Difference between revisions of "Collaboration:UNC"

From NAMIC Wiki
Jump to: navigation, search
m (Update from Wiki)
 
m (Update from Wiki)
 
(2 intermediate revisions by the same user not shown)
Line 1: Line 1:
 
== Goal ==
 
== Goal ==
  
−
* Discuss DTI tools
+
* Reviewing shape analysis with current NAMIC data
−
* Discuss DTI clinical projects
+
* Establishing a concrete plan and schedule for collaborations. Target projects are shape analysis and statistical analysis of anisotropy measure along fibers.
  
−
== Activities ==
+
== Agenda ==
  
−
* Demonstration of FiberViewer and FiberTracking software (Sampath Vetsa)
+
* 10am: UNC presentations for Psychiatrists/Psychologists:
−
** Training on step-by-step process for using software
+
** Shape Analysis of Caudate and Corpus Callosum Data (30 min)[[Image:2005_NAMIC_ShapeSchizoBWH.ppt|Image:2005 NAMIC ShapeSchizoBWH.ppt]]
−
*** Computing tensor image from diffusion weighted images
+
** ITK SNAP: A level Set Semi Automatic Segmentation tool and its use at UNC for the segmentation of brain structures [[Image:2005_NAMIC_ShapeSchizoBWH.ppt|Image:2005 NAMIC ShapeSchizoBWH.ppt]]
−
*** Identifying and drawing regions-of-interest using InsightSNAP
+
** UNC Tools for the Statistical Analysis of Anisotropy of Diffusion Tensor Measures along White Matter Fibers. (30min) [[Image:Isabelle100705-1.ppt|Image:Isabelle100705-1.ppt]]
−
*** Performing tractography
+
 
−
*** Analysis of FA,MD,eigenvalue properties along tracts of interest (splenium and genu used as examples)
+
* 11:15am: Open Discussion with PNL on immediate and future collaborations plans.
−
** Feedback from UCI group on software ease-of-use
+
** Establish what UNC needs from PNL and PNL from UNC.
−
** UCI group installed and tested software live on their machines - Jim Fallon tested software looking for challenging tracts in neonate data
+
** Resolve technical issues such authorship, clinical data, etc...
−
* Discussion of high-performance visualization of fiber tracts using modern graphics hardware (Vid Petrovic)
+
 
−
* Clinical projects using DTI
+
* 12pm: Lunch
−
** Explanation by Jim Fallon of previous studies in connection differences between schizophrenics and controls
+
* 1pm: Wrap up of PNL/UNC collaboration plans
−
** Discussion of Krabbe study between Martin Styner and Jim Fallon
+
* 2pm: UNC presentations for Computer Scientists.
 +
** Shape Analysis: UNC Shape Analysis Pipeline in ITK/NAMIC [[Image:2005_10_ShapePipeline.ppt|Image:2005 10 ShapePipeline.ppt]]
 +
** Shape Analysis: Statistical Non-Parametric Permutation tests for shape hypothesis testing, [[Image:2005_10_NonParamShapeStats.ppt|Image:2005 10 NonParamShapeStats.ppt]]
 +
** DTI Tensor Analysis [[Image:Isabelle100705-2.ppt|Image:Isabelle100705-2.ppt]]
  
 
== Participants ==
 
== Participants ==
  
−
* Jim Fallon (UC Irvine)
 
−
* Martina Panzenboeck (UC Irvine)
 
−
* Vid Petrovic (UC Irvine)
 
−
* Guido Gerig (UNC)
 
 
* Martin Styner (UNC)
 
* Martin Styner (UNC)
 
* Isabelle Corouge (UNC)
 
* Isabelle Corouge (UNC)
−
* Sampath Vetsa (UNC)
+
* Martha Shenton (PNL)
−
* Casey Goodlett (UNC)
+
* James Levitt (PNL)
 +
* Marek Kubicki (PNL)
 +
* C-F Westin (BWH)
 +
* Marc Niethammer (PNL)
 +
* Sylvain Bouix (PNL)
 +
 
