Difference between revisions of "2010 Winter Project Week SegmentationWizard"

From NAMIC Wiki
Jump to: navigation, search
(Created page with '__NOTOC__ <gallery> Image:PW-SLC2010.png|Projects List Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus…')
 
(→‎Key Investigators: Updated progress)
 
(12 intermediate revisions by 3 users not shown)
Line 2: Line 2:
 
<gallery>
 
<gallery>
 
Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]
 
Image:PW-SLC2010.png|[[2010_Winter_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>
 
</gallery>
−
 
−
==Instructions for Use of this Template==
 
−
#Please create a new wiki page with an appropriate title for your project using the convention Project/<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==
 
==Key Investigators==
−
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
+
* MRN: Jeremy Bockholt, Mark Scully
−
* Utah: Tom Fletcher, Ross Whitaker
+
* BWN: Steve Pieper
  
 
<div style="margin: 20px;">
 
<div style="margin: 20px;">
Line 21: Line 12:
  
 
<h3>Objective</h3>
 
<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 implement a high level wizard that performs all necessary pre-processing steps and then segments lesion images.
  
 +
</div>
  
 +
<div style="width: 27%; float: left; padding-right: 3%;">
  
 +
<h3>Approach, Plan</h3>
 +
'''1.''' Verify that all required sub-modules are production ready.
  
 +
'''2.''' Diagram all possible branches with requirements.
 +
 +
'''3.''' Use QT to create the UI and tie all relevant modules together.
  
  
 
</div>
 
</div>
  
−
<div style="width: 27%; float: left; padding-right: 3%;">
+
<div style="width: 40%; float: left;">
 +
 
 +
<h3>Progress</h3>
 +
''Prior to the meeting'':
  
−
<h3>Approach, Plan</h3>
+
'''1.''' Identified a number of modules to incorporate assuming they are production ready (SkullStripping, BiasCorrection, ProbabilisticBiasCorrection, RegisterImages, BrainsConstellation, etc).
  
−
Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below.  The main challenge to this approach is <foo>.
+
'''2.''' Implemented a number of other modules that were needed but didn't yet exist (JointIntensityStandardization, LupusLesionSegmenter)
  
−
Our plan for the project week is to first try out <bar>,...
 
  
−
</div>
+
''At the meeting'':
  
−
<div style="width: 40%; float: left;">
+
'''1.''' Met with individuals responsible for relevant modules and identified potential issues.
  
−
<h3>Progress</h3>
+
'''2.''' Met with Steve Pieper on using QT for the wizard
−
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.
 
  
 +
'''3.''' Worked with Hans to adapt his BRAINSABC tool to work on our data.  This accomplishes most of our preprocessing needs.
  
 +
'''4.''' Started implementing the wizard in QT.
 
</div>
 
</div>
 
</div>
 
</div>
Line 52: Line 53:
  
 
==References==
 
==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>
 
</div>

Latest revision as of 15:45, 8 January 2010

Home < 2010 Winter Project Week SegmentationWizard

Key Investigators

  • MRN: Jeremy Bockholt, Mark Scully
  • BWN: Steve Pieper

Objective

To implement a high level wizard that performs all necessary pre-processing steps and then segments lesion images.

Approach, Plan

1. Verify that all required sub-modules are production ready.

2. Diagram all possible branches with requirements.

3. Use QT to create the UI and tie all relevant modules together.


Progress

Prior to the meeting:

1. Identified a number of modules to incorporate assuming they are production ready (SkullStripping, BiasCorrection, ProbabilisticBiasCorrection, RegisterImages, BrainsConstellation, etc).

2. Implemented a number of other modules that were needed but didn't yet exist (JointIntensityStandardization, LupusLesionSegmenter)


At the meeting:

1. Met with individuals responsible for relevant modules and identified potential issues.

2. Met with Steve Pieper on using QT for the wizard

3. Worked with Hans to adapt his BRAINSABC tool to work on our data. This accomplishes most of our preprocessing needs.

4. Started implementing the wizard in QT.

References

Retrieved from "https://www.na-mic.org/w/index.php?title=2010_Winter_Project_Week_SegmentationWizard&oldid=47541"