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--></style></head><body lang=EN-US link=blue vlink="#954F72"><div class=WordSection1><p class=MsoNormal>Hi MG,</p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sometimes, the progressive deformation from the center of rotation to the edge of the image is caused by wrong sdd/sid ratio. Such as change in the geometry will lead to distortion of the image and wrong magnification.</p><p class=MsoNormal>Maybe you can play with that parameter and report your result. </p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Cheers,</p><p class=MsoNormal>Louie<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Sent from <a href="http://go.microsoft.com/fwlink/?LinkId=550986">Mail</a> for Windows 10</p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p><div style='mso-element:para-border-div;border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;border:none;padding:0in'><br><b>From: </b><a href="mailto:simon.rit@creatis.insa-lyon.fr">Simon Rit</a><br><b>Sent: </b>Tuesday, January 26, 2016 13:24<br><b>To: </b><a href="mailto:mgvallet.pro@gmail.com">MG Vallet</a><br><b>Cc: </b><a href="mailto:rtk-users@public.kitware.com">rtk-users@public.kitware.com</a><br><b>Subject: </b>Re: [Rtk-users] Sophia beads reconstruction</p></div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p><div><div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>Hi,</span><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>I think it's likely a problem with parameters. The best would be to obtain them from the Matlab code they provide.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>Good luck,<o:p></o:p></span></p></div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>Simon<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet <<a href="mailto:mgvallet.pro@gmail.com" target="_blank">mgvallet.pro@gmail.com</a>> wrote:<o:p></o:p></span></p><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in'><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>Hi Simon,<o:p></o:p></span></p><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>this was a point I missed. I had to do the log mapping.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>I must say, I do not use RTK from shell. I just plugged the objects<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from RTK into a visualisation software. That's the reason I'm not absolutely sure about the length parameter setting.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>Anyway, I'm now pretty close to your result. I believe the only difference is the progressive deformation of beads with the distance to center.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>What's your opinion : is there another step I might have missed, or is it more likely a problem with parameters ?<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif;color:#888888'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif;color:#888888'>MG<o:p></o:p></span></p></div></div><div><div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>2016-01-21 14:22 GMT-05:00 Simon Rit <<a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank">simon.rit@creatis.insa-lyon.fr</a>>:<o:p></o:p></span></p><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in'><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the projections and converts them depending on the type: for mha or mhd, it just reads it and nothing else. For tif, it assumes that I is passed, try to guess I0 (or gets it from the cmd line) and computes ln(I0/I).<br>So from each tif projection, instead of letting them go through the ProjectionsReader in RTK, directly use the ImageReader, stack them and pass it to the reconstruction algorithm. In other words, if you use SimpleRTK, use ImageSeriesReader instead of ProjectionsReader.<br>Regarding the geometry, it would be nice to be confident in the geometry parameters, maybe from their Matlab code?<span style='color:#888888'><br>Simon</span><o:p></o:p></span></p><div><div><p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>On 21/01/2016 20:02, MG Vallet wrote:<o:p></o:p></span></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>Hi Simon and Cyril, <o:p></o:p></span></p><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>I really appreciate your insight.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>By examining the parameters of the acquisition, I saw that the center must effectively be offset (4.8 mm in both directions). For the attached image, I also increases sdd and sid by a factor 1000, just in case I would be wrong in units. It reduces the first default I pointed out in my first message. Also note that my input dataset was </span><span style='font-size:9.5pt;font-family:"Times New Roman",serif'>SophiaBeads_512_averaged.</span><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.5pt;font-family:"Times New Roman",serif'>Regarding the pre-processing mentioned by Simon, I need more help. Is it as simple as the FDK filter assumes that the input is intensity, but the dataset provides -ln(I/I0) ?</span><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.5pt;font-family:"Times New Roman",serif'>Regards,</span><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.5pt;font-family:"Times New Roman",serif'>mg</span><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p></o:p></span></p></div></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>2016-01-20 3:33 GMT-05:00 Simon Rit <<a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank">simon.rit@creatis.insa-lyon.fr</a>>:<o:p></o:p></span></p><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in'><div><div><div><div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>Hi,<o:p></o:p></span></p></div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what is provided is directly the line integral. RTK will process the tif images as if it were a photon count so I converted the tif projections to mha to avoid this. For the conversion, I used another piece of software but you can easily do the same thing with SimpleRTK.