<html><head></head><body><div class="ydp3246d4a8yahoo-style-wrap" style="font-family:times new roman, new york, times, serif;font-size:16px;"><div><div dir="ltr" data-setdir="false">Hi,</div><div dir="ltr" data-setdir="false">This response might be late. And I am not sure if you found the solution.</div><div dir="ltr" data-setdir="false">I just want to share my experience on creating voxelized phantom from CT image, using GATE 7.2 back then. I experienced the same error and thought that was nothing to do with the image format since GATE 7.2 accept the uint or int image. I was using Analyze or Interfile format during that time since 7.2 version was not able to accept Dicom.</div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">The error occurred because the CT image and the HU calibration txt does not have the same min or max HU. In your case, GATE detected the HU of -1000, however, in HU calibration txt, the min HU started at higher than -1000. Therefore, GATE was not able to define and calibrate the HU less than -1000.</div><div dir="ltr" data-setdir="false">Whether you can rescale back the CT image according to the HU calibration txt or vice versa, the problem will be solved.</div><div dir="ltr" data-setdir="false"><br></div><div dir="ltr" data-setdir="false">Good luck.</div><div><br></div><div class="ydp3246d4a8signature"><div><font color="#00007f" face="bookman old style, new york, times, serif"></font> </div><div style="font-size:13px;"><br><br></div></div></div>
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On Friday, December 18, 2020, 06:39:01 AM GMT+8, Bryan McIntosh <mcintoshster@gmail.com> wrote:
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<div><div id="yiv7940788375"><div dir="ltr"><div>Hi everyone,</div><div><br></div><div>I am working on a side project to do some HDR brachytherapy dosimetry in GATE 8.2, and am having a very difficult time creating a voxelized phantom based on the DICOM CT data of our prostate phantom. However, as my simulation starts I get the following error as the voxelized phantom is turned into an image volume:</div><div><br></div><div>"GateVImageVolume.cc (l.742): I find R=-1000 in the image, while range stop at -1001"<br></div><div><br></div><div>The only reference I could find in the mailing list archives to this was back in 2016, before GATE had DICOM import capability. The same issue happens if I try to import the volume split across multiple files (the default from our planning CT system) or as a single file (using AMIDE to export the multi-file data). I'd rather not change the data to an Interfile format, since GATE won't import Interfile data unless it's an unsigned INT; that would make it pretty difficult to have CT data for the air-equivalent part of the phantom that represents the colon!</div><div><br></div><div>So, has anyone found a way to work around this? Is this fixed in GATE 9.0 and I just need to install the new version, or is there some other fix i need to go through? I'll post the beginning of my macro and system configuration below.<br></div><div><br></div><div>Thanks for your time,</div><div><br></div><div>-Bryan McIntosh</div><div><br></div><div>My configuration:<br></div><div>Linux Mint 19.3<br></div><div>GATE 8.2, GEANT4 10.5.p01, root 6.14, ITK 5.1.2</div><div>Ryzen 7 3700X, 16 GB RAM, Gigabyte X470</div><div><br></div><div>Phantom-defining macro content<br></div><div>------<br></div><div>/gate/geometry/setMaterialDatabase GateMaterials.db<br><br># World<br>/gate/world/geometry/setXLength 3 m<br>/gate/world/geometry/setYLength 3 m<br>/gate/world/geometry/setZLength 3 m<br>/gate/world/setMaterial Air<br><br>#Generate Hounsfield unit table (commented out after 1st run)<br>#/gate/HounsfieldMaterialGenerator/SetMaterialTable data/Schneider2000MaterialsTable.txt<br>#/gate/HounsfieldMaterialGenerator/SetDensityTable data/Schneider2000DensitiesTable.txt<br>#/gate/HounsfieldMaterialGenerator/SetDensityTolerance 0.1 g/cm3<br>#/gate/HounsfieldMaterialGenerator/SetOutputMaterialDatabaseFilename data/patient-HUmaterials.db<br>#/gate/HounsfieldMaterialGenerator/SetOutputHUMaterialFilename data/patient-HU2mat.txt<br>#/gate/HounsfieldMaterialGenerator/Generate<br><br># Voxelized prostate phantom<br># VOXELIZED PHANTOM BASED ON PATIENT DATA<br>/gate/world/daughters/name prostate<br><br>/gate/world/daughters/insert ImageNestedParametrisedVolume<br>/gate/prostate/geometry/setImage data/CT.T111112.1.dcm<br>/gate/geometry/setMaterialDatabase data/patient-HUmaterials.db<br>/gate/prostate/geometry/setRangeToMaterialFile data/patient-HU2mat.dat</div><div><br></div><div><br></div></div></div>_______________________________________________<br>Gate-users mailing list<br><a ymailto="mailto:Gate-users@lists.opengatecollaboration.org" href="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</a><br><a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a></div>
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