2009 Winter Project Week WFU1 - Revision history

Vidyaraj: /* Key Investigators */

2009-01-08T20:34:01Z

Key Investigators

Vidyaraj: /* Key Investigators */

2009-01-02T19:08:45Z

Key Investigators

Wyatt: /* References */

2008-12-29T13:28:05Z

References

Wyatt: New page: {| |Project Week Main Page ]] |[[Image:Rhesus_HpcCorScrnShot.jpg|thumb|220px|Subcortical Segmentation of Rhesus sub...

2008-10-23T13:05:21Z

New page: {| |thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page ]] |[[Image:Rhesus_HpcCorScrnShot.jpg|thumb|220px|Subcortical Segmentation of Rhesus sub...

New page

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:Rhesus_HpcCorScrnShot.jpg|thumb|220px|Subcortical Segmentation of Rhesus subject]]
|}

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===Key Investigators===
* Virgina Tech: Chris Wyatt
* Virginia Tech: Vidya Rajagopalan
* TBD

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<h1>Objective</h1>
We are developing methods for analysis of structural images from nonhuman primates for identifying regional differences in brain morphometry caused by interactions of stress and alcohol exposure. The current workflow for segmentation of the subject images involves a collection of tools that make it difficult to export to the neuroscience community. The goal of this project is to move our entire workflow into Slicer 3.

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<h1>Approach, Plan</h1>

At the [[NA-MIC/Projects/External Collaboration/Measuring Alcohol and Stress Interaction|2008 NA-MIC Summer Project Week]] we optimized EMSegmenter in slicer2 for segmentation of tissue classes and subcortical structures (above image). We have since moved to using the EMSegmenter module in Slicer3. Comparisons between the resulting segmentations show only small differences.

Our plan for the project week is to move our entire NHP segmentation workflow into Slicer3 so that it is easier for collaborators and others to use. This requires replacing our current registration procedure based on FSL-FLIRT and writing command-line modules for a few custom tools.
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<h1>Progress</h1>
TO-DO:
* replace FLS-flirt with rigid and affine CLPs
* write and test CLP module using our existing ITK-based deformable registration code
* write and test CLP module using our existing ITK-based brain extraction code
* develop a cleanup process using the Slicer3 editor
* create XNAT delivery mechanism for NHP atlas and test subject data
* write new tutorial using all-Slicer3 workflow

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===References===

← Older revision		Revision as of 13:28, 29 December 2008
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	===References===		===References===
		+	[[NA-MIC_NCBC_Collaboration:Measuring_Alcohol_and_Stress_Interaction]]

@@ Line 34: / Line 34: @@
 <h1>Progress</h1>
-TO-DO:
+IN PROGRESS
 * replace FLS-flirt with rigid and affine CLPs
-* develop a cleanup process using the Slicer3 editor
+* replace FLS-flirt with rigid and affine CLPs (working with Jim Miller)
@@ Line 45: / Line 44: @@
 * write and test CLP module using our existing ITK-based brain extraction code
 * write new tutorial using all-Slicer3 workflow