Difference between revisions of "2012 Summer Project Week:Overlapping structures"

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Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
 
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
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Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
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Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
 
 
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* MGH: Greg Sharp
 
* MGH: Greg Sharp
 
* Isomics: Steve Pieper
 
* Isomics: Steve Pieper
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* GE: Jim Miller
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* Queen's: Andras Lasso
  
 
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<h3>Objective</h3>
 
<h3>Objective</h3>
 
We are developing capabilities for Slicer to display and manipulate overlapping structures.
 
We are developing capabilities for Slicer to display and manipulate overlapping structures.
  
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
  
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The approach is to represent labelmaps in Slicer as a vector of unsigned characters, with one bit per structure.   
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An initial approach, used in plastimatch, is to represent structure sets as a vector of unsigned characters, with one bit per structure.   
  
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<h3>Progress</h3>
 
<h3>Progress</h3>
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To be established.
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* Discussions of target data types and capabilities:
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** Typically around 100meg for a Head/Neck CT
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** Typically no more than 100 structures
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* Goal is to provide lossless representation of original data, with conversion from contours to images for editing and warping
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** Keep original contours as slicer models (view in slices as slice intersections)
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** Provide routines to rasterize contours into label volumes on demand for editing on a per-structure basis
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** Caching if needed
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** Create vector image representation for running warp operations (warp all structures with single evaluation of pixel deformation function)
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* Caveats
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** Tilted planes are sometimes used (drawing on native MRI planes, but structures defined on CT)
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** Drawing done on saggital or coronal, would be good to see "caps" of structures
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** How to group structure sets (e.g. to exchange with module, CLI)?
  
 
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==References==
 
==References==
 
*Greg's progress notes.
 
*Greg's progress notes.
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*Mockup of UI (http://www.na-mic.org/Wiki/index.php/2012_Winter_Project_Week:RTSS)
 
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Latest revision as of 13:55, 22 June 2012

Home < 2012 Summer Project Week:Overlapping structures

Key Investigators

  • MGH: Greg Sharp
  • Isomics: Steve Pieper
  • GE: Jim Miller
  • Queen's: Andras Lasso

Objective

We are developing capabilities for Slicer to display and manipulate overlapping structures.

Approach, Plan

An initial approach, used in plastimatch, is to represent structure sets as a vector of unsigned characters, with one bit per structure.

Progress

  • Discussions of target data types and capabilities:
    • Typically around 100meg for a Head/Neck CT
    • Typically no more than 100 structures
  • Goal is to provide lossless representation of original data, with conversion from contours to images for editing and warping
    • Keep original contours as slicer models (view in slices as slice intersections)
    • Provide routines to rasterize contours into label volumes on demand for editing on a per-structure basis
    • Caching if needed
    • Create vector image representation for running warp operations (warp all structures with single evaluation of pixel deformation function)
  • Caveats
    • Tilted planes are sometimes used (drawing on native MRI planes, but structures defined on CT)
    • Drawing done on saggital or coronal, would be good to see "caps" of structures
    • How to group structure sets (e.g. to exchange with module, CLI)?

Delivery Mechanism

This work will be delivered to the NA-MIC Kit as a modification of Slicer interals

References

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