<o:p></o:p></span></p></div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>Second, I used the enclosed script which gives me a much better result. I have however a geometry problem. I think they provide a Matlab piece of code to get the center of rotation. If you can run it and find out what is this center, then you can use it to configure the geometry better with the options --proj_iso_x and --proj_iso_y.<o:p></o:p></span></p></div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>Good luck,<o:p></o:p></span></p></div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>Simon<o:p></o:p></span></p></div><div><div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet <<a href="mailto:mgvallet.pro@gmail.com" target="_blank">mgvallet.pro@gmail.com</a>> wrote:<o:p></o:p></span></p><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in'><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>Thanks Cyril! <o:p></o:p></span></p><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>going to carefully check my inputs and I give you some news.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>mgv<o:p></o:p></span></p></div></div><div><div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>2016-01-19 10:33 GMT-05:00 Cyril Mory <<a href="mailto:cyril.mory@uclouvain.be" target="_blank">cyril.mory@uclouvain.be</a>>:<o:p></o:p></span></p><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in'><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>Hi, <br><br>It looks like the geometry is wrong indeed, because I have never seen such artifacts.<br><br>Hope that helps,<br>Cyril <o:p></o:p></span></p><div><div><p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>Le 19/01/2016 16:19, MG Vallet a écrit :<o:p></o:p></span></p></div></div></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>Dear rtk-users, <o:p></o:p></span></p><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>I applied the </span><span style='font-size:9.0pt;font-family:"Courier New";color:black'>FDKConeBeamReconstructionFilter to a data set from </span><span style='font-size:10.5pt;font-family:"Arial",sans-serif;color:#333333'><a href="https://zenodo.org/record/16539" target="_blank">https://zenodo.org/record/16539</a>. </span><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Arial",sans-serif;color:#333333'>This is a plastic tube filled with glass beads that has been scanned.</span><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Arial",sans-serif;color:#333333'>Attached is a view of the reconstructed central slice. It is found that:</span><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><div><ol start=1 type=1><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1'><span style='font-size:12.0pt;font-family:"Arial",sans-serif;color:#333333'>the beads are quickly deformed outside the center</span><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p></o:p></span></li><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1'><span style='font-size:12.0pt;font-family:"Arial",sans-serif;color:#333333'>each one has a halo, or a shadow (dont know the proper term)</span><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p></o:p></span></li></ol></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Arial",sans-serif;color:#333333'>My question is if these are simply expected artifacts. I am not 100% sure I properly set the geometry parameters.</span><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Arial",sans-serif;color:#333333'>Regards,</span><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Arial",sans-serif;color:#333333'>mgv</span><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p></o:p></span></p></div></div><p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p></div></div><pre>_______________________________________________</pre><pre>Rtk-users mailing list</pre><pre><a href="mailto:Rtk-users@public.kitware.com" target="_blank">Rtk-users@public.kitware.com</a></pre><pre><a href="http://public.kitware.com/mailman/listinfo/rtk-users" target="_blank">http://public.kitware.com/mailman/listinfo/rtk-users</a></pre></blockquote><p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><br><br><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p></o:p></span></p><table class=MsoNormalTable border=0 cellspacing=0 cellpadding=0 style='border-collapse:collapse'><tr><td style='padding:0in 11.25pt 0in 6.0pt'><p class=MsoNormal><a href="https://www.avast.com/antivirus" target="_blank"></a><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p></o:p></span></p></td><td style='padding:.75pt .75pt .75pt .75pt'><p><span style='font-family:"Calibri",sans-serif;color:#3D4D5A'>L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast. <br><a href="https://www.avast.com/antivirus" target="_blank">www.avast.com</a> <o:p></o:p></span></p></td></tr></table><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p></div></blockquote></div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p></div></div></div><p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><br>_______________________________________________<br>Rtk-users mailing list<br><a href="mailto:Rtk-users@public.kitware.com" target="_blank">Rtk-users@public.kitware.com</a><br><a href="http://public.kitware.com/mailman/listinfo/rtk-users" target="_blank">http://public.kitware.com/mailman/listinfo/rtk-users</a><o:p></o:p></span></p></blockquote></div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p></div></div></div></blockquote></div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p></div></blockquote><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p></div></div></div></blockquote></div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p></div></div></div></blockquote></div></div><p class=MsoNormal><span style='font-size:12.0pt;font-family:"Times New Roman",serif'><o:p> </o:p></span></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>