Difference between revisions of "2011 Summer Project Week DTI PairWise Registration"

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<gallery>
 
<gallery>
 
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
 
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
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Image:notfound.png|Interesting picture to be added...
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Image:DTIPairWiseRegistrationModule.jpg|Screenshot
 
</gallery>
 
</gallery>
  
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'''Full Title of Project'''
 
  
 
==Key Investigators==
 
==Key Investigators==
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* Harvard Medical School: Mohsen Mahvash
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* UNC: Clement Vachet, Francois Budin, Martin Styner
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* IOWA: Joy Matsui, Mark Scully, Hans Johnson
  
 
<div style="margin: 20px;">
 
<div style="margin: 20px;">
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<h3>Objective</h3>
 
<h3>Objective</h3>
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We are developing a pipeline which performs DTI pair-wise registration. The goal is to create a user-friendly Slicer3 extension which performs such a registration automatically, instead of running Slicer3 modules individually (dtiprocess, BRAINSFit, BRAINSDemonWarp, ResampleDTI Volume...). Such a wrapper will generate and use scalar features (e.g FA,MD) to drive the registration between two DTI images.
  
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#:Segmentaion and 3d
 
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#:reconstruction of pericardial sac
 
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#: (a thin tissue layer that covers the heart)
 
  
 
</div>
 
</div>
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
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#:Trying 3dslicer modules  
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#:for segmentation
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Our approach is to develop a C++ based Slicer3 extension, which writes a BatchMake script, in order to call external modules as threads to perform individual steps of the pipeline.
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#:and 3d reconstruction 
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 +
Our plan for the project week is to develop/enhance the module.
  
 
</div>
 
</div>
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<h3>Progress</h3>
 
<h3>Progress</h3>
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* Command line / UI via GenerateCLP (cf. screenshot)
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* Main BatchMake script written
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* Individual steps called as threads via BatchMake
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* Improvement on registration: Affine + warping (BRAINSDemonWarp)
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* Further improvement / testing needs to be achieved...
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  bin/DWIProcessPipeline  [--returnparameterfile <std::string>]
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                          [--processinformationaddress <std::string>]
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                          [--xml] [--echo] [--runChoice <Do_not_run|Run
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                          |Condor>] [--registration <MD|FA>]
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                          [--interpolation <linear|bs|ws>] [--copy]
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                          [--nolog] [--skullStrip] [--scale] [--computeAD]
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                          [--computeRD] [--computeColorFA] [--computeMD]
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                          [--computeFA] [--initialTransform <std::string>]
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                          [-f <std::string>] [--createIDWI] [--createB0]
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                          [--manualOrientation <std::string>]
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                          [--computeOrientation] [--imNN2 <std::string>]
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                          [--imNN1 <std::string>] [--im3 <std::string>]
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                          [--im2 <std::string>] [--im1 <std::string>]
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                          [--rootName <std::string>] [--outputDir
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                          <std::string>] [--templateType <DTI|scalar>] [-t
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                          <std::string>] [--inputType <DWI|DTI|scalar>]
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                          [-i <std::string>] [--] [--version] [-h]
  
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<!-- Fill this out before Friday's summary presentations - list what you did and how well it worked. -->
 
  
  
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<div style="width: 97%; float: left;">
 
<div style="width: 97%; float: left;">
  
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==References==
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==Delivery Mechanism==
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D’Avila A, Scanavacca M, Sosa E, Riskin JN, Reddy VY. Pericardial anatomy for the Interventional Electrophysiologist. J Cardiovasc Electrophysiol 2003;14:422-430
 
  
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==Delivery Mechanism==
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This work will be delivered to the NA-MIC Kit as a Slicer extension.
  
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<!-- List here how you plan to deliver your results to user communities -->
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==References==
  
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This work will be delivered to the NAMIC Kit as a
 
  
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#NITRIC distribution
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</div>
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#Slicer Module
 
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##Built-in:
 
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##Extension -- commandline: 
 
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##Extension -- loadable:
 

Latest revision as of 14:47, 24 June 2011

Home < 2011 Summer Project Week DTI PairWise Registration


Key Investigators

  • UNC: Clement Vachet, Francois Budin, Martin Styner
  • IOWA: Joy Matsui, Mark Scully, Hans Johnson

Objective

We are developing a pipeline which performs DTI pair-wise registration. The goal is to create a user-friendly Slicer3 extension which performs such a registration automatically, instead of running Slicer3 modules individually (dtiprocess, BRAINSFit, BRAINSDemonWarp, ResampleDTI Volume...). Such a wrapper will generate and use scalar features (e.g FA,MD) to drive the registration between two DTI images.


Approach, Plan

Our approach is to develop a C++ based Slicer3 extension, which writes a BatchMake script, in order to call external modules as threads to perform individual steps of the pipeline.

Our plan for the project week is to develop/enhance the module.

Progress

  • Command line / UI via GenerateCLP (cf. screenshot)
  • Main BatchMake script written
  • Individual steps called as threads via BatchMake
  • Improvement on registration: Affine + warping (BRAINSDemonWarp)
  • Further improvement / testing needs to be achieved...
 bin/DWIProcessPipeline  [--returnparameterfile <std::string>]
                          [--processinformationaddress <std::string>]
                          [--xml] [--echo] [--runChoice <Do_not_run|Run
                          |Condor>] [--registration <MD|FA>]
                          [--interpolation <linear|bs|ws>] [--copy]
                          [--nolog] [--skullStrip] [--scale] [--computeAD]
                          [--computeRD] [--computeColorFA] [--computeMD]
                          [--computeFA] [--initialTransform <std::string>]
                          [-f <std::string>] [--createIDWI] [--createB0]
                          [--manualOrientation <std::string>]
                          [--computeOrientation] [--imNN2 <std::string>]
                          [--imNN1 <std::string>] [--im3 <std::string>]
                          [--im2 <std::string>] [--im1 <std::string>]
                          [--rootName <std::string>] [--outputDir
                          <std::string>] [--templateType <DTI|scalar>] [-t
                          <std::string>] [--inputType <DWI|DTI|scalar>]
                          [-i <std::string>] [--] [--version] [-h]


Delivery Mechanism

This work will be delivered to the NA-MIC Kit as a Slicer extension.

References

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