Difference between revisions of "2009 Summer Project Week DWI / DTI QC and Prepare Tool: DTIPrep"

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(Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png|Project Week Main Page Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus ...')
 
 
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<gallery>
 
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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:DTIPrep-gui.png|DTIPrep GUI
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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:DTIPrep-protocol.png|DTIPrep Protocol
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Image:DTIPrep-result.png|DTIPrep result
 
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</gallery>
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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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* UNC: Zhexing Liu, Heather Cody Hazlett, Martin Styner
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* Utah: Tom Fletcher, Ross Whitaker
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* Utah: Casey Goodlett, Guido Gerig, Tom Fletcher
  
 
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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 developing a GUI/command line tool for DWI/DTI QC and preparation.
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* Both a GUI and command line tool
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* "Study-specific Protocol" based
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** Handles NRRD and MINC2 formats
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** Image/diffusion information check
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** Padding/Cropping of data
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** Slice-wise, interlace-wise and gradient-wise intensity and motion check
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** Motion/Eddy current correction
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** DTI computing
  
  
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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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The tool allows a "protocol" based execution via parameter files. The parameter file contains all the settings/preferences/options and can be created using the tool's GUI. This tool performs automated quality control, correct data if possible, possibly reject parts of the data and provide a reporting facility.
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Our plan for the project week is to:
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* Add MINC2 support
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* Tune intergrations with other tools
  
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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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</div>
 
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</div>
 
  
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<div style="width: 970%; float: left;">
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* Separate command-line tools for DWI QC has been uploaded into UNC [http://www.ia.unc.edu/dev/ NeuroLib] ($NeuroLib/Applications/DWIQC)
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** DWIQCSliceChecker: for slice-wise intensity-related artifacts detection and gradient exclusion(optimized for both single and multiple b-valued DWIs).
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** DWIQCInterlaceChecker: for interlace-wise Venetian blind artifacts detection and gradient exclusion(optimized for both single and multiple b-valued DWIs).
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** DWIQCGradientChecker: for gradient-wise motion artifacts detection and gradient exclusion.
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** DWIBaselineAverager: for optimized multiple-b0 volumes average in a nrrd DWI file(optimizing is base on either all b0 volumes or all DW volumes).
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* DTIPrep will be updated soon with the upper new DWI QC tools to give better QC quality and more flexibility to the DWI/DTI QC/Prep pipeline.
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* Discussed with Ran(U. Utah) the improvement of her eddy-current and motion artifact correction tool.
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* I am still struggling with MINC2 :(.
  
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==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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* 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 .
 
  
 
</div>
 
</div>

Latest revision as of 15:38, 26 June 2009

Home < 2009 Summer Project Week DWI < DTI QC and Prepare Tool: DTIPrep

Key Investigators

  • UNC: Zhexing Liu, Heather Cody Hazlett, Martin Styner
  • Utah: Casey Goodlett, Guido Gerig, Tom Fletcher

Objective

We are developing a GUI/command line tool for DWI/DTI QC and preparation.

  • Both a GUI and command line tool
  • "Study-specific Protocol" based
    • Handles NRRD and MINC2 formats
    • Image/diffusion information check
    • Padding/Cropping of data
    • Slice-wise, interlace-wise and gradient-wise intensity and motion check
    • Motion/Eddy current correction
    • DTI computing


Approach, Plan

The tool allows a "protocol" based execution via parameter files. The parameter file contains all the settings/preferences/options and can be created using the tool's GUI. This tool performs automated quality control, correct data if possible, possibly reject parts of the data and provide a reporting facility.

Our plan for the project week is to:

  • Add MINC2 support
  • Tune intergrations with other tools


Progress

  • Separate command-line tools for DWI QC has been uploaded into UNC NeuroLib ($NeuroLib/Applications/DWIQC)
    • DWIQCSliceChecker: for slice-wise intensity-related artifacts detection and gradient exclusion(optimized for both single and multiple b-valued DWIs).
    • DWIQCInterlaceChecker: for interlace-wise Venetian blind artifacts detection and gradient exclusion(optimized for both single and multiple b-valued DWIs).
    • DWIQCGradientChecker: for gradient-wise motion artifacts detection and gradient exclusion.
    • DWIBaselineAverager: for optimized multiple-b0 volumes average in a nrrd DWI file(optimizing is base on either all b0 volumes or all DW volumes).
  • DTIPrep will be updated soon with the upper new DWI QC tools to give better QC quality and more flexibility to the DWI/DTI QC/Prep pipeline.
  • Discussed with Ran(U. Utah) the improvement of her eddy-current and motion artifact correction tool.
  • I am still struggling with MINC2 :(.


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