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

[Luis Ibanez]

Hi Nick,

This is great.

I wasn't aware of that development in the
application front.

It looks like it will be very useful for the tutorial.

Are all these underlying functionalities already
in the ITK Git repository ?

It is important to run the tutorial by showcasing
only functionalities that are indeed deployed in
ITKv4.


   Please let us know,


      Thanks


           Luis


-------------------------------------------------------------
On Tue, Apr 17, 2012 at 2:50 PM, Nicholas Tustison <ntustison at gmail.com>wrote:

> 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<https://www.securecms.com/ISBI2012/RegularProgram.asp?location=Room+127>
>
>
> Please see here the Conference Program<https://www.securecms.com/ISBI2012/RegularProgram.asp>
>
>
> Full details in the following link:
>
>    - Use of ITKv4 (and VTK) in biological imaging<http://www.biomedicalimaging.org/index.php/programme/tutorials/16-tutorials/87-tutorial-03>
>
>
> 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/20120422/419b310a/attachment.htm>