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

From NAMIC Wiki
Jump to: navigation, search
 
(48 intermediate revisions by the same user not shown)
Line 2: Line 2:
 
<gallery>
 
<gallery>
 
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
 
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
 +
Image:DTIPrep-gui.png|DTIPrep GUI
 +
Image:DTIPrep-protocol.png|DTIPrep Protocol
 +
Image:DTIPrep-result.png|DTIPrep result
 
</gallery>
 
</gallery>
  
 
==Key Investigators==
 
==Key Investigators==
 
* UNC: Zhexing Liu, Heather Cody Hazlett, Martin Styner
 
* UNC: Zhexing Liu, Heather Cody Hazlett, Martin Styner
* Utah: Casey Goodlett, Guido Gerig, Tom Fletcher, Ran Tao
+
* Utah: Casey Goodlett, Guido Gerig, Tom Fletcher
  
 
<div style="margin: 20px;">
 
<div style="margin: 20px;">
Line 12: Line 15:
  
 
<h3>Objective</h3>
 
<h3>Objective</h3>
We are developing a GUI/command line tool for DWI QC and DTI preparing.
+
We are developing a GUI/command line tool for DWI/DTI QC and preparation.
  
 
* Both a GUI and command line tool
 
* Both a GUI and command line tool
Line 21: Line 24:
 
** Slice-wise, interlace-wise and gradient-wise intensity and motion check
 
** Slice-wise, interlace-wise and gradient-wise intensity and motion check
 
** Motion/Eddy current correction  
 
** Motion/Eddy current correction  
** DTI data, as well as FA/MD
+
** DTI computing
  
  
Line 30: Line 33:
 
<h3>Approach, Plan</h3>
 
<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 handles the conversion of DICOM data to NRRD format, perform automated quality control, correct data if possible, possibly reject parts of the data and provide a reporting facility.  
+
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:
 
Our plan for the project week is to:
* Add MINC2 suppor
+
* Add MINC2 support
* Tune intergration with other tools
+
* Tune intergrations with other tools
  
  
Line 42: Line 45:
  
 
<h3>Progress</h3>
 
<h3>Progress</h3>
 +
 +
* Separate command-line tools for DWI QC has been uploaded into UNC [http://www.ia.unc.edu/dev/ 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 :(.
  
  
 
</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 :(.