View source for ProjectWeek200706:ContrastingTractographyMeasures

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|[[Image:Cingulum1.jpg|thumb|left|100px|Cingulum Bundle]]
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===Key Investigators===
* BWH: Marek Kubicki (Core 3), Carl-Fredrik Westin (NAC collaborator), Sonia Pujol (Core 5), Doug Markant (Core 3), Doug Terry (Core 3), Katharina Quintus (Core 3), Jorge Alvarado (Core 3), Tri Ngo (Core 3), Sylvain Bouix (Core 3), Marc Niethammer (Core 3)
* MGH: Randy Gollub (Core 5), Bruce Fischl (Core 1), Denis Jen (Core 1), Karl Helmer (Morphometry BIRN collaborator)
* Utah: Tom Fletcher (Core 1), Ross Whitaker (Cores 1 & 5), Guido Gerig (Cores 1 & 5), Casey Goodlett (Core 1), Saurav Basu (Core 1), Davis McKay (Core 1)
* UNC: Martin Styner (Core 1)
* GA Tech: Eric Pichon (Core 1), John Melonakos (Core 1), Xavier LaFaucheur (Core 1), Vandana Mohan (Core 1), Allen Tannenbaum (Core 1)
* MIT: Lauren O'Donnell (Core 1), Polina Golland (Core 1)
* UIowa: Vince Magnotta (Collaborator)
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<h1>Objective</h1>
A new initiative has begun in response to a shared vision among Cores 1, 3 and 5 that the field of medical image analysis would be well served by work in the area of validation, calibration and assessment of reliability.  Discussions have continued among our participants since then and as a result a plan for the initial work on this front has been articulated. 

*  There are many outstanding questions in this domain that we agree are interesting and worth considering such as:

1. What benchmarks should be used to assess performance of a NA-MIC Toolkit algorithm?
<p>2. How can we assess the performance of an algorithm if we have no access to the ground truth of what it is measuring (e.g. the white matter of the brain with tractography)?</P>
<p>3. What statistical methods are most appropriate for quanitfying and testing significance of these assessments? </p>

The answers to these questions will vary depending on the specific algorithm and its application. The group agreed that the best way to proceed was to chose one very specific example that is highly relevant to the NA-MIC work to date and focus efforts on that. The methods that arise from this can then be applied to additional areas.

We agreed to begin by studying the results obtained by applying each of the tractography tools to a single dataset and then gathering to present the results to one another and discuss how best to quantify the similarities and differences. 

*  Final goals are: 

1. To write up the results for publication with all of us as contributing authors.
<p>2. To make the dataset and our analyzed results available to the scientific community </p>
<p>3. To use our findings to begin to establish benchmarking methods for the NA-MIC toolkit.</p>

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<h1>Approach</h1>

Details:
* Data sets are provided by Marek Kubicki (put link to descriptor page and download instructions here).  Cohort includes 5 subjects with schizophrenia and 5 matched healthy controls that are de-identified and not marked as to diagnosis.  Each subject has a 3T high resolution DTI scan, structural MRI scan and expert generated Regions of Interest (ROIs) for each subject that are needed for tract definition. Acquisition parameters can be found here: [[Projects/Diffusion/2007_Project_Week_Contrasting Tractography Measures/Acquisition Parameters|Acquisition Parameters]].  

* The 10 tracts to be studied are the cingulum bundle, the uncinate fasiculus, fornix, internal capsule, and the arcuate fasiculus on the left and right sides. To see how the ROI's were defined, click here: [[Projects/Diffusion/2007_Project_Week_Contrasting Tractography Measures/ROI_Definitions|ROI Definitions]].

* Each tool developer is responsible for downloading and analyzing the data, optimizing their own algorithm as needed.  Keep careful notes on your final processing methods as you will need to teach them to Sonia Pujol at the Santa Fe retreat.  She will repeat the analysis independently using all the tools herself on the data, these are the result that will be included in summary manuscript(s).

* Metrics to be collected will be finalized by this group in an upcoming T-con.  Suggestions include measure of FA along the tract, size and/or volume of tract, spatial localization of tract, measure of connectivity.  Perhaps also some way to look at group results towards the goal of being able to make statements about differences in health and disease? 

* Participating algorithms (and tester) include:
# Fiber tracking the UNC way (Guido Gerig, Casey Goodlett or his designee)
# Slicer tract tool (Doug Terry/Marek Kubicki)
# POI tool ? not yet sure this one will participate (Bruce Fischl/Dennis Jen/Karl Helmer)
# Volumetric connectivity (Ross Whitaker/Tom Fletcher)
# [[Projects/Diffusion/Contrasting_Tractography_Measures#GATech |Finsler ]](Allen Tannenbaum/John Melonakos)
# Medinrea (PF Filliard)
# GTRACT (Vince Magnotta)
# Cluster tool (Lauren O'Donnell)
# Stochastic Tractography (Tri Ngo/Carl-Fredrik Westin)

In preparation for the upcoming T-con, each algorithm team needs to [[Projects/Diffusion/Contrasting_Tractography_Measures | update this wiki page ]] with proposed input and outputs for comparison. UNC and Iowa are done already.

* We will then hold a 2 day workshop/retreat in Santa Fe, NM.  Candidate dates are Oct 1-2.  That window avoids MICCAI, BIRN, SFN, New Mexico's ballonfest, and the Jewish High Holidays.  Please let us know immediately if that week is a NO GO for your group. The workshop/retreat will include a presentation from each group of their results AND a recommendation for how to statstically compare and quantify similarities and differences within and across tools. The outcome of the workshop/retreat will be a set of final agreed upon measurement metrics and method for compare and quantify similarities and differences within and across tools.  And the training of Sonia Pujol to run each of the analysis tools.

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<h1>Progress</h1>

Data can be found on BIRN in the following directory:

/home/Projects/NAMIC__0003/Files/PNL/3T_data_sample

with subdirectories:

:dwi (raw diffusion data)
:dwi-EdCor (raw diffusion data eddy current corrected)
:dougt_DTI_ROI (directory of labelmaps)


Interest in project confirmed during Project Week and dates for Sante Fe meeting agreed upon by group.  Next step is to convene a planning T-con to organize the final meeting preparations including how to share results in advance, who will attend and clarify roles for participants.

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==Additional Information==
*[[DBP2:Harvard|Harvard DBP (II) Homepage]]

== Historical Background==
*[[Training:Tractography.Validation | Tractography Validation]]