2012 Summer Project Week:DicomToNrrd - Revision history

Hjmjohnson: /* Key Investigators */

2012-06-21T20:59:18Z

Key Investigators

Kentwilliams at 20:02, 7 June 2012

2012-06-07T20:02:04Z

Dmwelch: First draft

2012-05-22T21:37:38Z

First draft

Dmwelch: Template

2012-05-14T21:22:05Z

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 12: / Line 12: @@
 <h3>Objective</h3>
 Revise and refactor the DicomToNrrd program to build properly with ITK 4.1.  Enhance it to accept a wider variety of DICOM Diffusion Weighted Images.
 </div>
@@ Line 26: / Line 28: @@
 Add more regression tests, incorporating new test images that were not readable with the old version of DicomToNRRD.
 </div>
@@ Line 32: / Line 36: @@
 <h3>Progress</h3>
-The work is complete. The program successfully reads all test images as the earlier ITK3-only version of DicomToNrrd. It can also handle several image 'flavors' that caused the earlier version to fail.  Test images contributed by the Slicer community have been added to the testing data corpus, which is stored on MIDAS (http://midas.kitware.com)
+Intial goals for this project are complete.
 </div>
 </div>

@@ Line 11: / Line 11: @@
 <h3>Objective</h3>
-Complete implementation of DicomToNrrd converter for Slicer 4.1
+Revise and refactor the DicomToNrrd program to build properly with ITK 4.1.  Enhance it to accept a wider variety of DICOM Diffusion Weighted Images.
 </div>
@@ Line 18: / Line 18: @@
 <h3>Approach, Plan</h3>
-TODO
+Starting from the original DIcomToNrrd program (as it exists in the Slicer3/Slicer4 source code),
 </div>
@@ Line 25: / Line 32: @@
 <h3>Progress</h3>
-We have already completed most of the reimplementation and code cleanup on our BRAINSia fork of Slicer on Github.
+The work is complete. The program successfully reads all test images as the earlier ITK3-only version of DicomToNrrd. It can also handle several image 'flavors' that caused the earlier version to fail.  Test images contributed by the Slicer community have been added to the testing data corpus, which is stored on MIDAS (http://midas.kitware.com)
 </div>
 </div>
@@ Line 34: / Line 40: @@
 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
+#ITK Module - NO
 #Slicer Module
-##Built-in YES
+##Built-in - NO
-##Extension -- commandline
+##Extension -- commandline - YES
-##Extension -- loadable
+##Extension -- loadable - NO
 #Other
 ==References==

@@ 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: Kent Williams, Hans Johnson
 <div style="margin: 20px;">
@@ Line 21: / Line 11: @@
 <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.
+Complete implementation of DicomToNrrd converter for Slicer 4.1
 </div>
@@ Line 33: / Line 18: @@
 <h3>Approach, Plan</h3>
+TODO
 </div>
@@ Line 43: / Line 25: @@
 <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.
+We have already completed most of the reimplementation and code cleanup on our BRAINSia fork of Slicer on Github.
 </div>
 </div>
 ==Delivery Mechanism==
@@ Line 57: / Line 36: @@
 #ITK Module
 #Slicer Module
-##Built-in
+##Built-in YES
 ##Extension -- commandline
 ##Extension -- loadable
-#Other (Please specify)
+#Other
 ==References==