[Insight-developers] ITKv4 Tutorial - ISBI 2012 - Barcelona - Wed May 2nd

[Nicholas Tustison]

Hi Luis,

I'm not sure if you are aware of it but after completing a 
good portion of the registration framework, we wanted
to put together an application which combined the ITKv4 
registration components.  This includes all the available
transforms and transform parameter adaptors, the new 
intensity metrics, the convergence monitoring, the image
registration methods (which includes SyN from ANTS and
a couple which haven't even been presented to the public
yet like BSplineSyN and TimeVaryingBSplineVelocityField),
etc.  We made it easy to use by interfacing it with our small
command line module (see short help menu below).  Add
to that the significant modularization by Hans and Kent, we
think it (antsRegistration) is a pretty nice piece of code which, 
in some ways, is more intuitive, easier to use, and more 
flexible than the original ANTS.

As I mentioned to you, I had to give a workshop on open 
source at SPIE and I spent quite a bit of time talking about the
new registration framework with much of the time devoted
to simply running antsRegistration on examples.  It's
currently available in the ANTS sourceforge repository and,
if you think it would help, I would be more than willing to help
get it up and running for the tutorial. 

Nick


[ntustison at Nietzschean-Numerics Tue Apr 17 14:38:54] $ antsRegistration -h

COMMAND: 
     antsRegistration

OPTIONS: 
     -d, --dimensionality 2/3
     -o, --output outputTransformPrefix
                  [outputTransformPrefix,<outputWarpedImage>,<outputInverseWarpedImage>]
     -q, --initial-fixed-transform initialTransform
                                   [initialTransform,<useInverse>]
     -r, --initial-moving-transform initialTransform
                                    [initialTransform,<useInverse>]
     -m, --metric CC[fixedImage,movingImage,metricWeight,radius,<samplingStrategy={Regular,Random}>,<samplingPercentage=[0,1]>]
                  MI[fixedImage,movingImage,metricWeight,numberOfBins,<samplingStrategy={Regular,Random}>,<samplingPercentage=[0,1]>]
                  Mattes[fixedImage,movingImage,metricWeight,numberOfBins,<samplingStrategy={Regular,Random}>,<samplingPercentage=[0,1]>]
                  MeanSquares[fixedImage,movingImage,metricWeight,radius,<samplingStrategy={Regular,Random}>,<samplingPercentage=[0,1]>]
                  Demons[fixedImage,movingImage,metricWeight,radius,<samplingStrategy={Regular,Random}>,<samplingPercentage=[0,1]>]
                  GC[fixedImage,movingImage,metricWeight,radius,<samplingStrategy={Regular,Random}>,<samplingPercentage=[0,1]>]
     -t, --transform Rigid[gradientStep]
                     Affine[gradientStep]
                     CompositeAffine[gradientStep]
                     Similarity[gradientStep]
                     Translation[gradientStep]
                     BSpline[gradientStep,meshSizeAtBaseLevel]
                     GaussianDisplacementField[gradientStep,updateFieldSigmaInPhysicalSpace,totalFieldSigmaInPhysicalSpace]
                     BSplineDisplacementField[gradientStep,updateFieldMeshSizeAtBaseLevel,totalFieldMeshSizeAtBaseLevel,<splineOrder=3>]
                     TimeVaryingVelocityField[gradientStep,numberOfTimeIndices,updateFieldSigmaInPhysicalSpace,updateFieldTimeSigma,totalFieldSigmaInPhysicalSpace,totalFieldTimeSigma]
                     TimeVaryingBSplineVelocityField[gradientStep,velocityFieldMeshSize,<numberOfTimePointSamples=4>,<splineOrder=3>]
                     SyN[gradientStep,updateFieldSigmaInPhysicalSpace,totalFieldSigmaInPhysicalSpace]
                     BSplineSyN[gradientStep,updateFieldMeshSizeAtBaseLevel,totalFieldMeshSizeAtBaseLevel,<splineOrder=3>]
     -c, --convergence MxNxO
                       [MxNxO,<convergenceThreshold=1e-6>,<convergenceWindowSize=10>]
     -s, --smoothing-sigmas MxNxO...
     -f, --shrink-factors MxNxO...
     -u, --use-histogram-matching 
     -l, --use-estimate-learning-rate-once 
     -w, --winsorize-image-intensities [lowerQuantile,upperQuantile]
     -x, --masks [fixedImageMask,movingImageMask]
     -h 
     --help 



On Apr 17, 2012, at 2:28 PM, Luis Ibanez wrote:

> 
> Dear Community Members,
> (http://www.kitware.com/blog/home/post/263)
> 
> 
> 
> We will present an ITK tutorial at the upcoming
> ISBI conference in Barcelona.
> 
>          http://www.biomedicalimaging.org/
> 
> 
> Please see details in the following link:
> 
>       http://www.itk.org/Wiki/ITK/Tutorials/ISBI2012
> 
> 
> The tutorial will take place
> 
> Wednesday May 2nd
> 8:30am to 12:30pm
> Room 127
> 
> 
> Please see here the Conference Program
> 
> 
> Full details in the following link:
> 
> Use of ITKv4 (and VTK) in biological imaging
> 
> 
> 
> This tutorial will introduce attendees to the new features of ITKv4, including among others:
> 
> The modularization of the toolkit
> The new frameworks for
> Statistics
> Image registration
> Level sets
> The refactored FEM framework
> The new support for video processing and
> The new simplified layer SimpleITK.
> The tutorial will follow a hands-on format, in which the attendees will receive USB memory sticks with a fully configured Virtual Machine containing an installation of ITKv4, OpenCV, VXL and their respective bridges. Hands on exercises will include a familiarization with the new process by which contributions can be brought back into the toolkit. 
> 
> 
> 
> --
> 
>      Luis
> 
> 
> _______________________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://www.itk.org/mailman/listinfo/insight-developers

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.itk.org/pipermail/insight-developers/attachments/20120417/178f43b0/attachment.htm>