<div dir="ltr"><div><div>Hi,<br></div>The geometry files look ok to me. What is the projection information? If you're still getting the same message as before, I think it's because you don't have enough data. If you send the mhd file of the projections (just the mhd, not the raw data), I can try to test it on simulated data to let you know my feeling.<br></div>Simon<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Dec 8, 2015 at 5:41 PM, Shiras Abdurahman <span dir="ltr"><<a href="mailto:shiraska@gmail.com" target="_blank">shiraska@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">Dear Simon,<div><br></div><div>I tried this option and unfortunately it did not work. I added zero projections and modified geometry files. However, I am getting same artifacts in the volume. Voxel values changed a little bit that indicates during backprojection it still considers extreme projections. I am also getting an output message same as before.</div><div><br></div><div>I am attaching geometry files.</div><div><br></div><div>With regards,</div><div>Shiras</div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Dec 8, 2015 at 10:15 AM, Simon Rit <span dir="ltr"><<a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank">simon.rit@creatis.insa-lyon.fr</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"><div>So calling AddProjection before and after the loop with an adequate gantry_angle should work.<span><font color="#888888"><br></font></span></div><span><font color="#888888">Simon<br></font></span></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Dec 8, 2015 at 9:52 AM, Shiras Abdurahman <span dir="ltr"><<a href="mailto:shiraska@gmail.com" target="_blank">shiraska@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">Drear Simon, <div><br></div><div>I generate the geometry with system geometry parameters and using AddProjection method.</div><div><br></div><div>Here is the code</div><div><br></div><div><br></div><div><div><span style="white-space:pre-wrap"> </span>rtk::ThreeDCircularProjectionGeometry::Pointer rtk_sys_geometry_;</div><div><span style="white-space:pre-wrap"> </span>rtk_sys_geometry_ = rtk::ThreeDCircularProjectionGeometry::New();</div><div><span style="white-space:pre-wrap"> </span>for (uint16_t proj_index = 0; proj_index < num_projections_; proj_index++)</div><div><span style="white-space:pre-wrap"> </span>{</div><div><span style="white-space:pre-wrap"> </span>rtk_sys_geometry_->AddProjection(rtk_geom_params_.at(proj_index).sid_mm,</div><div><span style="white-space:pre-wrap"> </span>rtk_geom_params_.at(proj_index).sdd_mm,</div><div><span style="white-space:pre-wrap"> </span>rtk_geom_params_.at(proj_index).gantry_angle_deg,</div><div><span style="white-space:pre-wrap"> </span>rtk_geom_params_.at(proj_index).proj_offset_x_mm,</div><div><span style="white-space:pre-wrap"> </span>rtk_geom_params_.at(proj_index).proj_offset_y_mm,</div><div><span style="white-space:pre-wrap"> </span>rtk_geom_params_.at(proj_index).out_plane_angle_deg,</div><div><span style="white-space:pre-wrap"> </span>rtk_geom_params_.at(proj_index).in_plane_angle_deg,</div><div><span style="white-space:pre-wrap"> </span>rtk_geom_params_.at(proj_index).src_offset_x_mm,</div><div><span style="white-space:pre-wrap"> </span>rtk_geom_params_.at(proj_index).src_offset_y_mm);</div><div><span style="white-space:pre-wrap"> </span>}</div></div><div><br></div><div><span style="white-space:pre-wrap"> And then write to xml file.</span></div><span><font color="#888888"><div><br></div><div>Shiras</div><div><br></div><div><br></div></font></span></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Dec 8, 2015 at 9:23 AM, Simon Rit <span dir="ltr"><<a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank">simon.rit@creatis.insa-lyon.fr</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"><div><div><div><div><div><div>Hi,<br></div>rtkfdk.cxx just read the geometry from a file so the best is to modify the geometry file. How do you generate the geometry?<br></div>For example, if you use rtksimulated geometry, let's say that you were using:<br></div>rtksimulatedgeometry -n 200 -a 200 -o g.xml<br></div>then you'll have to replace it with<br>rtksimulatedgeometry -n 202 -a 202 -o g.xml -f -1<br></div>Don't forget to add dummy projection at the beginning and the end. If you use a more complex geometry, maybe <a href="http://wiki.openrtk.org/index.php?title=SimpleRTK" target="_blank">SimpleRTK</a> can be helpful (I'd use that) or you'd have to modify the cxx code to add these additional projections in the geometry and the projection stack.<span><font color="#888888"><br></font></span></div><span><font color="#888888">Simon<br><div><div><div><br></div></div></div></font></span></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Dec 8, 2015 at 8:51 AM, Shiras Abdurahman <span dir="ltr"><<a href="mailto:shiraska@gmail.com" target="_blank">shiraska@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">Dear Simon,<div><br></div><div>Thanks a lot for the reply. Can you please inform me how can I set where the arc starts?</div><div>Do I need to modify geometry also?</div><div>If you can point the line of code rtkfdk.cxx, it will be really helpful.</div><div><br></div><div>With regards,</div><div>Shiras</div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Dec 8, 2015 at 7:56 AM, Simon Rit <span dir="ltr"><<a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank">simon.rit@creatis.insa-lyon.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"><span>
Dear Shiras,<br>
Yes, for practical reasons the first and the last projections are
set to 0 and the arc used in the Parker weighting starts between the
first two projections and ends between the lasts two projections.
There is a simple solution: add a projection at the beginning and
the end of the arc, which can contain any pixel values but should be
set where you want this arc to start. In the future, I think someone
should once take the time to correct this but I haven't so far. I'll
keep you posted on the mailing list when it's corrected.<br>
Simon<br>
<br>
<div>On 07/12/2015 12:04, Shiras Abdurahman
wrote:<br>
</div>
</span><blockquote type="cite"><div><div>
<div dir="ltr">Hi all,
<div><br>
</div>
<div>I am trying to reconstruct a volume from projection data
generated with C-arm CT. There are 248 projections with an
angular range of 199 degree. Technically, parker weighting
should run without any problems. However, I am getting an
output message that "You do not have enough data for proper
parker weighting". After parker weighting, the two extreme
projections (projection number 1 and 248) were completely zero
and thus reconstructed volume contained artifacts. When I
increased the angular range, this problem did not happen. How
can I solve this problem without increasing angular range? Is
there any threshold constant that I can change in command line
or in my code?</div>
<div><br>
</div>
<div>I really appreciate any help you can provide.</div>
<div><br>
</div>
<div>With regards,</div>
<div>Shiras</div>
</div>
<br>
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