<div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Feb 10, 2016 at 2:50 PM, Deepak Roy Chittajallu <span dir="ltr"><<a href="mailto:cdeepakroy@gmail.com" target="_blank">cdeepakroy@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Alternatively, without using the grid parameters in the .cal file, once i know the following 9 geometric parameters that RTK needs for each projection:<div><br></div><div>-- sourceToRotationCenterDistance</div><div>-- sourceToDetectorDistance</div><div>-- sourceOffsetX</div><div>-- sourceOffsetY</div><div>-- projectionOffsetX</div><div>-- projectionOffsetY</div><div>-- In-plane angle</div><div>-- Out-of-plane angle</div><div>-- gantryAngle</div><div><br></div><div>Can i use the above to determine the size and orientation/direction of the reconstruction grid that enclosed the object?</div></div></blockquote><div>No, that says nothing on where you've place your object.<br> <br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><br></div><div>In my case, the object rotates instead of the source and detector? Would this be an issue affecting the geometric parameters in some way?</div></div></blockquote><div><div><div><div>I think there is a confusion. The fact that the object is
still or the source/detector is still doesn't change anything in the
reference frame of the object. I think it's simpler to account for the
grid rotation in the direction. Don't try to account for it in the
projection parameters even if it's of course possible to do so.<br></div> <br></div></div></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><br></div><div>Also when i peeked into the geometry object given by the digisens reader i see that the In-plane and out-of-plane angle change a bit for each projection probably because of <a href="https://github.com/SimonRit/RTK/blob/master/code/rtkDigisensGeometryReader.cxx#L110" target="_blank">this</a>. Shouldnt these be constant? In my case the rotation axis is slightly off of the y-axis. I think RTK assumes it should be the y-axis. </div></div></blockquote><div>InPlane
and Out-of-plane are not 0 because your rotation axis is not (0,1,0),
that's expected. I guess they should be constant if your rotation axis is, if not there might be a
problem in the conversion from axis-angle to euler angles. You'd have
to check...<br>Good luck,<br>Simon <br><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><br></div><div>Maybe thats why the In-plane and Out-of-plane angles change?</div></div><div class=""><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Feb 10, 2016 at 8:32 AM, Deepak Roy Chittajallu <span dir="ltr"><<a href="mailto:cdeepakroy@gmail.com" target="_blank">cdeepakroy@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Sorry for those multiple emails. I felt they were not going through to the mailing list as they were not showing up in the archives.<div><br></div><div>Simon, thanks a lot for the reply. I tried "center - 0.5 * scale * (resolution - 1)". I will try what you suggest and see.</div><div><br></div><div>The four valued rotation parameter --- <span style="font-size:12.8px"><rotation>0 0 0.705858 0.708353</rotation> </span>--- in the .cal file is apparently a quaternion of unit length. Can i make an itk::Versor object from the four quaternion values. And then use its GetMatrix() as the direction as shown below:</div><div><br></div><div>itk::Versor<double> gridRot(0, 0, 0.705858, 0.708353);</div><div>dummyReconImage->SetDirection( gridRot.GetMatrix() );</div><div><br></div><div>I tried this and it still dint seem to give the right reconstruction. Any suggestions?</div><div><br></div><div>Should i be rotating the origin using this matrix before setting it using SetOrigin() maybe?</div></div><div class="gmail_extra"><div><div><br><div class="gmail_quote">On Wed, Feb 10, 2016 at 7:44 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:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
Hi,<br>
I haven't used the Digisens geometry reader so I hope that it works
fine. Be careful with it because I don't think it's been thoroughly
tested.<br>
Regarding the definition of the volume, in ITK, the origin is the
coordinate of the first voxel. This is what allows you to place the
volume at the right location. Using your grid parameters, I would
say that you have to set the origin as (coordinate-by-coordinate)<br>
scale * 0.5 * (resolution-1) + center<br>
so that the center of the reconstructed volume is around the
"center" parameter of your xml file.<br>
The direction would allow you to tilt your volume but since I don't
understand the digisens parameter, I can't help you. I advise you to
work on it later.<br>
I hope this helps. Good luck!<br>
Simon<div><div><br>
<br>
<div>On 10/02/2016 02:03, Deepak Roy
Chittajallu wrote:<br>
</div>
</div></div><blockquote type="cite"><div><div>
<div dir="ltr"><span style="font-size:12.8px">Hello All,</span>
<div style="font-size:12.8px"><br>
</div>
<div style="font-size:12.8px">I have at hand a stack of
projection images and the projection geometry defined in a
.cal file of digisens. I am trying to use RTK to do the
reconstruction.</div>
<div style="font-size:12.8px"><br>
</div>
<div style="font-size:12.8px">I used <a href="http://www.openrtk.org/Doxygen/classrtk_1_1DigisensGeometryReader.html" target="_blank">rtk::DigisensGeometryReader</a> to read the
