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<p class="MsoNormal">Dear all,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am trying to work with Elastix (<a href="http://elastix.isi.uu.nl">http://elastix.isi.uu.nl</a>) and therefore need to convert structure sets from DICOM RT-STRUCT files to the proper format accepted by Elastix. Elastix seems to require
files with a metaimage format in .mhd/.raw format.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">On my search on the internet I found an older thread in this e-mail list referencing a tool (part of vv) to convert RT-STRUCT files to the required format (<a href="https://www.creatis.insa-lyon.fr/pipermail/vv/2013-February/000285.html">https://www.creatis.insa-lyon.fr/pipermail/vv/2013-February/000285.html</a>).<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I got the Docker container running as suggested per <a href="https://www.creatis.insa-lyon.fr/rio/vv?action=show&redirect=VV#line-109">
https://www.creatis.insa-lyon.fr/rio/vv?action=show&redirect=VV#line-109</a> on Windows 7 using the following:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> docker pull tbaudier/vv<o:p></o:p></p>
<p class="MsoNormal"> docker run –name vv -e DISPLAY= $(docker-machine ip):0 -v $(pwd):/home tbaudier/vv<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">in combination with XMing running with the following command line (had to add the –ac switch to the default command line)<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> Xming.exe :0 -ac -clipboard –multiwindow<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">After that I am able to start the container and run vv in a X11 terminal on Windows 7. Besides I am able to attach a shell:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> docker exec -it vv /bin/bash<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">From that I can run the command line tools. But when I try to extract data from my RT-STRUCT file like this:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">p=P0162C0006I13345846;<o:p></o:p></p>
<p class="MsoNormal">rtstruct=RTSTRUCT/1.2.246.352.71.2.78480665410.4114624.20161221081018/RTSTRUCT.1.2.246.352.71.4.78480665410.142535.20161221114758.dcm;<o:p></o:p></p>
<p class="MsoNormal">ct=CT/1.3.6.1.4.1.32722.162.6.55613550350070884234080940853841385982/CT.1.3.6.1.4.1.32722.162.6.98938198109550082302924371538367888818.dcm;<o:p></o:p></p>
<p class="MsoNormal">d=/home/DICOM;<o:p></o:p></p>
<p class="MsoNormal">params=-v<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">clitkDicomRTStruct2Image $params \<o:p></o:p></p>
<p class="MsoNormal">-i $d/$p/$rtstruct \<o:p></o:p></p>
<p class="MsoNormal">-j $d/$p/$ct \<o:p></o:p></p>
<p class="MsoNormal">-o $d/$p/test.mhd<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I seem to run into issues, as clitkDicomRTStruct2Image seems to, consequently, return correct .mhd files, but .raw with a size of 256kB that contain only NULL values (512 * 512 * 1 = 262144).<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I would have expected to have some data in it as the RT-STRUCT file does contain contours. Even if I extract a specific contour for all slices of the CT set referenced from the RT-STRUCT I seem to get no data in any file.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Am I doing something wrong? Am I expecting something wrong?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Kind regards,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Jonathan<o:p></o:p></p>
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