Difference between revisions of "Projects:RegistrationLibrary:RegLib C35"

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m (Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/")
 
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=== Modules ===
 
=== Modules ===
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*'''Slicer 3.6.1 recommended modules:'''  [http://www.slicer.org/slicerWiki/index.php/Modules:SurfaceRegistration '''SurfaceRegistration'''],    [http://www.slicer.org/slicerWiki/index.php/Modules:Transforms '''Transforms (manual registration)'''],  [http://www.slicer.org/slicerWiki/index.php/Modules:FastMarchingSegmentation-Documentation-3.6 '''Fast Marching Segmentation'''],  [http://www.slicer.org/slicerWiki/index.php/Modules:HistogramMatching-Documentation-3.6 '''Histogram Matching'''],  [http://www.slicer.org/slicerWiki/index.php/Modules:ModelMaker-Documentation-3.6 '''Model Maker'''],
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*'''Slicer 3.6.1 recommended modules:'''  [https://www.slicer.org/wiki/Modules:PythonSurfaceICPRegistration-Documentation-3.6 '''SurfaceRegistration'''],    [https://www.slicer.org/wiki/Modules:Transforms '''Transforms (manual registration)'''],  [https://www.slicer.org/wiki/Modules:FastMarchingSegmentation-Documentation-3.6 '''Fast Marching Segmentation'''],  [https://www.slicer.org/wiki/Modules:HistogramMatching-Documentation-3.6 '''Histogram Matching'''],  [https://www.slicer.org/wiki/Modules:ModelMaker-Documentation-3.6 '''Model Maker'''],
  
 
===Objective / Background ===
 
===Objective / Background ===
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*DATA
 
*DATA
 
**[[Media:RegLib_C35_Data.zip‎|'''Registration Library Case 35 '''<small> (Data,  zip file 46 MB) </small>]]
 
**[[Media:RegLib_C35_Data.zip‎|'''Registration Library Case 35 '''<small> (Data,  zip file 46 MB) </small>]]
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*See detailed pipeline with parameter settings below
 
  
 
=== Keywords ===
 
=== Keywords ===
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===Registration Challenges===
 
===Registration Challenges===
 
*The image content to be registered is less than 10% of the total image and of low energy (close to background);  
 
*The image content to be registered is less than 10% of the total image and of low energy (close to background);  
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[[Image:RegLibC35_Histogram.png|150px|lleft|histogram of image content: target structure (colon, red) is very small amount of total image energy, making intensity-based automated approach unlikely to succeed]]  
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[[Image:RegLib_C35_Histogram.png|150px|lleft|histogram of image content: target structure (colon, red) is very small amount of total image energy, making intensity-based automated approach unlikely to succeed]]  
 
*there's large portions of the colon for which no matching/corresponding structures exist, i.e. a straightforward one-one mapping is not avail.
 
*there's large portions of the colon for which no matching/corresponding structures exist, i.e. a straightforward one-one mapping is not avail.
 
*other landmarks (kidneys etc.) are very different in position and size
 
*other landmarks (kidneys etc.) are very different in position and size
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*This is a '''challenge case''' and currently unsolved. Best hopes are combinations of manual, fiducial and surface-based registration
 
*This is a '''challenge case''' and currently unsolved. Best hopes are combinations of manual, fiducial and surface-based registration
 
*'''Slicer 3.6.1 recommended modules:  
 
*'''Slicer 3.6.1 recommended modules:  
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** [http://www.slicer.org/slicerWiki/index.php/Modules:SurfaceRegistration Surface Registration]
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** [https://www.slicer.org/wiki/Modules:PythonSurfaceICPRegistration-Documentation-3.6 Surface Registration]
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** Plastimatch
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** [https://www.slicer.org/wiki/Modules:Plastimatch Plastimatch]
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=== Registration Results===
 
=== Registration Results===

Latest revision as of 18:07, 10 July 2017

Home < Projects:RegistrationLibrary:RegLib C35

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Back to Registration Use-case Inventory

v3.6.1 Slicer3-6Announcement-v1.png Slicer Registration Library Case #35: Mouse Colon Brain MRI

Input

case A lleft case B
fixed image 1/target
MRI mouse 1 		moving image
MRI mouse 2

Modules

Objective / Background

Aim is to register the two MRIs such that the colon aligns.

Download

Keywords

MRI, colon, mouse, masking, non-human, non-rigid,manual, unsolved

Input Data

  • reference/fixed MRI: 0.12 x 0.12 x 0.1 mm, 512 x 512 x 94
  • moving MRI: 0.09 x 0.09 x 0.1 mm, 512 x 512 x 94

Registration Challenges

  • The image content to be registered is less than 10% of the total image and of low energy (close to background);

histogram of image content: target structure (colon, red) is very small amount of total image energy, making intensity-based automated approach unlikely to succeed

  • there's large portions of the colon for which no matching/corresponding structures exist, i.e. a straightforward one-one mapping is not avail.
  • other landmarks (kidneys etc.) are very different in position and size

Key Strategies

  • This is a challenge case and currently unsolved. Best hopes are combinations of manual, fiducial and surface-based registration
  • Slicer 3.6.1 recommended modules:

Registration Results

very rough surface models of colon help visualize misalignment very rough surface models of colon help visualize misalignment
original unregistered original, not registered
after surface registration (rigid) + manual correction after surface registration (rigid) + manual correction

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