<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hello,<div><br></div><div>I am working on integrating displacement fields into SimpleITK right now, so in just a couple days I should be able easily demonstrate this in SimpleITK Notebooks.</div><div><br></div><div>To use you WarpFilter on a results a a registration, you will be resampling the fixed image onto the moving image, as the is the direction of the transform.</div><div><br></div><div>Have you been able to use the following example:</div><div><br></div><div><a href="http://www.itk.org/Doxygen/html/Filtering_2WarpImageFilter1_8cxx-example.html#_a4">http://www.itk.org/Doxygen/html/Filtering_2WarpImageFilter1_8cxx-example.html#_a4</a></div><div><br></div><div>With the command line arguments as "FixedImage" DisplacementFieldImage" "OutputImage"?</div><div><br></div><div>Does the moving and fixed image have the same domain prior to registration or is there an additional large transformation going on with the displacement field?</div><div><br></div><div>Also if you could share your data or a small test case illustrating the problem this may help others more extensively help you.</div><div><br></div><div>Brad</div><div><br><div><div>On Dec 9, 2013, at 9:06 AM, Tim Bhatnagar <<a href="mailto:tim.bhatnagar@gmail.com">tim.bhatnagar@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr"><div><div><div>I appreciate the response, Brad.<br><br></div>Can you tell me how the implementation of the 'WarpImageFilter' works, such that when I input my Demons-generated displacement field, and my 'movingImage' (from Demons) as input, I get what looks like my 'fixedImage' (from Demons) as output... making me think that the displacement field is actually mapping my movingImage into my fixedImage?<br>
<br></div>Also, I use Paraview to visualize my field, and when visualized, it illustrates what you are suggesting (the mapping that would take fixed -> moving). But how then, does the WarpFilter use the SAME FIELD to warp my movingImage into a very nice estimation of my fixedImage?<br>
<br></div>Sorry if any of that is convoluted..<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Dec 9, 2013 at 6:00 AM, Bradley Lowekamp <span dir="ltr"><<a href="mailto:brad@lowekamp.net" target="_blank">brad@lowekamp.net</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">Hello,<div><br></div><div>It not uncommon for resampling-type algorithms to have some points be mapped out side the the domain. This is why a boundary condition and extrapolators are used. If there are just a limited number of pixel being mapped out side, then the simplest way be by to just check if the pixel is within the image's region.</div>
<div><br></div><div>ITK's registration frameworks solve for a transform which maps from the "Fixed" image to the "Moving" image. This is well described int Chapter Eight of the old Software guide:</div>
<div><br></div><div><a href="http://www.itk.org/ItkSoftwareGuide.pdf" target="_blank">http://www.itk.org/ItkSoftwareGuide.pdf</a></div><div><br></div><div>Brad</div><div><br><div><div><div class="h5"><div>On Dec 8, 2013, at 6:38 PM, Tim Bhatnagar <<a href="mailto:tim.bhatnagar@gmail.com" target="_blank">tim.bhatnagar@gmail.com</a>> wrote:</div>
<br></div></div><blockquote type="cite"><div><div class="h5"><div dir="ltr"><div><div>Hello,<br><br></div>I've created a displacement field via Demons non-rigid registration. I am now trying to create the inverse (using InverseDisplacementFieldImageFilter), but when I am using the indexes to ascribe the inverted field, my program crashes mid-way through, because it appears I am trying to call a <b>negative</b> index (specifically, the 3rd index parameter.. the 'z'-parameter).<br>
<br>I don't do anything to the displacement field except write it to a vtk file before i invert it.. can anyone suggest a solution? I thought I could try and specify the 'direction' of the field, but I'm not sure where in my pipeline I can set the direction of the <b>inverted</b> displacement field...<br>
<br></div>sorry if that's messy.. any thoughts would be appreciated!<br><br>Thanks,<br><br>Tim<br clear="all"><div><br>-- <br>Tim Bhatnagar<br>PhD Candidate<br>Orthopaedic Injury Biomechanics Group<br>Department of Mechanical Engineering<br>
University of British Columbia<br><br>Rm 5000 - 818 West 10th Ave.<br>Vancouver, BC<br>Canada<br>V5Z 1M9<br><br>Ph: <a href="tel:%28604%29%20675-8845" value="+16046758845" target="_blank">(604) 675-8845</a><br>Fax: <a href="tel:%28604%29%20675-8820" value="+16046758820" target="_blank">(604) 675-8820</a><br>
Web: <a href="http://oibg.mech.ubc.ca/" target="_blank">oibg.mech.ubc.ca</a><br>
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</div></blockquote></div><br></div></div></blockquote></div><br><br clear="all"><br>-- <br>Tim Bhatnagar<br>PhD Candidate<br>Orthopaedic Injury Biomechanics Group<br>Department of Mechanical Engineering<br>University of British Columbia<br>
<br>Rm 5000 - 818 West 10th Ave.<br>Vancouver, BC<br>Canada<br>V5Z 1M9<br><br>Ph: (604) 675-8845<br>Fax: (604) 675-8820<br>Web: <a href="http://oibg.mech.ubc.ca/" target="_blank">oibg.mech.ubc.ca</a><br>
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