Difference between revisions of "2009 Summer Project Week DWI / DTI QC and Prepare Tool: DTIPrep"
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<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 | + | * Utah: Casey Goodlett, Guido Gerig, Tom Fletcher |
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<h3>Objective</h3> | <h3>Objective</h3> | ||
| − | We are developing a GUI/command line tool for DWI QC and | + | 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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| + | <div style="width: 27%; float: left; padding-right: 3%;"> | ||
| − | </ | + | <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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</div> | </div> | ||
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<div style="width: 40%; float: left;"> | <div style="width: 40%; float: left;"> | ||
| − | < | + | <h3>Progress</h3> |
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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) | ||
| + | ** 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
DTIPrep GUI
DTIPrep Protocol
DTIPrep result
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 :(.
