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<p class="MsoNormal"><span style="color:#1F497D">Thank you Andras, this helps a lot! Glad to see that the solutions are simple and elegant.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Best regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Mikael<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;color:#1F497D">
.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#1F497D">Mikael Eriksson<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#1F497D">R&D Physicist Trainee<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#1F497D">Philips Medical Systems MR Finland, Feasibility studies<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#1F497D">+358 40 631 8500<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#1F497D"><a href="mailto:mikael.k.eriksson@philips.com">mikael.k.eriksson@philips.com</a><o:p></o:p></span></p>
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.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Andras Lasso [mailto:lasso@queensu.ca]
<br>
<b>Sent:</b> 1. syyskuuta 2014 17:41<br>
<b>To:</b> Eriksson, Mikael; community@itk.org<br>
<b>Subject:</b> Re: [ITK] Registration of multislice images<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">Hi Mikael,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">You can copy the voxels from each slice into a volume and use that as fixed image, use a mask that has non-zero values only at valid pixels (usually you can use the constructed image itself as a mask), then
do a usual volumetric registration. This works quite well, if you have orthogonal images and their resolution is similar (see for example
<a href="http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=5975205" target="_parent">
http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=5975205</a>). You can use ITK as is, no modifications are needed.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">Alternatively, you can modify a similarity metric to accept multiple images and compute the metric value as sum of the metric value of each image (this is necessary when the image slices are not orthogonal).
An IJCARS paper is in press, a high-level overview is given in this abstract: <a href="http://perk.cs.queensu.ca/contents/target-localization-mriguided-transperineal-prostate-biopsy-using-multislicetovolume-regist" target="_parent">
http://perk.cs.queensu.ca/contents/target-localization-mriguided-transperineal-prostate-biopsy-using-multislicetovolume-regist</a> .<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">Andras<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;letter-spacing:.25pt">From:</span></b><span style="font-size:12.0pt;letter-spacing:.25pt"> <a href="mailto:mikael.k.eriksson@philips.com" target="_parent">Eriksson, Mikael</a><br>
<b>Sent:</b> ύMondayύ, ύSeptemberύ ύ1ύ, ύ2014 ύ1ύ:ύ26ύ ύAM<br>
<b>To:</b> <a href="mailto:community@itk.org" target="_parent">community@itk.org</a></span><span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal">Hello,<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">I have obtained multislice image data for trying to do real-time registration for motion correction purposes. Specifically, every 0.x seconds, one coronal, one sagittal and one axial slice is obtained during the imaging, and I would like
to register pairs of such sets with each other, e.g. each set after the first set at time zero should be registered to this time zero set. The slices cover the entire body in the axial plane, and the upper body from the hips to the neck in the sagittal and
coronal planes with a size of 336 x 336 and pixel spacing of 1.19 x 1.19. I have searched for possible implementations in ITK and havent found anything. An interesting article on the subject which describes what I want to do can be found here:
<a href="http://www.researchgate.net/publication/221623301_Intersection_based_registration_of_slice_stacks_to_form_3D_images_of_the_human_fetal_brain" target="_parent">
http://www.researchgate.net/publication/221623301_Intersection_based_registration_of_slice_stacks_to_form_3D_images_of_the_human_fetal_brain</a><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Essentially, what they did was to optimize the (rigid) transform the slices in the moving set until their
<i>intensity profiles along the intersections with orthogonal slices</i> match the intensity profiles at the corresponding intersections in the fixed set, within a certain tolerance. Now, this is one way that I would be more than happy to try out on my data,
but likewise, if there are other methods already implemented in ITK Ill try them out as well. If there isnt anything already implemented, could someone please give me some hints as for how to write a program which does something along the lines of what I
described above (and is described in more detail in the link)? Oh, and just knowing whether anything like this already exists and can be used in ITK will be a huge help, since it would allow me to plan my work.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Best regards,<o:p></o:p></p>
<p class="MsoNormal">Mikael<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#1F497D">
.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#1F497D">Mikael Eriksson</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#1F497D">R&D Physicist Trainee</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#1F497D">Philips Medical Systems MR Finland, Feasibility studies</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#1F497D"><a href="mailto:mikael.k.eriksson@philips.com" target="_parent">mikael.k.eriksson@philips.com</a></span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#1F497D">
.</span><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:12.0pt"><o:p> </o:p></span></p>
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