Difference between revisions of "DBP2:UNC:Cortical Thickness Roadmap"

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Next we discuss the main modules and details of current status and development work:
 
Next we discuss the main modules and details of current status and development work:
  
−
; A - White matter/gray matter segmentation :
+
=== White matter/gray matter segmentation ===
 
:* UNC has a segmentation technique implemented in an ITK framework for segmenting white matter and gray matter in the young brain. This technique will be converted into a Slicer3 [[Slicer3:Execution Model Documentation | command line module]]
 
:* UNC has a segmentation technique implemented in an ITK framework for segmenting white matter and gray matter in the young brain. This technique will be converted into a Slicer3 [[Slicer3:Execution Model Documentation | command line module]]
 
:** Since this segmentation technique exists in an ITK framework, the integration into Slicer3 is low risk and should be completed over the next couple of months (mid fall)
 
:** Since this segmentation technique exists in an ITK framework, the integration into Slicer3 is low risk and should be completed over the next couple of months (mid fall)
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:** This will be a good test case for applying the Slicer3 EM Segment module to a slightly different application. UNC should work through the training material on the Slicer3 EM Segment module and then refer to Brad Davis and Kilian Pohl as needed.
 
:** This will be a good test case for applying the Slicer3 EM Segment module to a slightly different application. UNC should work through the training material on the Slicer3 EM Segment module and then refer to Brad Davis and Kilian Pohl as needed.
 
:** This also should be completed before the AHM.
 
:** This also should be completed before the AHM.
−
; B - Local cortical thickness measurement :
+
=== Local cortical thickness measurement ===
 
:* UNC has an algorithm to measure local cortical thickness given a labeling of white matter and gray matter.  This technique will be converted into a Slicer3 command line module
 
:* UNC has an algorithm to measure local cortical thickness given a labeling of white matter and gray matter.  This technique will be converted into a Slicer3 command line module
 
:** This technique is non-symmetric and sparse (only computing distances where they can be computed reliably).   
 
:** This technique is non-symmetric and sparse (only computing distances where they can be computed reliably).   
 
:** It is expected that this module should be available before the AHM.
 
:** It is expected that this module should be available before the AHM.
 
:* Marc Niethammer was developing a [[Algorithm:Harvard:Thickness Slicer3 Module|technique]] at a previous project week that would be symmetric. This could be an alternative used as a comparison.
 
:* Marc Niethammer was developing a [[Algorithm:Harvard:Thickness Slicer3 Module|technique]] at a previous project week that would be symmetric. This could be an alternative used as a comparison.
−
; C - Local correspondence :
+
=== Local correspondence ===
 
:* Regional as well as local subject comparisons are needed
 
:* Regional as well as local subject comparisons are needed
 
:* Regional analysis will require precise deformable registration to a young brain atlas
 
:* Regional analysis will require precise deformable registration to a young brain atlas
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:** Freesurfer could be used for the local analysis (but it is not in the NA-MIC Kit)
 
:** Freesurfer could be used for the local analysis (but it is not in the NA-MIC Kit)
 
:** Ipek is developing local analysis tools and may have a tool available in Fall 2008.
 
:** Ipek is developing local analysis tools and may have a tool available in Fall 2008.
−
; D - Hypothesis testing
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=== Hypothesis testing ===
−
; E - Performance characterization and validation :
+
=== Performance characterization and validation ===
 
:* Characterize response based on signal noise, patient motion, etc.
 
:* Characterize response based on signal noise, patient motion, etc.
 
:* Comparison to other tools (FreeSurfer)
 
:* Comparison to other tools (FreeSurfer)
  
−
===To do===
+
=== To do ===
 
* Assign owners to tasks
 
* Assign owners to tasks
 
* Define schedule
 
* Define schedule
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−
===Schedule===
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=== Schedule ===
  
 
* '''xx/xx/2007''' - White matter/gray matter segmentation of the young brain using UNC technique as a Slicer3 module
 
* '''xx/xx/2007''' - White matter/gray matter segmentation of the young brain using UNC technique as a Slicer3 module
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===Team and Institute===
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=== Team and Institute ===
 
*Co-PI: Heather Cody Hazlett, PhD, (heather_cody at med.unc.edu, Ph: 919-966-4099)
 
*Co-PI: Heather Cody Hazlett, PhD, (heather_cody at med.unc.edu, Ph: 919-966-4099)
 
