<div dir="ltr"><div>Hi Cyril,</div><div> </div><div>I am testing SART reconstruction according to what you described, specifying dimension, spacing and origin:</div><div> </div><div>rtksart \<br>   --geometry varianGeometry \<br>   --regexp .*.hnd \<br>   --path ../Scan0 \<br>   --output sart_rec.mha \<br>   --verbose \<br>   --spacing 2.0\<br>   --dimension 128,100,128 \</div><div>   --origin -127.5,-99,-127.5</div><div> </div><div>but the reconstruction gave a plain image with no object/contrast. I checked the grayscale values on the reconstructed images and did see they ranged from -1.78 to 3 (this may not be precise but give you some idea). I tried to adjust window level but couldn't see any contrast. I must miss something here. Please advise. Thanks!</div><div> </div><div>-howard</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Sep 18, 2014 at 10:59 AM, Cyril Mory <span dir="ltr"><<a href="mailto:cyril.mory@creatis.insa-lyon.fr" target="_blank">cyril.mory@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">
    Howard,<br>
    <br>
    For SART reconstructions, you do not need padding, and you can't do
    Hann windowing because no ramp filtering is applied. SART usually
    outputs smoother images, so you probably will not need this
    denoising trick anyway.<br>
    However, you should be careful about one thing : your object has to
    be fully contained in the reconstructed volume, or you will observe
    important border effects. Use the --dimension, --spacing and
    --origin options to ensure this. <br>
    <br>
    All the best,<br>
    Cyril<div><div class="h5"><br>
    <br>
    <div>On 09/18/2014 04:47 PM, Howard wrote:<br>
    </div>
    <blockquote type="cite">
      <div dir="ltr">Thanks very much, Cyril & Simon. Now the fdk
        reconstruction is working beautifully. Jus another quick
        question: for rtksart executable, are we still able to do
        padding and hanning window trick as well?</div>
      <div class="gmail_extra"><br>
        <div class="gmail_quote">On Thu, Sep 18, 2014 at 9:47 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;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid">
            <div dir="ltr">Hi,<br>
              I fully agree with Cyril. Something else : you might want
              to mask out what is outside the field-of-view using the
              rtkfieldofview executable. Your ring corresponds to that
              border. See an example here:<br>
              <a href="http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction" target="_blank">http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction<span><font color="#888888"><span></span><span></span></font></span></a><span><font color="#888888"><br>
                  Simon<br>
                </font></span></div>
            <div>
              <div>
                <div class="gmail_extra"><br>
                  <div class="gmail_quote">On Thu, Sep 18, 2014 at 10:12
                    AM, Cyril Mory <span dir="ltr"><<a href="mailto:cyril.mory@creatis.insa-lyon.fr" target="_blank">cyril.mory@creatis.insa-lyon.fr</a>></span>
                    wrote:<br>
                    <blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid">
                      <div bgcolor="#FFFFFF" text="#000000"> Hi Howard,<br>
                        <br>
                        The bright ring artifact is typically caused by
                        high-pass filtering (the ramp filter used in
                        FDK) of truncated projection data (when
                        projections have non-zero values on the sides,
                        the edge of the projection makes a sharp
                        transition to zero). A classical answer to this
                        problem is to pad the projections, for example
                        with values starting from the values on the side
                        and slowly decreasing to zero. <br>
                        <br>
                        rtkfdk can do this padding for you. Just add
                        "--pad 0.1" to your options (or more than 0.1 if
                        it isn't enough).<br>
                        Also, I noticed that your reconstructed image
                        seems quite noisy. You might want to use a Hann
                        windowing of the ramp filter to reduce the noise
                        amplification effect of high-pass filtering. You
                        can do that by adding "--hann 0.5" to your
                        options. Note that the argument is a cut-off
                        frequency, so smaller values mean more
                        smoothing.<br>
                        <br>
                        Best regards,<br>
                        Cyril
                        <div>
                          <div><br>
                            <br>
                            <div>On 09/18/2014 05:21 AM, Howard wrote:<br>
                            </div>
                          </div>
                        </div>
                        <blockquote type="cite">
                          <div>
                            <div>
                              <div dir="ltr">
                                <div>Hi,</div>
                                <div> </div>
                                <div>I use rtkfdk to reconstruct varian
                                  cbct images following the example on
                                  rtk wiki page. The projections were
                                  obtained with half fan mode because it
                                  is an abdominal region with the
                                  patient lateral x AP dimension of
                                  550x550. The reconstructed cbct images
                                  have a big bright circle around</div>
                                <div>the image. Please see the image:</div>
                                <div><a href="http://expirebox.com/download/2f55c9d8f0bc83138b954d2fec08e78c.html" target="_blank">http://expirebox.com/download/2f55c9d8f0bc83138b954d2fec08e78c.html</a></div>
                                <div> </div>
                                <div>I am using Ubuntu Linux box to
                                  reconstruct. Two sequential commands
                                  were used:</div>
                                <div> </div>
                                <div>./rtkvarianobigeometry --xml_file
                                  ProjectionInfo.xml --path Scan0/
                                  --regexp Proj_.*.hnd -o varianGeometry<br>
                                </div>
                                <div>and </div>
                                <div> </div>
                                <div>rtkfdk \<br>
                                     --geometry varianGeometry \<br>
                                     --regexp .*.hnd \<br>
                                     --path ../Scan0 \<br>
                                     --output rec.mha \<br>
                                     --verbose \<br>
                                     --spacing 2.0,2.0,2.0 \<br>
                                     --dimension 256,100,256 \<br>
                                </div>
                                <div>The projections are stored in the
                                  standard varian format: Scan0 and
                                  ProjectionInfo.xml with 644 projection
                                  images.  I assume that rtkfdk handled
                                  the half fan geometry properly. What
                                  did I do wrong then?  Many thanks!</div>
                                <div> </div>
                                <div>-howard</div>
                              </div>
                              <br>
                              <fieldset></fieldset>
                              <br>
                            </div>
                          </div>
                          <span>
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                          </span></blockquote>
                        <span><font color="#888888"> <br>
                            <pre cols="72">-- 
--
Cyril Mory, Post-doc
CREATIS
Leon Berard cancer treatment center
28 rue Laënnec
69373 Lyon cedex 08 FRANCE

Mobile: <a href="tel:%2B33%206%2069%2046%2073%2079" target="_blank" value="+33669467379">+33 6 69 46 73 79</a></pre>
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                      <br>
                    </blockquote>
                  </div>
                  <br>
                </div>
              </div>
            </div>
          </blockquote>
        </div>
        <br>
      </div>
    </blockquote>
    <br>
    <pre cols="72">-- 
--
Cyril Mory, Post-doc
CREATIS
Leon Berard cancer treatment center
28 rue Laënnec
69373 Lyon cedex 08 FRANCE

Mobile: <a href="tel:%2B33%206%2069%2046%2073%2079" target="_blank" value="+33669467379">+33 6 69 46 73 79</a></pre>
  </div></div></div>

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