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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Hi Simon,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">My bad, you are right again when changing the rotation direction everything works fine.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Your indication made me double check my dataset generation code, and there was indeed a little convention mismatch in
my new generation code compared to the initial one.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Thanks again and have a nice day,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Albert<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">De :</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Simon Rit [mailto:simon.rit@creatis.insa-lyon.fr]
<br>
<b>Envoyé :</b> dimanche 20 août 2023 08:32<br>
<b>À :</b> Albert MURIENNE <Albert.MURIENNE@b-com.com><br>
<b>Cc :</b> rtk-users@openrtk.org<br>
<b>Objet :</b> Re: [Rtk-users] Problem reconstructing from synthetic data<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal">Hi Albert,<o:p></o:p></p>
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<p class="MsoNormal">It seems that you have changed the rotation direction. Setting -a option of rtksimulatedgeometry to 360 (the default value) seems to fix the problem.
<o:p></o:p></p>
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<p class="MsoNormal">Simon<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Fri, Aug 18, 2023 at 2:10 PM Albert MURIENNE <<a href="mailto:Albert.MURIENNE@b-com.com" target="_blank">Albert.MURIENNE@b-com.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hello again Simon,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Going further away with my gVirtualXRay/RTK tests, I tried to switch to a new projections
set, using the previous indications you gave me.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Unfortunately the results are not very good, and I can’t understand why.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">This time the data corresponds to a human phantom, with a 600mm SID and 1200mm SDD, 2.0mm
pixel size with a 512x512 image resolution.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I used the following scripts without success:</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><i><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">rtksimulatedgeometry -n 360 -a -360 -o projections_p4_512x512_2.0_600_1200/geometry.xml
--sdd 1200 --sid 600</span></i><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><i><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">rtkfdk -p projections_p4_512x512_2.0_600_1200 -r '</span></i><i><span lang="EN-US">
</span></i><i><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">attenuation-([0-9]*).tif' -o fdk.mha --neworigin -511.0,-511.0,0 --newspacing 2.0 --nsort --submatch 1 --hardware cuda –g projections_p4_512x512_2.0_600_1200/geometry.xml</span></i><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">This new dataset’s images, as well as the xml geometry I generated, are available for
download at this link:</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><a href="https://filesender.renater.fr/?s=download&token=acf071a0-1299-4725-81d3-4a41b5a8a158" target="_blank">https://filesender.renater.fr/?s=download&token=acf071a0-1299-4725-81d3-4a41b5a8a158</a></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks for your help,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Regards,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Albert</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">De :</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Simon
Rit [mailto:<a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank">simon.rit@creatis.insa-lyon.fr</a>]
<br>
<b>Envoyé :</b> lundi 26 juin 2023 11:49<br>
<b>À :</b> Albert MURIENNE <<a href="mailto:Albert.MURIENNE@b-com.com" target="_blank">Albert.MURIENNE@b-com.com</a>><br>
<b>Cc :</b> <a href="mailto:rtk-users@openrtk.org" target="_blank">rtk-users@openrtk.org</a><br>
<b>Objet :</b> Re: [Rtk-users] Problem reconstructing from synthetic data</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Yes, the origin is the center of the first pixel in ITK see e.g.
</span><a href="https://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch4.html#x45-54001r1" target="_blank"><span lang="EN-US">figure 4.1 of ITK's software guide</span></a><span lang="EN-US">.</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Simon</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">On Mon, Jun 26, 2023 at 11:03 AM Albert MURIENNE <</span><a href="mailto:Albert.MURIENNE@b-com.com" target="_blank"><span lang="EN-US">Albert.MURIENNE@b-com.com</span></a><span lang="EN-US">>
wrote:</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hello Simon,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Glad to hear you’re still actively maintaining RTK
</span><span lang="EN-US" style="font-size:11.0pt;font-family:Wingdings;color:#1F497D">J</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I made some tests following your advices, and everything is now working fine!</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I had already started playing with the projections origin, but I was missing the point
about the rotation convention.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I guess the xxx.75 origin coordinates are related to the origin being at the “center”
of the pixel?</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Regards,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Albert
</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">De :</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Simon
Rit [mailto:</span><a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">simon.rit@creatis.insa-lyon.fr</span></a><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">]
<br>
<b>Envoyé :</b> jeudi 22 juin 2023 11:47<br>
<b>À :</b> Albert MURIENNE <</span><a href="mailto:Albert.MURIENNE@b-com.com" target="_blank"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">Albert.MURIENNE@b-com.com</span></a><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">><br>
<b>Cc :</b> </span><a href="mailto:rtk-users@openrtk.org" target="_blank"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">rtk-users@openrtk.org</span></a><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><br>
<b>Objet :</b> Re: [Rtk-users] Problem reconstructing from synthetic data</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Hi Albert,</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Nice to hear that you are still working on CT. There are two things that must be accounted for</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">- there is a difference in convention for the rotation angle between gVirtualXRay and RTK,</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">- the projections are not centered if the origin is 0.</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">The following command lines work for me:</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-family:"Courier New"">rtksimulatedgeometry -n 360 -a -360 -o g --sdd 1000 --sid 500<br>
rtkfdk -p . -r 'projection([0-9]*).tif' -o fdk.mha --neworigin -159.75,-119.75,0 --newspacing 0.5 --nsort --submatch 1 --hardware cuda -g g</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Let me know if something is unclear,</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Simon</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">On Wed, Jun 21, 2023 at 10:04 AM Albert MURIENNE <</span><a href="mailto:Albert.MURIENNE@b-com.com" target="_blank"><span lang="EN-US">Albert.MURIENNE@b-com.com</span></a><span lang="EN-US">>
wrote:</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Hello,<br>
<br>
I'm struggling to reconstruct properly a synthetic projection images sequence using RTK.<br>
The sequence was generated using gVirtualXRay (</span><a href="https://gvirtualxray.fpvidal.net/" target="_blank"><span lang="EN-US">https://gvirtualxray.fpvidal.net/</span></a><span lang="EN-US">) and a dragon 3D model, and represents a full 360 degrees CBCT
tomographic sequence, with a 500mm SID and 1000mm SDD, 0.5mm pixel size with a 640x480 image resolution, and without any offsets (perfect circular geometry). I tried reconstructions with the simplest FDK and SART implementations, inspired by RTK provided code
examples, using rtk::ProjectionsReader to read the images and rtk::ThreeDCircularProjectionGeometry to read the geometry, but the results are not good, and I don't really know if the problem comes from the data or from my reconstruction implementation.<br>
<br>
The images data, as well as the xml geometry I generated, are available for download at this link:<br>
<br>
</span><a href="https://filesender.renater.fr/?s=download&token=bc8f87b4-989c-46d7-8c4b-dac39a4df0e1" target="_blank"><span lang="EN-US">https://filesender.renater.fr/?s=download&token=bc8f87b4-989c-46d7-8c4b-dac39a4df0e1</span></a><span lang="EN-US"><br>
<br>
Could you help me pinpoint the origin of my problem? Does it come from the data itself?<br>
<br>
Thanks,<br>
<br>
Albert<br>
Murienne <br>
<br>
_______________________________________________<br>
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