Update: by setting transform matrices to identity in order to experiment with them, I notices that my code for using <span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; "><div style="display: inline; height: auto; position: absolute; visibility: hidden; width: auto; ">
</div>DeformableMesh3DFilter was not wrong, but that filter does not respect direction cosines either. With identity cosines it worked without weird deformations I was experiencing with sagittal images.</span><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br>
</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">And since many (most?) filters which deal with images ignore direction cosines, again we come to the need of having a filter which will reorient image pixels in order to have identity cosines matrix (DICOM LPS orientation, ITK RAI orientation). And creating this filter does not have to be considered admitting "ITK is not perfect", it can be considered as a stopgap measure until all filters use <span class="Apple-style-span" style="border-collapse: separate; font-family: arial; ">TransformPhysicalPointToIndex and other built-in transformation routines instead of custom (and incomplete) transformation code (such as in </span></span></font>TriangleMeshToBinaryImageFilter).</div>
<div><br></div><div>Regards,</div><div>Dženan</div><div><br><div class="gmail_quote">2010/5/26 Dženan Zukić <span dir="ltr"><<a href="mailto:dzenanz@gmail.com">dzenanz@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi everyone!<div><br></div><div>While wrestling with DeformableMesh3DFilter, I wanted to create binary mask of my initial mesh (so I could use it with examples), but I ran into a problem. TriangleMeshToBinaryImageFilter is not designed to produce images with direction cosines matrix different from identity matrix. When I supply it with such an image and mesh which is valid with respect to ITK's physical coordinate handling routines (TransformPhysicalPointToContinuousIndex and friends), it crashes.</div>
<div><br></div><div><div>typedef itk::TriangleMeshToBinaryImageFilter<MeshType,VisualizingImageType> MeshFilterType;</div><div>MeshFilterType::Pointer meshFilter = MeshFilterType::New();</div><div>meshFilter->SetInfoImage(visualizing); //TransformMatrix = 0 1 0 -0.0939968 0 -0.995573 -0.995573 0 0.0939968</div>
</div><div>meshFilter->SetInput(mesh);</div><div><div>meshFilter->Update(); //crashes</div></div><div><br></div><div>For usage in examples, I can edit my transform matrix in .mha files and set it to identity, but what about normal usage? Is there some quick (and possibly dirty) way to get this right, or do I have to do all the math on paper in order to transform between representations with and without direction cosines?</div>
<div><br></div><div>Thanks,</div><div>Dženan</div>
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