2013 Summer Project Week:MRML Infrastructure Airway Inspector - Revision history

Demian: /* Key Investigators */

2013-06-21T12:31:21Z

Key Investigators

Demian at 12:11, 17 June 2013

2013-06-17T12:11:53Z

Raul: Created page with 'NOTOC Image:PW-MIT2013.png|Projects List Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus…'

2013-06-11T21:36:11Z

Created page with '__NOTOC__ <gallery> Image:PW-MIT2013.png|Projects List Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus…'

New page

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_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 2013_Summer_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>

==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 .

@@ Line 26: / Line 26: @@
 <div style="width: 40%; float: left;">
 <h3>Progress</h3>
-TBD
+A Loadable module with the MRML nodes for storage, data representation and visualization has been created. The next steps are to create the Logic and GUI components.
 </div>
 </div>
 ==Delivery Mechanism==

@@ Line 2: / Line 2: @@
 <gallery>
 Image:PW-MIT2013.png|[[2013_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:EmphysemaGUI.png|Emphysema Analysis Tool
-Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
+Image:AIScreenshot.png|Airway Analysis Tool
 </gallery>
-==Instructions for Use of this Template==
+==Key Investigators==
-#Please create a new wiki page with an appropriate title for your project using the convention 2013_Summer_Project_Week:<Project Name>
+* BWH: Demian Wassermann, Raul San Jose, Rola Harmouche (BWH)
-#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
+<h3>Background</h3>
-#Delete this section from the created page
+Airway Inspector (www.airwayinspector.org) is a tool for CT-based image quantitative analysis of the lung to allow the  exploration of  airway morphology and desitometric characteristics [1]. In order to become a part of 3D Slicer 4, the Airway inspector needs to have a consistent MRML representation of data and visualization
 <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.
+To develop a MRML Infrastructure for the airway inspector
 </div>
 <div style="width: 27%; float: left; padding-right: 3%;">
 <h3>Approach, Plan</h3>
+We will base the developement in the current infrastructure for tractography in 3D slicer. This is well modularized and encompasses data representation, I/O and GUI
 </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.
+TBD
 ==Delivery Mechanism==
 #Slicer Module
-##Built-in
+##Extension — loadable modules
 ==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.
+* San Jose Estepar R, Washko GG, Silverman EK, Reilly JJ, Kikinis R, Westin CF. Airway inspector: An open source application for lung morphometry. In First International Workshop on Pulmonary Image Processing. New York City, USA, 2008;293-302. Available on-line: www.lulu.com/content/3507981.

2013 Summer Project Week:MRML Infrastructure Airway Inspector - Revision history

Demian: /* Key Investigators */

Demian at 12:11, 17 June 2013

Raul: Created page with '__NOTOC__ Image:PW-MIT2013.png|Projects List Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus…'

Raul: Created page with 'NOTOC Image:PW-MIT2013.png|Projects List Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus…'