2012 Summer Project Week:DTIPrep - Revision history

Dmwelch: /* Key Investigators */

2012-06-18T16:39:18Z

Key Investigators

Tkapur at 03:01, 18 June 2012

2012-06-18T03:01:57Z

Dmwelch: /* Key Investigators */ Added some specifics for Objectives

2012-05-29T16:40:57Z

Key Investigators: Added some specifics for Objectives

Dmwelch: Added documentation links to page

2012-05-15T14:01:15Z

Added documentation links to page

Dmwelch: Filled in from template

2012-05-14T21:57:43Z

Filled in from template

Dmwelch: Template

2012-05-14T21:21:24Z

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: @@
 DTIPrep is a useful tool for automated QA of DWI images, but it has areas where improvement and increased usability could be achieved.  We will identify ways to improve user interaction and experience, as well as address any architectural decisions that affect future development.  Specific goals are:
 # Fix the behavior of the '--outputFolder' flag to something more intuitive or add alternative method and document current behavior
-# Fix the report of excluded gradients so that the .txt and .xml files are consistant
+# Fix the xml reporting scheme for batch processing mode and make it conform to the interactive mode
 #*; Example : [[Media:DTIPrepMisimatchingTXT.txt]] [[Media:DTIPrepMismatchingXML.xml]]
@@ Line 26: / Line 26: @@
 <h3>Approach, Plan</h3>
-We will meet with the main developers of DTIPrep and discuss user experiences and ways to improve the interface.  We will also address any additional enhancements and solutions that is needed for the tool.
+We will meet with the main developers of DTIPrep and discuss user experiences and ways to improve the interface.    We will also address any additional enhancements and solutions that is needed for the tool.
 </div>

@@ Line 18: / Line 18: @@
 # Fix the behavior of the '--outputFolder' flag to something more intuitive or add alternative method and document current behavior
 # Fix the report of excluded gradients so that the .txt and .xml files are consistant
-#*; Example : [[File:DTIPrepMisimatchingTXT.txt]] [[File:DTIPrepMismatchingXML.xml]]
+#*; Example : [[Media:DTIPrepMisimatchingTXT.txt]] [[Media:DTIPrepMismatchingXML.xml]]

@@ Line 15: / Line 15: @@
 <h3>Objective</h3>
-DTIPrep is a useful tool for automated QA of DWI images, but it has areas where improvement and increased usability could be achieved.  We will identify ways to improve user interaction and experience, as well as address any architectural decisions that affect future development.
+DTIPrep is a useful tool for automated QA of DWI images, but it has areas where improvement and increased usability could be achieved.  We will identify ways to improve user interaction and experience, as well as address any architectural decisions that affect future development.  Specific goals are:
+# Fix the behavior of the '--outputFolder' flag to something more intuitive or add alternative method and document current behavior
+# Fix the report of excluded gradients so that the .txt and .xml files are consistant
+#*; Example : [[File:DTIPrepMisimatchingTXT.txt]] [[File:DTIPrepMismatchingXML.xml]]

@@ Line 54: / Line 54: @@
 ==References==
-* Z. Liu et al., "Quality control of diffusion weighted images" Proc. SPIE 2010, vol. 1, no. 1, p. 76280J-76280J-9.
+* Z. Liu et al., [http://www.nitrc.org/docman/view.php/283/753/spie2010-dwi-qc.pdf| "Quality control of diffusion weighted images"] Proc. SPIE 2010, vol. 1, no. 1, p. 76280J-76280J-9.
 </div>

@@ Line 2: / Line 2: @@
 <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:|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.
+Image:|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
 </gallery>
 ==Key Investigators==
-* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
+* UIowa: David Welch, Hans Johnson
-* Utah: Tom Fletcher, Ross Whitaker
+* Utah: Clement Vachet, Sylvian Gouttard
 <div style="margin: 20px;">
@@ Line 21: / Line 15: @@
 <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.
+DTIPrep is a useful tool for automated QA of DWI images, but it has areas where improvement and increased usability could be achieved.  We will identify ways to improve user interaction and experience, as well as address any architectural decisions that affect future development.
@@ Line 33: / Line 27: @@
 <h3>Approach, Plan</h3>
+We will meet with the main developers of DTIPrep and discuss user experiences and ways to improve the interface.  We will also address any additional enhancements and solutions that is needed for the tool.
 </div>
@@ Line 43: / Line 34: @@
 <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.
+N/A
@@ Line 63: / Line 54: @@
 ==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.
+* Z. Liu et al., "Quality control of diffusion weighted images" Proc. SPIE 2010, vol. 1, no. 1, p. 76280J-76280J-9.
 </div>