<div dir="ltr">Hi Simon,<div><br></div><div>this was a point I missed. I had to do the log mapping.</div><div><br></div><div>I must say, I do not use RTK from shell. I just plugged the objects</div><div>FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from RTK into a visualisation software. That's the reason I'm not absolutely sure about the length parameter setting.</div><div><br></div><div>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.</div><div><br></div><div>What's your opinion : is there another step I might have missed, or is it more likely a problem with parameters ?</div><div><br></div><div>MG</div></div><div class="gmail_extra"><br><div class="gmail_quote">2016-01-21 14:22 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>
    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 class="HOEnZb"><font color="#888888"><br>
    Simon</font></span><div><div class="h5"><br>
    <br>
    <div>On 21/01/2016 20:02, MG Vallet wrote:<br>
    </div>
    <blockquote type="cite">
      <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>
              <div>
                <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"></a><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"></a><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 color="#000000" face="Courier New"><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 color="#333333" face="Roboto,
                                                  sans-serif"><span style="line-height:20px">the
                                                    beads are quickly
                                                    deformed outside the
                                                    center</span></font></li>
                                              <li><font color="#333333" face="Roboto,
                                                  sans-serif"><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>
    </blockquote>
    <br>
  </div></div></div>

</blockquote></div><br></div>