Difference between revisions of "2009 Summer Project Week Slicer3 registration"

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Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
 
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
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Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
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Image:Aparc-overlay-affine.png|Overlay of affine registered freesurfer label map on DTI data.
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Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
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Image:T2-base masked rigid-linear-affine.png|Rigid-Affine-Bspline registration of T2 to DTI data.
 
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==Instructions for Use of this Template==
 
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#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name>
 
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#Copy the entire text of this page into the page created above
 
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#Link the created page into the list of projects for the project event
 
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#Delete this section from the created page
 
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#Send an email to tkapur at bwh.harvard.edu if you are stuck
 
  
 
==Key Investigators==
 
==Key Investigators==
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* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
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* BWH: Andrew Rausch, Doug Terry, Sylvain Bouix, Marek Kubicki
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* Utah: Tom Fletcher, Ross Whitaker
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* Kitware: Luis Ibanez
  
 
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<h3>Objective</h3>
 
<h3>Objective</h3>
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We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.
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We are determining which methods of registration in slicer (and other tools) work best for registration of various types of volumes. Our focus is currently on registering data from structural to DTI space.
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
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We're going through each type of registration and registration pipeline in Slicer 3 with a specific image to test which methods give the best results.  We are also performing comparisons with FSL's FLIRT and FNIRT tools.
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Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below.  The main challenge to this approach is <foo>.
 
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Our plan for the project week is to first try out <bar>,...
 
  
 
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<h3>Progress</h3>
 
<h3>Progress</h3>
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Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.
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Some of Slicer 3's registration works ok, but it currently has no good way to register from structural to DTI, and no way to apply a similar transform to a label map from structural space. Currently we must use FSL tools to accomplish this. Luis Ibanez has been helping us with developing tools outside of Slicer that seem to be performing well.
  
  
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==References==
 
==References==
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*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
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http://www.na-mic.org/Wiki/index.php/Projects:DBP2:Harvard:Registration_Documentation
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* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
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* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
 
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* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .
 
  
 
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Latest revision as of 16:50, 22 June 2009

Home < 2009 Summer Project Week Slicer3 registration

  • Overlay of affine registered freesurfer label map on DTI data.

  • Rigid-Affine-Bspline registration of T2 to DTI data.

Key Investigators

  • BWH: Andrew Rausch, Doug Terry, Sylvain Bouix, Marek Kubicki
  • Kitware: Luis Ibanez

Objective

We are determining which methods of registration in slicer (and other tools) work best for registration of various types of volumes. Our focus is currently on registering data from structural to DTI space.



Approach, Plan

We're going through each type of registration and registration pipeline in Slicer 3 with a specific image to test which methods give the best results. We are also performing comparisons with FSL's FLIRT and FNIRT tools.

Progress

Some of Slicer 3's registration works ok, but it currently has no good way to register from structural to DTI, and no way to apply a similar transform to a label map from structural space. Currently we must use FSL tools to accomplish this. Luis Ibanez has been helping us with developing tools outside of Slicer that seem to be performing well.


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