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

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:* 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
:** NA-MIC Kit tools can be applied here
+
:** NA-MIC toolkit can be applied here, Slicer 3 has a b-spline based MI registration which needs to be tested
 +
:** Parcellation atlas for regional analysis is the current atlas used by the DBP
 
:* Local analysis requires techniques which are not currently in the NA-MIC Kit
 
:* 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)
+
:** Freesurfer can 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 Oguz is developing local analysis tools and should be available in Fall 2008. The tool necessitates the following steps (also performed within Freesurfer)
 +
:*** 1) spherical topology of white matter: Marc Niethammer has Slicer module for this step, testing will be necessary to ensure appropriateness in the cortical case
 +
:*** 2) inflation of cortical surface: A Slicer module exists for this step, but likely not with the properties. Tests and possible additional implementation will need to be done.
 +
:*** 3) computation of correspondence on inflated surface using particle system: No module exists, first prototype programs are in development in collaboration with Utah (I Oguz, J Cates)
 +
 
 
=== Hypothesis testing ===
 
=== Hypothesis testing ===
 
=== Performance characterization and validation ===
 
=== Performance characterization and validation ===

Revision as of 21:09, 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 open source segmentation tool called itkEMS (binary download) 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 a 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 module is well suited for regional analysis, but additional work to interpolate dense measurements along the boundaries from the sparse ones would be necessary for a local analysis.
    • It is expected that this module should be available before the AHM (for the current, sparse measurements).
  • Marc Niethammer developed a technique at a previous project week that would be symmetric. This could be used for the local cortical thickness analysis, if our comparison studies show appropriate results.

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 toolkit can be applied here, Slicer 3 has a b-spline based MI registration which needs to be tested
    • Parcellation atlas for regional analysis is the current atlas used by the DBP
  • Local analysis requires techniques which are not currently in the NA-MIC Kit
    • Freesurfer can be used for the local analysis (but it is not in the NA-MIC Kit)
    • Ipek Oguz is developing local analysis tools and should be available in Fall 2008. The tool necessitates the following steps (also performed within Freesurfer)
      • 1) spherical topology of white matter: Marc Niethammer has Slicer module for this step, testing will be necessary to ensure appropriateness in the cortical case
      • 2) inflation of cortical surface: A Slicer module exists for this step, but likely not with the properties. Tests and possible additional implementation will need to be done.
      • 3) computation of correspondence on inflated surface using particle system: No module exists, first prototype programs are in development in collaboration with Utah (I Oguz, J Cates)

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

  • Tissue segmentation
  • 15/10/2007 - White matter/gray matter segmentation of the young brain using itkEMS as a Slicer3 module (C Vachet) - at AHM
  • 01/12/2007 - White matter/gray matter segmentation of the young brain using the Slicer3 EM Segment module (C Vachet) - at AHM
  • 15/12/2007 - Comparison study itEMS vs EM Segment in Slicer 3 (C Vachet) - at AHM
  • Cortical thickness
  • 23/12/2007 - UNC Cortical thickness measurement as a Slicer3 module (C Vachet) - at AHM
  • 23/12/2007 - Niethammer's Laplacian Cortical thickness measurement module code working at UNC as a Slicer3 module (C Vachet) - at AHM
  • 01/03/2008 - Regional comparison between UNC and Laplacian cortical thickness (C Vachet)
  • Cortical correspondence
  • 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