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Hi Daniel,<br>
<br>
Please keep the discussion about RTK on the mailing list : this
conversation might come in handy to someone else in the future. <br>
Regarding the data acquisition, here is what you need :<br>
- Raw pixel data and meta-data of the projection images (number of
pixels per line and column, number of lines and columns, number of
projections, bits per pixel, size of the pixels in mm)<br>
- Geometry data (you can find some information on the RTK geometry
on the wiki, <a class="moz-txt-link-freetext" href="http://wiki.openrtk.org/index.php/Main_Page#Geometry">http://wiki.openrtk.org/index.php/Main_Page#Geometry</a>).
It usually consists in a few (from 9 to 15) floats per projection<br>
<br>
I worked with a Philips C-Arm during my PhD indeed. I was employed
by Philips, so I had the tools to export the raw data and geometry
information readily available. <br>
Depending on how well-documented the data you have is, it may range
from very easy to very difficult to extract this information (if you
have to look for it manually in undocumented Dicom fields, for
example, it may take time, while if all you need is a geometry
converter, it's a matter of a few hours).<br>
<br>
Can you be precise on what kind of data you are able to extract from
the Zeego ? <br>
<br>
Regards,<br>
Cyril<br>
<br>
<div class="moz-cite-prefix">On 08/15/2014 04:16 PM, Schoenke,
Daniel wrote:<br>
</div>
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<div class="WordSection1">
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"
lang="EN-US">Thanks!<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"
lang="EN-US">My goal is to use RTK for Reconstruction of
Siemens Artis Zeego projection data. You´ve worked with a
Philips Scanner – so as I understood from your PhD thesis.
If you have any advices regarding writing code for the
read-in of data this would be very helpful for me (I´m a
physicist and no real programmer…)<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"
lang="EN-US">Again thanks a lot and have a nice weekend!<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"
lang="EN-US">Daniel<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext"
lang="EN-US">Von:</span></b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext"
lang="EN-US"> Cyril Mory
[<a class="moz-txt-link-freetext" href="mailto:cyril.mory@creatis.insa-lyon.fr">mailto:cyril.mory@creatis.insa-lyon.fr</a></span><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">]
<br>
<b>Gesendet:</b> Donnerstag, 14. August 2014 14:58<br>
<b>An:</b> Schoenke, Daniel; <a class="moz-txt-link-abbreviated" href="mailto:rtk-users@openrtk.org">rtk-users@openrtk.org</a><br>
<b>Betreff:</b> Re: [Rtk-users] SART with Elekta Dataset<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt">Hi Daniel,<br>
<br>
Welcome to RTK. It's always a pleasure to have new people
around.<br>
Your problem is a frequently encountered issue with SART: your
reconstruction volume is too small, and some of the object
lies outside of it. <br>
<br>
Another user recently had a similar issue, so I'll copy/paste
what I wrote for her : <br>
An intuitive way to understand this is the following: the
algorithm tries to "explain" the attenuation it sees on the
projections. If the data has been partially truncated, some
rays have "extra attenuation" that has to go somewhere in the
reconstructed volume. The center of the reconstructed volume
is constrained by all the other rays, so this "extra
attenuation" is pushed to the borders (or the corners). If, on
the other hand, the reconstructed volume is large enough, this
"extra attenuation" can go where it belongs, and does not
cause hyper attenuation on the borders.<br>
<br>
I've run the same command as you with spacing 2, and it gives
a nice reconstruction result (except for the border artifacts
on the bottom of the phantom, caused by the exact same
phenomenon, which you can get rid of by increasing the
reconstructed volume's size again). So just make sure your
object is fully contained in the reconstructed volume, and it
should work.<br>
<br>
Best regards,<br>
Cyril<br>
<br>
<o:p></o:p></p>
<div>
<p class="MsoNormal">On 08/14/2014 11:46 AM, Schoenke, Daniel
wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Calibri","sans-serif"">Hello,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Calibri","sans-serif"">I´ve
just begun to work with RTK. <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Calibri","sans-serif"">Question:
Why do I get strange results for the SART reco with the
Elekta dataset?<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Calibri","sans-serif"">My
commands:<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Calibri","sans-serif"">rtkelektasynergygeometry
--image_db ../../../elekta/elekta/IMAGE.DBF --frame_db
../../../elekta/elekta/FRAME.DBF --dicom_uid
1.3.46.423632.135428.1351013645.166 -o elektaGeometry<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Calibri","sans-serif"">rtksart
-g elektaGeometry -p
../../../elekta/elekta/img_1.3.46.423632.135428.1351013645.166/
-r .*.his -o sart.elekta.mha --verbose --spacing 1
--dimension 128<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Calibri","sans-serif"">One
slice of the result:<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Calibri","sans-serif""><img
moz-do-not-send="true" id="_x0000_i1025"
src="cid:7a88d6f7-52d2-4b5c-bd5f-534b77cd64c2"
height="32" width="32"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Calibri","sans-serif"">With
rtkfdk its working fine (like in the wiki).<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Calibri","sans-serif"">Can
you help me please?<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Calibri","sans-serif"">Thanks.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Calibri","sans-serif"">Daniel<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
</div>
<p class="MsoNormal"><br>
<br>
<br>
<o:p></o:p></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>Rtk-users mailing list<o:p></o:p></pre>
<pre><a moz-do-not-send="true" href="mailto:Rtk-users@public.kitware.com">Rtk-users@public.kitware.com</a><o:p></o:p></pre>
<pre><a moz-do-not-send="true" href="http://public.kitware.com/mailman/listinfo/rtk-users">http://public.kitware.com/mailman/listinfo/rtk-users</a><o:p></o:p></pre>
</blockquote>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<pre>-- <o:p></o:p></pre>
<pre>--<o:p></o:p></pre>
<pre>Cyril Mory, Post-doc<o:p></o:p></pre>
<pre>CREATIS<o:p></o:p></pre>
<pre>Leon Berard cancer treatment center<o:p></o:p></pre>
<pre>28 rue Laënnec<o:p></o:p></pre>
<pre>69373 Lyon cedex 08 FRANCE<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Mobile: +33 6 69 46 73 79<o:p></o:p></pre>
</div>
</blockquote>
<br>
<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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