View source for 2009 Summer Project Week DWI / DTI QC and Prepare Tool: DTIPrep

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Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
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==Key Investigators==
* UNC: Zhexing Liu, Heather Cody Hazlett, Martin Styner
* Utah: Casey Goodlett, Guido Gerig, Tom Fletcher

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<h3>Objective</h3>
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


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<h3>Approach, Plan</h3>

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


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<h3>Progress</h3>

* 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 volume average in a nrrd DWI file.
* DTIPrep will be updated soon with these upper new DWI QC tools to give better quality and more flexibility to the DWI/DTI QC/Prep pipeline.
* I am still struggling with MINC2 :(.


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