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</o:shapelayout></xml><![endif]--></head><body bgcolor=white lang=DE link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I get one image file (.bin or .nrrd format like data at <a href="http://www5.cs.fau.de/conrad/data/heart/">http://www5.cs.fau.de/conrad/data/heart/</a>) with all projections and a geometry matrix file (same formats available) from the Data Conversion Tool provided by Siemens. Today I get the recommendation to use the CONRAD toolkit for my purpose because it´s adapted for these data files. So I will at first try to get CONRAD. If this shall not work I´ll get in touch again. Thanks a lot!<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Daniel</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></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'>Von:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext'> Cyril Mory [mailto:cyril.mory@creatis.insa-lyon.fr] <br><b>Gesendet:</b> Montag, 18. August 2014 16:52<br><b>An:</b> Schoenke, Daniel; rtk-users@openrtk.org<br><b>Betreff:</b> Re: AW: [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>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 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<o:p></o:p></p><div><p class=MsoNormal>On 08/15/2014 04:16 PM, Schoenke, Daniel wrote:<o:p></o:p></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks!</span><o:p></o:p></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>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…)</span><o:p></o:p></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Again thanks a lot and have a nice weekend!</span><o:p></o:p></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Daniel</span><o:p></o:p></p><p class=MsoNormal><span lang=EN-US> </span><o:p></o:p></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext'>Von:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext'> Cyril Mory [<a 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 href="mailto:rtk-users@openrtk.org">rtk-users@openrtk.org</a><br><b>Betreff:</b> Re: [Rtk-users] SART with Elekta Dataset</span><o:p></o:p></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><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,</span><o:p></o:p></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. </span><o:p></o:p></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?</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif"'>My commands:</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif"'> </span><o:p></o:p></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</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif"'> </span><o:p></o:p></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</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif"'> </span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif"'>One slice of the result:</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif"'> </span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif"'><img border=0 width=32 height=32 id="_x0000_i1025" src="cid:7a88d6f7-52d2-4b5c-bd5f-534b77cd64c2"></span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif"'> </span><o:p></o:p></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).</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif"'>Can you help me please?</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif"'>Thanks.</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif"'>Daniel</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif"'> </span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif"'> </span><o:p></o:p></p></div><p class=MsoNormal><br><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 href="mailto:Rtk-users@public.kitware.com">Rtk-users@public.kitware.com</a><o:p></o:p></pre><pre><a 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><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></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></body></html>