View source for 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 ==

* 10am: UNC presentations for Psychiatrists/Psychologists:
** Shape Analysis of Caudate and Corpus Callosum Data (30 min)[[Image:2005_NAMIC_ShapeSchizoBWH.ppt|Image:2005 NAMIC ShapeSchizoBWH.ppt]]
** 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]]
** 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]]

* 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...

* 12pm: Lunch
* 1pm: Wrap up of PNL/UNC collaboration plans
* 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 ==

* 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

<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?