2013 Summer Project Week:Nipype CLI Integration - Revision history

Rharmo: /* Key Investigators */

2013-06-21T14:16:00Z

Key Investigators

Rharmo: /* Key Investigators */

2013-06-21T02:27:46Z

Key Investigators

Raul at 16:37, 16 June 2013

2013-06-16T16:37:39Z

Raul at 16:36, 16 June 2013

2013-06-16T16:36:27Z

Raul at 15:50, 16 June 2013

2013-06-16T15:50:34Z

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…'

2013-06-11T21:36:27Z

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 28: / Line 28: @@
 * The tools had been previously developed using C++ and ITK and have been validated and used in the works described previously.
 * This week we decided to deliver the tools through several extensions consisting of python modules. Each module executes a flow of commands by calling CLIs
 * We completed the CLIs for 1 of the extensions (as an example), and are working on the scripted module
 </div>

@@ Line 26: / Line 26: @@
 <h3>Progress</h3>
-The tools have been developed using C++ and ITK and have been validated and used in the works described previously.
+* The tools had been previously developed using C++ and ITK and have been validated and used in the works described previously.
 </div>

@@ Line 1: / Line 1: @@
 __NOTOC__
 <gallery>
-Image:EmphysemaGUI.png|[[2013_Summer_Project_Week#Projects|Projects List]]
+Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
 </gallery>

@@ Line 2: / Line 2: @@
 <gallery>
 Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
 </gallery>
 ==Key Investigators==
-* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
+* BWH: Rola Harmouche,Demian Wassermann, Raul San Jose (BWH)
 <div style="margin: 20px;">
@@ Line 21: / Line 12: @@
 <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.
+We have developed a library of tools (Chest Imaging Platform) for the processing and the analysis of chest images. The main objective is to make the tools available to the public by incorporating them into Slicer as command line extension modules and through a nipype work flow for their deployment in high performance computing environments.
 </div>
@@ Line 33: / Line 19: @@
 <h3>Approach, Plan</h3>
+The library contains a set of tools for image processing, segmentation and airway and vessel generation using particles and inspection. Some of these tools are described in the works by Ross et al. and Kindlmann et. al. Our plan for the project week is to port most of these tools to the CLI infrastructure and to define nipype interfaces.
 </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.
+The tools have been developed using C++ and ITK and have been validated and used in the works described previously.
 </div>
@@ Line 50: / Line 32: @@
 ==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)
+Slicer Module
 Extension -- commandline
 ==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.
+* James C. Ross, R. San Jose Estepar, G. Kindlmann, Alejandro Diaz, C.-F. Westin, Edwin K. Silverman, George R. Washko, [Automatic Lung Lobe Segmentation Using Particles, Thin Plate Splines, and Maximum a Posteriori Estimation] Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2010 Volume 6363, Pages 163-171, 2010
-* 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.
+* Gordon Kindlmann, Raúl San José Estépar, Stephen M. Smith, Carl-Fredrik Westin. Sampling and Visualizing Creases with Scale-Space Particles. IEEE Transactions on Visualization and Computer Graphics. 2009; 15(6):1415-1424.
-* 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.
+* San José Estépar, R. et al., 2012. Computational Vascular Morphometry for the Assessment of Pulmonary Vascular Disease based on Scale-Space Particles. In Proceedings of the 9th IEEE International Symposium on Biomedical Imaging (ISBI) 2012. Barcelona, pp. 1479–1482.

2013 Summer Project Week:Nipype CLI Integration - Revision history

Rharmo: /* Key Investigators */

Rharmo: /* Key Investigators */

Raul at 16:37, 16 June 2013

Raul at 16:36, 16 June 2013

Raul at 15:50, 16 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…'