Hi Nick,<br><br>This is great. <br><br>I wasn't aware of that development in the <br>application front.<br><br>It looks like it will be very useful for the tutorial.<br><br>Are all these underlying functionalities already <br>
in the ITK Git repository ?<br><br>It is important to run the tutorial by showcasing<br>only functionalities that are indeed deployed in<br>ITKv4.<br><br><br> Please let us know,<br><br><br> Thanks<br><br><br> Luis<br>
<br><br>-------------------------------------------------------------<br><div class="gmail_quote">On Tue, Apr 17, 2012 at 2:50 PM, Nicholas Tustison <span dir="ltr"><<a href="mailto:ntustison@gmail.com" target="_blank">ntustison@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Luis,<div><br></div><div>I'm not sure if you are aware of it but after completing a </div>
<div>good portion of the registration framework, we wanted</div><div>to put together an application which combined the ITKv4 </div><div>registration components. This includes all the available</div><div>transforms and transform parameter adaptors, the new </div>
<div>intensity metrics, the convergence monitoring, the image</div><div>registration methods (which includes SyN from ANTS and</div><div>a couple which haven't even been presented to the public</div><div>yet like BSplineSyN and TimeVaryingBSplineVelocityField),</div>
<div>etc. We made it easy to use by interfacing it with our small</div><div>command line module (see short help menu below). Add</div><div>to that the significant modularization by Hans and Kent, we</div><div>think it (antsRegistration) is a pretty nice piece of code which, </div>
<div>in some ways, is more intuitive, easier to use, and more </div><div>flexible than the original ANTS.</div><div><br></div><div>As I mentioned to you, I had to give a workshop on open </div><div>source at SPIE and I spent quite a bit of time talking about the</div>
<div>new registration framework with much of the time devoted</div><div>to simply running antsRegistration on examples. It's</div><div>currently available in the ANTS sourceforge repository and,</div><div>if you think it would help, I would be more than willing to help</div>
<div>get it up and running for the tutorial. </div><div><br></div><div>Nick</div><div><br></div><div><br></div><div><div>[ntustison@Nietzschean-Numerics Tue Apr 17 14:38:54] $ antsRegistration -h</div><div><br></div><div>
COMMAND: </div><div> antsRegistration</div><div><br></div><div>OPTIONS: </div><div> -d, --dimensionality 2/3</div><div> -o, --output outputTransformPrefix</div><div> [outputTransformPrefix,<outputWarpedImage>,<outputInverseWarpedImage>]</div>
<div> -q, --initial-fixed-transform initialTransform</div><div> [initialTransform,<useInverse>]</div><div> -r, --initial-moving-transform initialTransform</div><div> [initialTransform,<useInverse>]</div>
<div> -m, --metric CC[fixedImage,movingImage,metricWeight,radius,<samplingStrategy={Regular,Random}>,<samplingPercentage=[0,1]>]</div><div> MI[fixedImage,movingImage,metricWeight,numberOfBins,<samplingStrategy={Regular,Random}>,<samplingPercentage=[0,1]>]</div>
<div> Mattes[fixedImage,movingImage,metricWeight,numberOfBins,<samplingStrategy={Regular,Random}>,<samplingPercentage=[0,1]>]</div><div> MeanSquares[fixedImage,movingImage,metricWeight,radius,<samplingStrategy={Regular,Random}>,<samplingPercentage=[0,1]>]</div>
<div> Demons[fixedImage,movingImage,metricWeight,radius,<samplingStrategy={Regular,Random}>,<samplingPercentage=[0,1]>]</div><div> GC[fixedImage,movingImage,metricWeight,radius,<samplingStrategy={Regular,Random}>,<samplingPercentage=[0,1]>]</div>
