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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<br>
<br>
<div class="moz-cite-prefix">On 09/18/2014 04:47 PM, Howard wrote:<br>
</div>
<blockquote
cite="mid:CAKr9h5WvPszaFGtEmSVsyLmcgKu2oMbg5ONMQN-X9+A5P1bzHw@mail.gmail.com"
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 moz-do-not-send="true"
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">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 moz-do-not-send="true"
href="http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction"
target="_blank">http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction<span
class="HOEnZb"><font color="#888888"><span></span><span></span></font></span></a><span
class="HOEnZb"><font color="#888888"><br>
Simon<br>
</font></span></div>
<div class="HOEnZb">
<div class="h5">
<div class="gmail_extra"><br>
<div class="gmail_quote">On Thu, Sep 18, 2014 at 10:12
AM, Cyril Mory <span dir="ltr"><<a
moz-do-not-send="true"
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 moz-do-not-send="true"
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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<pre cols="72">--
--
Cyril Mory, Post-doc
CREATIS
Leon Berard cancer treatment center
28 rue Laënnec
69373 Lyon cedex 08 FRANCE
Mobile: <a moz-do-not-send="true" href="tel:%2B33%206%2069%2046%2073%2079" target="_blank" value="+33669467379">+33 6 69 46 73 79</a></pre>
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<pre class="moz-signature" cols="72">--
--
Cyril Mory, Post-doc
CREATIS
Leon Berard cancer treatment center
28 rue Laënnec
69373 Lyon cedex 08 FRANCE
Mobile: +33 6 69 46 73 79</pre>
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