<div dir="ltr">Hi Simon and Cyril,<div><br></div><div>I really appreciate your insight.</div><div><br></div><div>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 style="font-size:12.8px">SophiaBeads_512_averaged.</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">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></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">Regards,</span></div><div><span style="font-size:12.8px">mg</span></div></div><div class="gmail_extra"><br><div class="gmail_quote">2016-01-20 3:33 GMT-05:00 Simon Rit <span dir="ltr"><<a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank">simon.rit@creatis.insa-lyon.fr</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div>Hi,<br></div>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.<br></div>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.<br></div>Good luck,<br></div>Simon<br></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet <span dir="ltr"><<a href="mailto:mgvallet.pro@gmail.com" target="_blank">mgvallet.pro@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Thanks Cyril!<div>going to carefully check my inputs and I give you some news.</div><div>mgv</div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">2016-01-19 10:33 GMT-05:00 Cyril Mory <span dir="ltr"><<a href="mailto:cyril.mory@uclouvain.be" target="_blank">cyril.mory@uclouvain.be</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
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<div><div><br>
<br>
<div>Le 19/01/2016 16:19, MG Vallet a
écrit :<br>
</div>
</div></div><blockquote type="cite"><div><div>
<div dir="ltr">Dear rtk-users,
<div><br>
</div>
<div>I applied the <font face="Courier New" color="#000000"><span style="font-size:12px">FDKConeBeamReconstructionFilter to
a data set from </span></font><span style="color:rgb(51,51,51);font-family:Roboto,sans-serif;font-size:14px;line-height:20px"><a href="https://zenodo.org/record/16539" target="_blank"></a><a href="https://zenodo.org/record/16539" target="_blank">https://zenodo.org/record/16539</a>. </span></div>
<div><span style="color:rgb(51,51,51);font-family:Roboto,sans-serif;line-height:20px">This
is a plastic tube filled with glass beads that has been
scanned.</span></div>
<div><span style="color:rgb(51,51,51);font-family:Roboto,sans-serif;line-height:20px"><br>
</span></div>
<div><span style="color:rgb(51,51,51);font-family:Roboto,sans-serif;line-height:20px">Attached
is a view of the reconstructed central slice. It is found
that:</span></div>
<div>
<ol>
<li><font face="Roboto, sans-serif" color="#333333"><span style="line-height:20px">the beads are quickly
deformed outside the center</span></font></li>
<li><font face="Roboto, sans-serif" color="#333333"><span style="line-height:20px">each one has a halo, or a
shadow (dont know the proper term)</span></font></li>
</ol>
</div>
<div><span style="color:rgb(51,51,51);font-family:Roboto,sans-serif;line-height:20px">My
question is if these are simply expected artifacts. </span><span style="color:rgb(51,51,51);font-family:Roboto,sans-serif;line-height:20px">I
am not 100% sure I properly set the geometry parameters.</span></div>
<div><span style="color:rgb(51,51,51);font-family:Roboto,sans-serif;line-height:20px"><br>
</span></div>
<div><span style="color:rgb(51,51,51);font-family:Roboto,sans-serif;line-height:20px">Regards,</span></div>
<div><span style="color:rgb(51,51,51);font-family:Roboto,sans-serif;line-height:20px">mgv</span></div>
</div>
<br>
<fieldset></fieldset>
<br>
</div></div><pre>_______________________________________________
Rtk-users mailing list
<a href="mailto:Rtk-users@public.kitware.com" target="_blank">Rtk-users@public.kitware.com</a>
<a href="http://public.kitware.com/mailman/listinfo/rtk-users" target="_blank">http://public.kitware.com/mailman/listinfo/rtk-users</a>
</pre>
</blockquote>
<br>
<br><br>
<hr style="border:none;color:#909090;background-color:#b0b0b0;min-height:1px;width:99%">
<table style="border-collapse:collapse;border:none">
<tbody><tr>
<td style="border:none;padding:0px 15px 0px 8px">
<a href="https://www.avast.com/antivirus" target="_blank">
<img src="http://static.avast.com/emails/avast-mail-stamp.png" alt="Avast logo" border="0">
</a>
</td>
<td>
<p style="color:#3d4d5a;font-family:"Calibri","Verdana","Arial","Helvetica";font-size:12pt">
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>
</p>
</td>
</tr>
</tbody></table>
<br>
</div>
</blockquote></div><br></div>
</div></div><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" rel="noreferrer" target="_blank">http://public.kitware.com/mailman/listinfo/rtk-users</a><br>
<br></blockquote></div><br></div>
</div></div></blockquote></div><br></div>