<div> -t, --transform Rigid[gradientStep]</div><div> Affine[gradientStep]</div><div> CompositeAffine[gradientStep]</div><div> Similarity[gradientStep]</div>
<div>
Translation[gradientStep]</div><div> BSpline[gradientStep,meshSizeAtBaseLevel]</div><div> GaussianDisplacementField[gradientStep,updateFieldSigmaInPhysicalSpace,totalFieldSigmaInPhysicalSpace]</div>
<div> BSplineDisplacementField[gradientStep,updateFieldMeshSizeAtBaseLevel,totalFieldMeshSizeAtBaseLevel,<splineOrder=3>]</div><div> TimeVaryingVelocityField[gradientStep,numberOfTimeIndices,updateFieldSigmaInPhysicalSpace,updateFieldTimeSigma,totalFieldSigmaInPhysicalSpace,totalFieldTimeSigma]</div>
<div> TimeVaryingBSplineVelocityField[gradientStep,velocityFieldMeshSize,<numberOfTimePointSamples=4>,<splineOrder=3>]</div><div> SyN[gradientStep,updateFieldSigmaInPhysicalSpace,totalFieldSigmaInPhysicalSpace]</div>
<div> BSplineSyN[gradientStep,updateFieldMeshSizeAtBaseLevel,totalFieldMeshSizeAtBaseLevel,<splineOrder=3>]</div><div> -c, --convergence MxNxO</div><div> [MxNxO,<convergenceThreshold=1e-6>,<convergenceWindowSize=10>]</div>
<div> -s, --smoothing-sigmas MxNxO...</div><div> -f, --shrink-factors MxNxO...</div><div> -u, --use-histogram-matching </div><div> -l, --use-estimate-learning-rate-once </div><div> -w, --winsorize-image-intensities [lowerQuantile,upperQuantile]</div>
<div> -x, --masks [fixedImageMask,movingImageMask]</div><div> -h </div><div> --help </div></div><div><br></div><div><br></div><div><br><div><div><div><div>On Apr 17, 2012, at 2:28 PM, Luis Ibanez wrote:</div>
<br></div></div><blockquote type="cite"><div><div><br><div class="gmail_quote">Dear Community Members,<br>(<a href="http://www.kitware.com/blog/home/post/263" target="_blank">http://www.kitware.com/blog/home/post/263</a>)<br>
<br><br><br>We will present an ITK tutorial at the upcoming<br>
ISBI conference in Barcelona.<br>
<br> <a href="http://www.biomedicalimaging.org/" target="_blank">http://www.biomedicalimaging.org/</a><br><br><br>Please see details in the following link:<br><br> <a href="http://www.itk.org/Wiki/ITK/Tutorials/ISBI2012" target="_blank">http://www.itk.org/Wiki/ITK/Tutorials/ISBI2012</a><br>
<br><br><p>The tutorial will take place
</p>
<ul><li> Wednesday May 2nd
</li><li> 8:30am to 12:30pm
</li><li> <a href="https://www.securecms.com/ISBI2012/RegularProgram.asp?location=Room+127" rel="nofollow" target="_blank">Room 127</a>
</li></ul><p><br></p><p>Please see here the <a href="https://www.securecms.com/ISBI2012/RegularProgram.asp" rel="nofollow" target="_blank">Conference Program</a>
</p><p><br>
Full details in the following link:
</p>
<ul><li> <a href="http://www.biomedicalimaging.org/index.php/programme/tutorials/16-tutorials/87-tutorial-03" rel="nofollow" target="_blank">Use of ITKv4 (and VTK) in biological imaging</a>
</li></ul>
<h1><span></span><span></span></h1><p><br></p><p>This tutorial will introduce attendees to the new features of ITKv4, including among others:
</p>
<ul><li> The modularization of the toolkit
</li><li> The new frameworks for
<ul><li> Statistics
</li><li> Image registration
</li><li> Level sets
</li></ul>
</li><li> The refactored FEM framework
</li><li> The new support for video processing and
</li><li> The new simplified layer SimpleITK.
</li></ul><p>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. <br></p><p><br></p><p>--<br></p><p> Luis<br></p>
</div><br></div></div>
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