Project Week/Template - Revision history

Grclirui: /* Instructions for Use of this Template */

2013-06-18T03:03:52Z

Instructions for Use of this Template

Grclirui: /* Key Investigators */

2013-06-18T03:03:23Z

Key Investigators

Grclirui: /* Delivery Mechanism */

2013-06-18T03:01:21Z

Delivery Mechanism

Grclirui: /* References */

2013-06-18T02:59:46Z

References

Grclirui at 02:56, 18 June 2013

2013-06-18T02:56:57Z

AnthonyBlumfield: Undo revision 81496 by AnthonyBlumfield (Talk)

2013-06-11T21:39:19Z

Undo revision 81496 by AnthonyBlumfield (Talk)

AnthonyBlumfield: Summer 2013 Radnostics page created

2013-06-11T21:35:41Z

Summer 2013 Radnostics page created

Anry: Undo revision 81173 by Anry (Talk)

2013-05-26T17:32:24Z

Undo revision 81173 by Anry (Talk)

Anry: Undo revision 81174 by Anry (Talk)

2013-05-26T17:32:02Z

Undo revision 81174 by Anry (Talk)

Anry at 17:23, 25 May 2013

2013-05-25T17:23:26Z

@@ Line 3: / Line 3: @@
 Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
 </gallery>
 ==Key Investigators==

@@ Line 33: / Line 33: @@
 <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>.
+Discuss with Jc and Steve regarding how to incorporate into Slicer. Currently it
+is used as a downloadable library during superbuild, similar to SlicerExecutionModel.
 </div>
@@ Line 42: / Line 41: @@
 <h3>Progress</h3>
 </div>

← Older revision		Revision as of 03:01, 18 June 2013
Line 50:		Line 50:
	==Delivery Mechanism==		==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)~~	+	https://github.com/grclirui/PythonCppAPI.git
−
−	~~#ITK Module~~
−	~~#Slicer Module~~
−	~~##Built-in~~
−	~~##Extension -- commandline~~
−	~~##Extension -- loadable~~
−	~~#Other (Please specify)~~

← Older revision		Revision as of 02:59, 18 June 2013
Line 58:		Line 58:
	##Extension -- loadable		##Extension -- loadable
	#Other (Please specify)		#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 .

@@ Line 2: / Line 2: @@
 <gallery>
 Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
 </gallery>
@@ Line 14: / Line 12: @@
 ==Key Investigators==
-* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
+* GRC: Rui Li, Jim Miller
-* Utah: Tom Fletcher, Ross Whitaker
+* Kitware: Jean-Christophe Fillion-Robin
 <div style="margin: 20px;">
@@ Line 21: / Line 20: @@
 <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.
+Python embedding library to manage calling python functions from C++. This will eliminate the code duplication  in Slicer.

@@ Line 1: / Line 1: @@
 __NOTOC__
 <gallery>
 Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
-Image:spine.png|CT Spine
+Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
-Image:SegmentedSpine.png|Automated Segmentation
+Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
 </gallery>
-<b>Osteoporosis</b>
+==Instructions for Use of this Template==
+#Please create a new wiki page with an appropriate title for your project using the convention 2013_Summer_Project_Week:<Project Name>
-A condition of bone mineral loss affecting the aging population
+#Copy the entire text of this page into the page created above
-* Impacts 200 million people WW
+#Link the created page into the list of projects for the project event
-* Leads to 9 million fractures each year
+#Delete this section from the created page
-* Inflicts pain, morbidity, and mortality
+#Send an email to tkapur at bwh.harvard.edu if you are stuck
 ==Key Investigators==
-* Radnostics: Anthony Blumfield
+* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
-* Albert Einstein College of Medicine: Einat Blumfield, MD
+* Utah: Tom Fletcher, Ross Whitaker
 <div style="margin: 20px;">
@@ Line 28: / Line 21: @@
 <h3>Objective</h3>
-Radnostics Osteoporosis Detection is a solution for early detection of osteoporosis in CT scans performed for other clinical indications
+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.
-*Tens of millions of CT scans are performed annually for various medical conditions
-*We measure osteoporosis biomarkers and detect patients at risk
-*100% automated & integrated into the clinical workflow
@@ Line 41: / Line 34: @@
 <h3>Approach, Plan</h3>
-Create a 3D Slicer v4 command line module for Radnostics Beta2.
+Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below.  The main challenge to this approach is <foo>.
 </div>
@@ Line 48: / Line 43: @@
 <h3>Progress</h3>
@@ Line 55: / Line 51: @@
 ==Delivery Mechanism==
-This work will be delivered to the NA-MIC Kit as a
+This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)
 #Slicer Module
 ##Extension -- commandline
 ==References==
-*http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine
+*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.
-*http://www.radnostics.com
+* 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.

@@ Line 6: / Line 6: @@
 </gallery>
 ==Key Investigators==
-* UAB: Arie Nakhmani, LiangJia Zhu, Allen Tannenbaum
+* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
-* BWH: Yi Gao, Ron Kikinis
+* Utah: Tom Fletcher, Ross Whitaker
 <div style="margin: 20px;">
@@ Line 16: / Line 21: @@
 <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.
@@ Line 29: / Line 34: @@
 <h3>Approach, Plan</h3>
 </div>
@@ Line 35: / Line 43: @@
 <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.
@@ Line 41: / Line 49: @@
 </div>
-==delivery Mechanism==
+==Delivery Mechanism==
-This work will be delivered to the NA-MIC Kit as a loadable commandline extension and antor effect.
+This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)
 ==References==
-* A. Nakhmani, A. Tannenbaum, "Tracking with Adaptive Sobolev Snakes." Submitted to
+*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.
-IEEE Transactions on Image Processing.
+* 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.
-* A. Nakhmani, A. Tannenbaum, "Self-Crossing Detection and Location for Parametric
+* 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 .