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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Hi Matthew,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><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;mso-fareast-language:EN-US">I am not at all an expert for dicom files as I am mainly working with “interfile” file format. But I had similar problems,
when I tried to use voxelized geometry and source with Gate in interfile format. I guess in both cases, there are some small differences in either my interfile header or in some of your dicom tags compared to what Gate wants as an input.
<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;mso-fareast-language:EN-US">For now, I simply use the mhd format instead and had no problems anymore. There are many ways (and softwares) to convert
file formats. You could for example use amide (<a href="http://amide.sourceforge.net/index.html">http://amide.sourceforge.net/index.html</a>), which is free, to convert your dicom file into a raw image and then simply create the mhd header textfile with your
image parameters. <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;mso-fareast-language:EN-US">The NAME.mhd requires these lines:<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;mso-fareast-language:EN-US"><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;mso-fareast-language:EN-US">NDims = 3<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;mso-fareast-language:EN-US">DimSize = 512 512 1028<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;mso-fareast-language:EN-US">ElementSpacing = 0.14 0.14 0.14
<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;mso-fareast-language:EN-US">ElementNumberOfChannels = 1<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;mso-fareast-language:EN-US">ElementByteOrderMSB = False<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;mso-fareast-language:EN-US">ElementType = MET_FLOAT<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;mso-fareast-language:EN-US">ElementDataFile = NAMEofIMAGE.raw<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;mso-fareast-language:EN-US"><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;mso-fareast-language:EN-US">I hope this workaround works for you too!<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;mso-fareast-language:EN-US"><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;mso-fareast-language:EN-US">Best,<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;mso-fareast-language:EN-US">Julia<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;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">Von:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Gate</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">-users
<gate-users-bounces@lists.opengatecollaboration.org> <b>Im Auftrag von </b>Matthew Strugari<br>
<b>Gesendet:</b> Dienstag, 29. Oktober 2019 17:45<br>
<b>An:</b> gate-users@lists.opengatecollaboration.org<br>
<b>Betreff:</b> [Gate-users] DICOM parameters appear incorrect<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black">Hi all,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black">I am attempting to implement a voxelized phantom and voxelized source for a study on Y90 radioembolization. To prepare my dicom data I had to stitch together 3 datasets which I
suspect may be causing some issues. Regardless, when I import the dicom data into GATE using the commands below, a number of the image parameters appear incorrect when compared to the metadata (see attached image). For example, the original image is 512x512x1028
while GATE states the matrix size as 71.68x71.68x1028 and resolution as 512x512x1028. Also, the voxel size is incorrect as it should be 0.14 mm isotropically which causes the loaded image to appear incorrect when I include the patient-HU2mat.txt file.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black">From what I can tell, my input dicom file appears okay but I am not sure what modifications are required to successfully load the dicom data. Any suggestions would be greatly appreciated.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black">Thank you,<o:p></o:p></span></p>
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<p style="background:white"><span style="font-family:"Calibri",sans-serif;color:black">Matthew<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri",sans-serif;color:black"># Voxelized phantom<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Calibri",sans-serif;color:black">/gate/world/daughters/name patient<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Calibri",sans-serif;color:black">/gate/world/daughters/insert ImageNestedParametrisedVolume<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Calibri",sans-serif;color:black">/gate/patient/geometry/setImage kidneyData/patient.dcm<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri",sans-serif;color:black">#/gate/patient/geometry/setHUToMaterialFile kidneyData/patient-HU2mat.txt<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="xmsonormal" style="background:white"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="xmsonormal" style="background:white"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">--</span><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
<p class="xmsonormal" style="background:white"><span style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">Matthew Strugari</span><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-size:10.5pt;font-family:"Calibri",sans-serif;color:black">Biomedical Translational Imaging Centre -
<span class="markcp47xw9my"><span style="background:white">BIOTIC</span></span>,<br>
5890 University Ave, <br>
Halifax, NS, B3K 6R8</span><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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