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

From NAMIC Wiki
Jump to: navigation, search
 
(10 intermediate revisions by the same user not shown)
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
 
<gallery>
 
<gallery>
−
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
+
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
 +
Image:DTIPairWiseRegistrationModule.jpg|Screenshot
 
</gallery>
 
</gallery>
  
Line 13: Line 14:
  
 
<h3>Objective</h3>
 
<h3>Objective</h3>
−
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 (fiber process, 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.
+
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.
  
  
Line 22: Line 23:
 
<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
  
−
Our approach is to develop a C++ based Slice3 extension, which writes a BatchMake script, in order to call external modules as threads to perform individual steps of the pipeline.
+
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 development/enhancement of the module.
+
Our plan for the project week is to develop/enhance the module.
  
 
</div>
 
</div>
Line 31: Line 32:
  
 
<h3>Progress</h3>
 
<h3>Progress</h3>
 +
* 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]
 +
  
  
Line 40: Line 65:
 
==Delivery Mechanism==
 
==Delivery Mechanism==
  
−
This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)
+
This work will be delivered to the NA-MIC Kit as a Slicer extension.
−
 
 
−
#ITK Module
 
−
#Slicer Module
 
−
##Built-in
 
−
##Extension -- commandline YES
 
−
##Extension -- loadable YES
 
−
#Other (Please specify)
 
  
 
==References==
 
==References==

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

Retrieved from "https://www.na-mic.org/w/index.php?title=2011_Summer_Project_Week_DTI_PairWise_Registration&oldid=69434"