 +
== Discussion overview ==
 +
 
 +
'''Statistical shape analysis:'''
 +
 
 +
Caudate (SPD):
 +
 
 +
* Spherical harmonics for shape description
 +
* local/global/parcellated significance and anlysis
 +
* Local and global differences on R, but only local on L
 +
* main shape difference in caudate head, small effect in caudate tail
 +
* volume reduction in SPD
 +
 
 +
Corpus callosum:
 +
 
 +
* model based 2D segmentation of corpus callosum
 +
* DTI fiber tracking based corpus callosum subdivision method (coloring based on connection to white matter parcellation -- given as a template) results in probabilistic subdivision of the corpus callosum
 +
 
 +
<br /> DTI:
 +
 
 +
* quantitative analysis of DTI data (along fibers; statistics within fiber bundles)
 +
 
 +
<br />'''PNL provides:'''
 +
 
 +
* an interpretation of the shape differences seen in SPD vs control group caudates
 +
* a larger dataset to improve the statistical significance (chronic SZ?)
 +
 
 +
<br />'''UNC provides:'''
 +
 
 +
* statistical shape analysis software
 +
* fiber viewer and fiber tracking software (in Namic sandbox see also [http://www.ia.unc.edu/dev software here])
 +
* tools for quantitiative analysis of DTI data (statistics of diffusion metrics and tensors along fibers and across fibers within a fiber bundle)
 +
 
 +
'''Issues:'''
 +
 
 +
* very small sample sizes (-> PNL will provide more and different data)
 +
* local shape difference significance measures are very conservative or not conservative enough (is there a middle groud?)
 +
* not clear how to compare fiber tracts between subjects (how to align?)
 +
 
 +
'''Possible future work:'''
 +
 
 +
* Do statistical caudate analysis for chronic SZ (expect larger changes than for SPD)?
 +
* Hippocampus study using the UNC software?

Latest revision as of 13:52, 18 December 2006

Home < Collaboration:UNC

Goal

  • Reviewing shape analysis with current NAMIC data
  • Establishing a concrete plan and schedule for collaborations. Target projects are shape analysis and statistical analysis of anisotropy measure along fibers.

Agenda

  • 11:15am: Open Discussion with PNL on immediate and future collaborations plans.
    • Establish what UNC needs from PNL and PNL from UNC.
    • Resolve technical issues such authorship, clinical data, etc...

Participants

  • Martin Styner (UNC)
  • Isabelle Corouge (UNC)
  • Martha Shenton (PNL)
  • James Levitt (PNL)
  • Marek Kubicki (PNL)
  • C-F Westin (BWH)
  • Marc Niethammer (PNL)
  • Sylvain Bouix (PNL)

Discussion overview

Statistical shape analysis:

Caudate (SPD):

  • Spherical harmonics for shape description
  • local/global/parcellated significance and anlysis
  • Local and global differences on R, but only local on L
  • main shape difference in caudate head, small effect in caudate tail
  • volume reduction in SPD

Corpus callosum:

  • model based 2D segmentation of corpus callosum
  • DTI fiber tracking based corpus callosum subdivision method (coloring based on connection to white matter parcellation -- given as a template) results in probabilistic subdivision of the corpus callosum


DTI:

  • quantitative analysis of DTI data (along fibers; statistics within fiber bundles)


PNL provides:

  • an interpretation of the shape differences seen in SPD vs control group caudates
  • a larger dataset to improve the statistical significance (chronic SZ?)


UNC provides:

  • statistical shape analysis software
  • fiber viewer and fiber tracking software (in Namic sandbox see also software here)
  • tools for quantitiative analysis of DTI data (statistics of diffusion metrics and tensors along fibers and across fibers within a fiber bundle)

Issues:

  • very small sample sizes (-> PNL will provide more and different data)
  • local shape difference significance measures are very conservative or not conservative enough (is there a middle groud?)
  • not clear how to compare fiber tracts between subjects (how to align?)

Possible future work:

  • Do statistical caudate analysis for chronic SZ (expect larger changes than for SPD)?
  • Hippocampus study using the UNC software?
Retrieved from "https://www.na-mic.org/w/index.php?title=Collaboration:UNC&oldid=4424"