.cal file and generate the geometry.</div>
<div style="font-size:12.8px"><br>
</div>
<div style="font-size:12.8px">Then i call <a href="http://www.openrtk.org/Doxygen/classrtk_1_1FDKConeBeamReconstructionFilter.html" target="_blank">rtk::FDKConeBeamReconstructionFilter</a> to
do the reconstruction by supplying to it as Inputs -- the
geometry, a dummy reference image of the reconstructed volume
(with origin, spacing, size, direction etc), and the stack of
projection images.</div>
<div style="font-size:12.8px"><br>
</div>
<div style="font-size:12.8px">But i am getting a blank volume as
reconstruction.</div>
<div style="font-size:12.8px"><br>
</div>
<div style="font-size:12.8px">I suspect the problem is with
positioning the reconstructed volume (specified via the dummy
reference image).</div>
<div style="font-size:12.8px"><br>
</div>
<div style="font-size:12.8px">As a sample attached is the
digisens .cal file that RTK uses for testing purposes which
looks very similar to mine.</div>
<div style="font-size:12.8px"><br>
</div>
<div style="font-size:12.8px">In lines 642-656, it seems to
define the postion, size, and spacing of the reconstructed
volume via the following schema:</div>
<div style="font-size:12.8px"><br>
</div>
<div style="font-size:12.8px">---------------------------------------------------------------------</div>
<div style="font-size:12.8px"><br>
</div>
<div style="font-size:12.8px">
<div> <Grid></div>
<div> <rotation>0 0 0.705858 0.708353</rotation></div>
<div> <center>-1.23119 -16.6554 10.2144</center></div>
<div> <scale>0.2 0.2 0.2</scale></div>
<div> <resolution>289 399 360</resolution></div>
<div> <autoRotation>true</autoRotation></div>
<div>
<cylinderConstraint>false</cylinderConstraint></div>
<div>
<cylinderConstraintFromGrid>false</cylinderConstraintFromGrid></div>
<div>
<name>C:/Documents/2011_02_14_15-15-12_FenteAl/reconstruction.vol</name></div>
<div> <format>2</format></div>
<div> <beamHardening>0</beamHardening></div>
<div> <background>0</background></div>
<div> <colorscaling>1 0</colorscaling></div>
<div> <rawOutput></rawOutput></div>
<div> </Grid></div>
</div>
<div style="font-size:12.8px"><br>
</div>
<div style="font-size:12.8px">-----------------------------------------------------------------------</div>
<div style="font-size:12.8px"><br>
</div>
<div style="font-size:12.8px">I understand the <scale>
(spacing in mm) and <resolution> (size) elements. These
can be used to SetSize() and SetSpacing() of the dummy
reconstructed volume provided as input to the reconstruction
filter.</div>
<div style="font-size:12.8px"><br>
</div>
<div style="font-size:12.8px">I dont know how to translate the
<rotation> and <center> to SetOrigin(), and
SetDirection() of the dummy reconstructed volume.</div>
<div style="font-size:12.8px"><br>
</div>
<div style="font-size:12.8px">Does anyone know how to do this?</div>
<div style="font-size:12.8px"><br>
</div>
<div style="font-size:12.8px">Or alternatively, is there a way
to automatically set these to reconstruct the maximum possible
extent of the object positioned in between the source and
detector?</div>
<div style="font-size:12.8px"><br>
</div>
<div style="font-size:12.8px">Regards,</div>
<div style="font-size:12.8px"><br>
</div>
<div style="font-size:12.8px">Deepak</div>
</div>
<br>
<fieldset></fieldset>
<br>
</div></div><pre>_______________________________________________
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</pre>
</blockquote>
<br>
</div>
</blockquote></div><br><br clear="all"><div><br></div></div></div><span><font color="#888888">-- <br><div><div dir="ltr"><div><div style="color:rgb(136,136,136);font-size:12.8px">Deepak Roy Chittajallu, Ph.D.<div>R&D Engineer, Medical Computing Team<br><div><a href="http://www.kitware.com/" style="color:rgb(17,85,204)" target="_blank">Kitware Inc</a>, Carrboro, NC, USA</div><div>E-mail: <a href="mailto:cdeepakroy@gmail.com" style="color:rgb(17,85,204)" target="_blank">cdeepakroy@gmail.com</a><br>URL: <a href="http://www.drchittajallu.info/" style="color:rgb(17,85,204)" target="_blank">http://www.drchittajallu.info</a></div></div></div><div style="color:rgb(136,136,136);font-size:12.8px">Linkedin: <a href="https://www.linkedin.com/in/cdeepakroy" style="color:rgb(17,85,204)" target="_blank">https://www.linkedin.com/in/cdeepakroy</a></div></div></div></div>
</font></span></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div><div dir="ltr"><div><div style="color:rgb(136,136,136);font-size:12.8px">Deepak Roy Chittajallu, Ph.D.<div>R&D Engineer, Medical Computing Team<br><div><a href="http://www.kitware.com/" style="color:rgb(17,85,204)" target="_blank">Kitware Inc</a>, Carrboro, NC, USA</div><div>E-mail: <a href="mailto:cdeepakroy@gmail.com" style="color:rgb(17,85,204)" target="_blank">cdeepakroy@gmail.com</a><br>URL: <a href="http://www.drchittajallu.info/" style="color:rgb(17,85,204)" target="_blank">http://www.drchittajallu.info</a></div></div></div><div style="color:rgb(136,136,136);font-size:12.8px">Linkedin: <a href="https://www.linkedin.com/in/cdeepakroy" style="color:rgb(17,85,204)" target="_blank">https://www.linkedin.com/in/cdeepakroy</a></div></div></div></div>
</div>
</div></div></blockquote></div><br></div></div>