2012 Summer Project Week:ITKv4 Integration - Revision history

Hjmjohnson: /* Key Investigators */

2012-06-22T13:49:52Z

Key Investigators

Dmwelch: Added screenshot

2012-06-22T13:04:34Z

Added screenshot

Lorensen: /* Key Investigators */

2012-06-21T20:15:59Z

Key Investigators

Lorensen at 18:55, 18 June 2012

2012-06-18T18:55:23Z

Blowekamp: /* Key Investigators */

2012-06-18T16:26:48Z

Key Investigators

Pieper: /* References */

2012-06-12T12:22:46Z

References

Hjmjohnson at 19:35, 7 June 2012

2012-06-07T19:35:43Z

Dmwelch: Template

2012-05-14T21:22:34Z

Template

New page

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
</gallery>

==Instructions for Use of this Template==
#Please create a new wiki page with an appropriate title for your project using the convention 2012_Winter_Project_Week:<Project Name>
#Copy the entire text of this page into the page created above
#Link the created page into the list of projects for the project event
#Delete this section from the created page
#Send an email to tkapur at bwh.harvard.edu if you are stuck

==Key Investigators==
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
* Utah: Tom Fletcher, Ross Whitaker

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.

Our plan for the project week is to first try out <bar>,...

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
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.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
*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.
* 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.
* 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.
* 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 .

</div>

@@ Line 17: / Line 17: @@
 <h3>Objective</h3>
-Move Slicer from ITKv3 to ITKv4
+# Move Slicer build from ITKv3 to ITKv4
 </div>
@@ Line 24: / Line 31: @@
 <h3>Approach, Plan</h3>
 Figure out how to get packaging working when building with ITKv4
 </div>
@@ Line 29: / Line 39: @@
 <h3>Progress</h3>
-Basic building is working (Has been for a long time).
 During Project Week we resolved the packaging issues.
-# ITKv4 now supports runtime only installs. This required changes to both Slicer and ITKv4. The Slicer changes are checked into the repo.
+# ITKv4 now supports runtime only installs. (Thanks Bill Lorensen)
-# The current changes to Slicer work with ITK 4.1.
+## This required changes to both Slicer and ITKv4 (for complete compliance).
-# Currenty, a few .h files are included in the Slicer package. Better support has been tested and will be available in ITK 4.2.
+### The Slicer changes are checked into the repo.
 </div>
 </div>

@@ Line 29: / Line 29: @@
 <h3>Progress</h3>
 Basic building is working (Has been for a long time).
 </div>
 </div>

@@ Line 10: / Line 10: @@
 * Kitware: JC, Julien
 * NLM (C): Bradley Lowekamp
 <div style="margin: 20px;">

@@ Line 9: / Line 9: @@
 * SPL: Steve Pieper
 * Kitware: JC, Julien
 <div style="margin: 20px;">

← Older revision		Revision as of 12:22, 12 June 2012
Line 37:		Line 37:

	==References==		==References==
		+
		+	http://www.na-mic.org/Bug/view.php?id=2007

	</div>		</div>

@@ Line 2: / Line 2: @@
 <gallery>
 Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
 </gallery>

@@ Line 2: / Line 2: @@
 <gallery>
 Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
 </gallery>
 ==Key Investigators==
-* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
+* Iowa: Hans Johnson, Kent Williams
-* Utah: Tom Fletcher, Ross Whitaker
+* GE: Jim Miller
 <div style="margin: 20px;">
@@ Line 21: / Line 14: @@
 <h3>Objective</h3>
-We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.
+Move Slicer from ITKv3 to ITKv4
 </div>
@@ Line 33: / Line 20: @@
 <h3>Approach, Plan</h3>
+Figure out how to get packaging working when building with ITKv4
 </div>
@@ Line 43: / Line 26: @@
 <h3>Progress</h3>
-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.
+Basic building is working (Has been for a long time).
 </div>
 </div>
@@ Line 53: / Line 34: @@
 ==Delivery Mechanism==
-This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)
+As part of the CMake build system
 ==References==
 </div>