorporating existing code base into Slicer)
# Population shape analysis – joint collaboration with UNC (Martin Styner). (Prototype pipeline expected by August 1, integration with Slicer an open issue to due code complexities)

* MGH

# QBALL (done)
# Tensor-based statistical group comparison (June 30)

* UTAH

# Tensor statistics and representations (April 30)
# DTI interpolation (June 30)
# DTI filtering (June 30)
# Hypothesis testing for tensors (expected by September but work is still in more speculative stage, and will require feedback from users before a more firm timetable is possible)

* UNC

# Tensor statistics and representations
# Clustering tools
# Prototype platform for analysis
# Shape representations and analysis tools

* Georgia Tech

# Rule based segmentation methods (June 30)
# Statistical based segmentation methods (Implemented in ITK)
# DTI analysis methods (June 30)
# Shape analysis tools (August 31)
# Expected Core 3 Collaborations

* MIT

# Population analysis of shape (with Martha Shenton)
# DTI analysis (with Andy Saykin)
# fMRI analysis (with Andy Saykin)

* MGH

# DTI group comparison of sz SNP subtypes (MGH-Irvine)

* UTAH

# DTI statistics and processing (with Martha Shenton)
# Tensor hypothesis testing (with Martha Shenton)

* UNC

# DTI properties – with BWH
# Shape analysis – with BWH

* Georgia Tech

# Segmentation of structures – with Irvine, BWH
# Level set analysis tools – with Utah
# Shape analysis – with UNC

== Suggested organizational structure: ==

* Set up a timeline for integration of tools
* Set up a specific plan for meeting with Core 3 partners
* Set up specific sets of data in coordination with Core 2 and Core 3

Algorithm:Future Plans - Revision history

Andy: Update from Wiki