Difference between revisions of "2011 Winter Project Week:TwoTensorTracts"

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(Created page with '__NOTOC__ <gallery> Image:PW-SLC2011.png|Projects List Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus…')
 
 
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<gallery>
 
<gallery>
 
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
 
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
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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:wholebrainclustersexample.jpg|Example whole brain clustering result.
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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:example2tensortracts.jpg|Example two-tensor tractography result.
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Image:clustersinSlicer4.png|Progress: Cluster output loaded into Slicer4 with new MRML file.
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Image:modelHierarchyClustersSlicer4.png|Progress: Model hierarchy created by initial Slicer4 module
 
</gallery>
 
</gallery>
  
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==Instructions for Use of this Template==
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==Key Investigators==
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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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* BWH: Lauren O'Donnell, Yogesh Rathi, C-F Westin
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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
 
  
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==Key Investigators==
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==Thank You==
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* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
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* BWH: Demian Wassermann (help with Python)
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* Utah: Tom Fletcher, Ross Whitaker
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* Kitware: JC, J2, for bug squishing.  Danielle Pace for pointers on Python modules for Slicer4.
  
 
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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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To test 2-tensor tractography in Slicer3/standalone and hook it up to full-brain clustering pipelines.
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
  
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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 goals for the project week are to test 2-tensor tractography, to update clustering I/O to read tracts as a single large polydata file per subject, and to produce output in Slicer3 MRML format.   
  
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Our plan for the project week is to first try out <bar>,...
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The next step is to ascertain what needs to be done to visualize/label the clusters in slicer3 or 4. This is in order to make atlases or study a particular tract. The old slicer2 interface allowed interactive selection of clusters (show/hide selected, and show/hide labeled or unlabeled) and anatomical naming/labeling.
  
 
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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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* Installed/tested 2-tensor slicer3 python module. Thank you Demian for help. Reported bug with voxel sizes to Yogesh Rathi.
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* Converted clustering output tcl script to output slicer3/slicer4 MRML format
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* Initial work on porting slicer2 ModelInteraction module to slicer4. Module will enable interactive model selection/grouping/naming. Slicer4 picking and improved model hierarchy functionality will be used when available.  The module is a QTScriptedModule python Slicer4 implementation.
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* Some progress towards general file formats as input to clustering code, to allow slicer2/3/4/other programs to input tract files (one or many vtk's)
 
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#ITK Module
 
#ITK Module
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#Slicer Module
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#Slicer Module YES
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##Built-in
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##Built-in YES!
 
##Extension -- commandline
 
##Extension -- commandline
 
##Extension -- loadable
 
##Extension -- loadable
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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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*Tensor Kernels for Simultaneous Fiber Model Estimation and Tractography. Y. Rathi, J. G. Malcolm, O. Michailovich, C.-F. Westin, M. E. Shenton, S. Bouix. Magn Reson Med. 2010
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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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*Quantitative examination of a novel clustering method using magnetic resonance diffusion tensor tractography. A. N. Voineskos, L. J. O'Donnell, N. J. Lobaugh, D. Markant, S. H. Ameis, M. Niethammer, B. H. Mulsant, B. G. Pollock BG, J. L. Kennedy, C. F. Westin, M. E. Shenton. NeuroImage 45(2):370-376, 2009
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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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*Automatic Tractography Segmentation Using a High-Dimensional White Matter Atlas. Lauren O'Donnell and Carl-Fredrik Westin. IEEE Transactions in Medical Imaging 26(11):1562-1575, 2007
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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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</div>
 
</div>

Latest revision as of 18:07, 14 January 2011

Home < 2011 Winter Project Week:TwoTensorTracts

  • Example whole brain clustering result.

  • Example two-tensor tractography result.

  • Progress: Cluster output loaded into Slicer4 with new MRML file.

  • Progress: Model hierarchy created by initial Slicer4 module

Key Investigators

  • BWH: Lauren O'Donnell, Yogesh Rathi, C-F Westin

Thank You

  • BWH: Demian Wassermann (help with Python)
  • Kitware: JC, J2, for bug squishing. Danielle Pace for pointers on Python modules for Slicer4.

Objective

To test 2-tensor tractography in Slicer3/standalone and hook it up to full-brain clustering pipelines.

Approach, Plan

Our goals for the project week are to test 2-tensor tractography, to update clustering I/O to read tracts as a single large polydata file per subject, and to produce output in Slicer3 MRML format.

The next step is to ascertain what needs to be done to visualize/label the clusters in slicer3 or 4. This is in order to make atlases or study a particular tract. The old slicer2 interface allowed interactive selection of clusters (show/hide selected, and show/hide labeled or unlabeled) and anatomical naming/labeling.

Progress

  • Installed/tested 2-tensor slicer3 python module. Thank you Demian for help. Reported bug with voxel sizes to Yogesh Rathi.
  • Converted clustering output tcl script to output slicer3/slicer4 MRML format
  • Initial work on porting slicer2 ModelInteraction module to slicer4. Module will enable interactive model selection/grouping/naming. Slicer4 picking and improved model hierarchy functionality will be used when available. The module is a QTScriptedModule python Slicer4 implementation.
  • Some progress towards general file formats as input to clustering code, to allow slicer2/3/4/other programs to input tract files (one or many vtk's)

Delivery Mechanism

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

  1. ITK Module
  2. Slicer Module YES
    1. Built-in YES!
    2. Extension -- commandline
    3. Extension -- loadable
  3. Other (Please specify)

References

  • Tensor Kernels for Simultaneous Fiber Model Estimation and Tractography. Y. Rathi, J. G. Malcolm, O. Michailovich, C.-F. Westin, M. E. Shenton, S. Bouix. Magn Reson Med. 2010
  • Quantitative examination of a novel clustering method using magnetic resonance diffusion tensor tractography. A. N. Voineskos, L. J. O'Donnell, N. J. Lobaugh, D. Markant, S. H. Ameis, M. Niethammer, B. H. Mulsant, B. G. Pollock BG, J. L. Kennedy, C. F. Westin, M. E. Shenton. NeuroImage 45(2):370-376, 2009
  • Automatic Tractography Segmentation Using a High-Dimensional White Matter Atlas. Lauren O'Donnell and Carl-Fredrik Westin. IEEE Transactions in Medical Imaging 26(11):1562-1575, 2007
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