Difference between revisions of "2011 Summer Project Week Integrate BRAINSCut into Slicer3"

From NAMIC Wiki
Jump to: navigation, search
m
 
(6 intermediate revisions by the same user not shown)
Line 2: Line 2:
 
<gallery>
 
<gallery>
 
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
 
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
−
File:BRAINSCutFigure.png|BRAINSCut Result Example
+
File:BRAINSCutFigure.png|BRAINSCut: Result Example After Rendering with Slicer Model Maker
 +
File:ProbabilityMaps.png|BRAINSCut: Probability Map Example for Sub-cortical regions of brain to identify ROI
 +
File:GradientFeatureComparison.png |BRAINSCut: One of Feature Images.
 +
File:Caudates.png|BRAINSCut: Caudate test statistics between BRAINSCut output and Manual Traces
 +
File:Putamens.png|BRAINSCut: Putamen test statistics between BRAINSCut output and Manual Trace
 +
File:BRAINSCutThalamus.png|BRAINSCut: Thalamus test statistics between BRAINSCut output and Manual Trace
 +
File:HippoWithSOnly.png|BRAINSCut: Hippocampus test statistics between BRAINSCut output and Manual Trace
 
</gallery>
 
</gallery>
  
Line 8: Line 14:
  
 
==Key Investigators==
 
==Key Investigators==
−
* University of Iowa: Eunyoung(Regina) Kim
+
* University of Iowa: Eunyoung(Regina) Kim, Hans Johnson, Mark Scully
  
  
 
<div style="margin: 20px;">
 
<div style="margin: 20px;">
−
<div style="width: 27%; float: left; padding-right: 3%;">
+
<div style="width: 40%; float: left; padding-right: 3%;">
  
 
<h3>Objective</h3>
 
<h3>Objective</h3>
  
−
#:Integration of BRAINSCut into Slicer3/Slicer4  
+
#Integration of BRAINSCut into Slicer3/Slicer4  
−
#:Integration of GMI feature images into BRAINSCut
+
#Integration of GMI feature images into BRAINSCut
−
#:Test BRAINSCut  
+
#Test BRAINSCut  
  
 
</div>
 
</div>
  
−
<div style="width: 27%; float: left; padding-right: 3%;">
+
<div style="width: 40%; float: left; padding-right: 3%;">
  
 
<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
−
#:Check dependencies of BRAINSCut  
+
# Check dependencies of BRAINSCut and integrate into Slicer CLM.
−
#:and integrate into Slicer CLM.
+
#Process test data set to verify
−
#:
+
# Submit caudate results to the CAUSE07 Challenge 'http://www.cause07.org/'
−
 
+
</div>
 
</div>
 
</div>
−
 
−
<div style="width: 40%; float: left;">
 
  
 
<h3>Progress</h3>
 
<h3>Progress</h3>
  
−
<!-- Fill this out before Friday's summary presentations - list what you did and how well it worked. -->
+
# BRAINSCut Incorporating with Slicer3 DONE
 +
# Generating BRAINSCut model for subcortical structures: caudate, putamen, thalamus, and hippocampus. DONE
 +
# Verifying generated model by comparing manual traces. DONE
 +
# Process 230 data to generate hippocampus. DONE
  
−
 
−
</div>
 
−
</div>
 
  
 
<div style="width: 97%; float: left;">
 
<div style="width: 97%; float: left;">
Line 45: Line 49:
 
==References==
 
==References==
  
 +
#Powell, S., Magnotta, V., Johnson, H., and . . . , V. J., “Registration and machine learning-based automated segmentation of subcortical and cerebellar brain . . . ,” NeuroImage (Jan 2008)
 +
#Eun Young Kim, Hans Johnson, "Multi-structure segmentation of multi-modal brain images using artificial neural networks", SPIE Proceedings Paper (Mar 2010)
 +
 +
==Download Page==
 +
 +
http://www.nitrc.org/projects/brainscut
  
 
==Delivery Mechanism==
 
==Delivery Mechanism==
−
 
−
<!-- List here how you plan to deliver your results to user communities -->
 
  
 
This work will be delivered to the NAMIC Kit as a  
 
This work will be delivered to the NAMIC Kit as a  

Latest revision as of 14:36, 24 June 2011

Home < 2011 Summer Project Week Integrate BRAINSCut into Slicer3

  • BRAINSCut: Result Example After Rendering with Slicer Model Maker

  • BRAINSCut: Probability Map Example for Sub-cortical regions of brain to identify ROI

  • BRAINSCut: One of Feature Images.

  • BRAINSCut: Caudate test statistics between BRAINSCut output and Manual Traces

  • BRAINSCut: Putamen test statistics between BRAINSCut output and Manual Trace

  • BRAINSCut: Thalamus test statistics between BRAINSCut output and Manual Trace

  • BRAINSCut: Hippocampus test statistics between BRAINSCut output and Manual Trace

Integrate BRAINSCut into Slicer3

Key Investigators

  • University of Iowa: Eunyoung(Regina) Kim, Hans Johnson, Mark Scully


Objective

  1. Integration of BRAINSCut into Slicer3/Slicer4
  2. Integration of GMI feature images into BRAINSCut
  3. Test BRAINSCut

Approach, Plan

  1. Check dependencies of BRAINSCut and integrate into Slicer CLM.
  2. Process test data set to verify
  3. Submit caudate results to the CAUSE07 Challenge 'http://www.cause07.org/'

Progress

  1. BRAINSCut Incorporating with Slicer3 DONE
  2. Generating BRAINSCut model for subcortical structures: caudate, putamen, thalamus, and hippocampus. DONE
  3. Verifying generated model by comparing manual traces. DONE
  4. Process 230 data to generate hippocampus. DONE


References

  1. Powell, S., Magnotta, V., Johnson, H., and . . . , V. J., “Registration and machine learning-based automated segmentation of subcortical and cerebellar brain . . . ,” NeuroImage (Jan 2008)
  2. Eun Young Kim, Hans Johnson, "Multi-structure segmentation of multi-modal brain images using artificial neural networks", SPIE Proceedings Paper (Mar 2010)

Download Page

http://www.nitrc.org/projects/brainscut

Delivery Mechanism

This work will be delivered to the NAMIC Kit as a

  1. NITRIC distribution
  2. Slicer Module
    1. Built-in:
    2. Extension -- commandline:
    3. Extension -- loadable:
Retrieved from "https://www.na-mic.org/w/index.php?title=2011_Summer_Project_Week_Integrate_BRAINSCut_into_Slicer3&oldid=69415"