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

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Details of the tool functionality were discussed [[2008_Core_1_UNC_Utah_DTI|between UNC and Utah]]:
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* "Protocol" based execution
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** Parameter files contain all settings
 +
* Handles conversion of DICOM data to volumetric formats (NRRD)
 +
* Automated quality control, corrects/rejects, provides reporting facility.
 +
* Motion correction
 +
* Eddy current correction
 +
* Interpolation of data
 +
* Rejection of interslice brightness
 +
* Local plausibility check with reconstructed DTI
 +
* FA/MD histogram comparison with atlas
 +
* Local dot product of principal direction with atlas
 +
* Full brain tracking for flips/permutations of axes
 +
* Focus QC on white matter only
 +
* DTI data, as well as FA/MD
  
  
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<div style="width: 27%; float: left; padding-right: 3%;">
  
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<h3>Approach, Plan</h3>
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<h1>Approach, Plan</h1>
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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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The tool will allow a "protocol" based execution via parameter files. The parameter files contain all the settings/preferences/options and this file can be created using the tool's GUI. This tool will handle the conversion of DICOM data to volumetric image formats (NRRD), perform automated quality control, correct data if possible, possibly reject parts of the data and provide a reporting facility.  
  
 
</div>
 
</div>
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<div style="width: 40%; float: left;">
 
<div style="width: 40%; float: left;">
  
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<h3>Progress</h3>
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<h1>Progress</h1>
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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 style="width: 970%; float: left;">
 
  
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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 .
 
  
 
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Revision as of 05:01, 11 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, Ran Tao

Objective

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


Details of the tool functionality were discussed between UNC and Utah:

  • "Protocol" based execution
    • Parameter files contain all settings
  • Handles conversion of DICOM data to volumetric formats (NRRD)
  • Automated quality control, corrects/rejects, provides reporting facility.
  • Motion correction
  • Eddy current correction
  • Interpolation of data
  • Rejection of interslice brightness
  • Local plausibility check with reconstructed DTI
  • FA/MD histogram comparison with atlas
  • Local dot product of principal direction with atlas
  • Full brain tracking for flips/permutations of axes
  • Focus QC on white matter only
  • DTI data, as well as FA/MD


Approach, Plan

The tool will allow a "protocol" based execution via parameter files. The parameter files contain all the settings/preferences/options and this file can be created using the tool's GUI. This tool will handle the conversion of DICOM data to volumetric image formats (NRRD), perform automated quality control, correct data if possible, possibly reject parts of the data and provide a reporting facility.

Progress


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