*Co-PI: Joseph Piven, MD
 
*Co-PI: Joseph Piven, MD
 
*NA-MIC Engineering Contact: Jim Miller, GE Research
 
*NA-MIC Engineering Contact: Jim Miller, GE Research
 
*NA-MIC Algorithms Contact: Martin Styner, UNC
 
*NA-MIC Algorithms Contact: Martin Styner, UNC

Revision as of 19:20, 25 September 2007

Home < DBP2:UNC:Cortical Thickness Roadmap

Objective

We would like to create an end-to-end application within Slicer3 allowing individual and group analysis of regional and local cortical thickness. Such a workflow applied to the young brain (2-4 years old) is one goal of the UNC DBP. This page describes the technology roadmap for cortical thickness analysis in the NA-MIC Kit. The basic components necessary for this end-to-end application are:

  • Tissue segmentation: Should be multi-modality, correcting for intensity inhomogeneity and work on non-skull-stripped data
  • Cortical thickness measurement: Local cortical thickness needs measurements at every location of the white-gray matter boundary, as well as at the gray-csf boundary. Regional analysis does not need such a dense measurement.
  • Cortical correspondence: Local analysis needs a full correspondence on both white-gray boundary and gray-csf boundary.
  • Statistical analysis/Hypothesis testing: Measurements need to be compared and tested localy incorporating multiple-comparison correction, correlative analysis would be necessary too.

Roadmap

Starting with several MRI images (weighted-T1, weighted-T2...) we want to obtain cortical thickness maps for each subject, compute cortical correspondences between subjects, and analyze the cortical thickness at these corresponding locations. Ultimately, the NA-MIC Kit will provide a workflow for individual and group analysis of cortical thickness. It will be implemented as a set of Slicer3 modules that can be used interactively within the Slicer3 application as well as in batch on a computing cluster using BatchMake.

Next we discuss the main modules and details of current status and development work:

White matter/gray matter segmentation

  • UNC has a segmentation technique implemented in an ITK framework for segmenting white matter and gray matter in the young brain. This technique will be converted into a Slicer3 command line module
    • Since this segmentation technique exists in an ITK framework, the integration into Slicer3 is low risk and should be completed over the next couple of months (mid fall)
  • UNC will also investigate adapting the Slicer3 EM Segment module to their young brain studies. Here, UNC will adapt the UNC atlas of the 2 year old brain to provide priors for the EM Segment module
    • This will be a good test case for applying the Slicer3 EM Segment module to a slightly different application. UNC should work through the training material on the Slicer3 EM Segment module and then refer to Brad Davis and Kilian Pohl as needed.
    • This also should be completed before the AHM.

Local cortical thickness measurement

  • UNC has an algorithm to measure local cortical thickness given a labeling of white matter and gray matter. This technique will be converted into a Slicer3 command line module
    • This technique is non-symmetric and sparse (only computing distances where they can be computed reliably).
    • It is expected that this module should be available before the AHM.
  • Marc Niethammer was developing a technique at a previous project week that would be symmetric. This could be an alternative used as a comparison.

Local correspondence

  • Regional as well as local subject comparisons are needed
  • Regional analysis will require precise deformable registration to a young brain atlas
    • NA-MIC Kit tools can be applied here
  • Local analysis requires techniques which are not currently in the NA-MIC Kit
    • Freesurfer could be used for the local analysis (but it is not in the NA-MIC Kit)
    • Ipek is developing local analysis tools and may have a tool available in Fall 2008.

Hypothesis testing

Performance characterization and validation

  • Characterize response based on signal noise, patient motion, etc.
  • Comparison to other tools (FreeSurfer)

To do

  • Assign owners to tasks
  • Define schedule


Schedule

  • xx/xx/2007 - White matter/gray matter segmentation of the young brain using UNC technique as a Slicer3 module
  • xx/xx/2007 - White matter/gray matter segmentation of the young brain using the Slicer3 EM Segment module
  • xx/xx/2007 - Cortical thickness measurement using UNC technique as a Slicer3 module
  • xx/xx/2007 - Cortical thickness measurement using Marc Niethammer's approach as a Slicer3 module
  • xx/xx/2007 - Deformable registration of young brain regional atlas
  • xx/xx/2007 - Regional analysis of cortical thickness as a Slicer3 module
  • xx/xx/2007 - BatchMake workflow
  • xx/xx/2007 - Groupwise regional analysis of cortical thickness as a NA-MIC Workflow
  • xx/xx/200x - Groupwise local analysis of cortical thickness as a NA-MIC Workflow


Team and Institute

  • Co-PI: Heather Cody Hazlett, PhD, (heather_cody at med.unc.edu, Ph: 919-966-4099)
  • Co-PI: Joseph Piven, MD
  • NA-MIC Engineering Contact: Jim Miller, GE Research
  • NA-MIC Algorithms Contact: Martin Styner, UNC
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