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Hi David,</div>
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No luck with "buildAndDumpLabeledImage". I implemented as <br>
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/gate/phantom/geometry/buildAndDumpLabeledImage data/Cropped_kidneyContour_binary.mhd<br>
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but there was no associated output.</div>
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I assume this is the correct usage as suggested by the --qt viewer.</div>
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Regards,</div>
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Matthew<br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> David Sarrut <David.Sarrut@creatis.insa-lyon.fr><br>
<b>Sent:</b> March 2, 2020 11:56 AM<br>
<b>To:</b> Matthew Strugari <matthew.strugari@dal.ca>; David Boersma <david.boersma@medaustron.at><br>
<b>Subject:</b> Re: [Gate-users] Potential bug in units to materials conversion</font>
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<div>Hi Matthew, <br>
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<div>quick idea: try "buildAndDumpLabeledImage" to see what happens ... <br>
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<div>DavidB : any idea ? <br>
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<div>Thanks, <br>
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<div>David<br>
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<div dir="ltr" class="x_gmail_attr">On Mon, Mar 2, 2020 at 4:33 PM Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca">matthew.strugari@dal.ca</a>> wrote:<br>
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Hi everyone,</div>
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As a followup to my previous email, it appears that the bug affects voxelized simulation results. After allowing the simulation to run to completion, the dose distribution due to 40 million Y-90 primaries does not show any back-scatter effects at the air-water
interface. I have attached an image which highlights a couple regions showing the extension of dose into "air". The dose decreases smoothly with distance from the source despite crossing the boundary.
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I use the following lines to define my voxelized phantom:<br>
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<span>/gate/world/daughters/name phantom<br>
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<div>/gate/world/daughters/insert ImageNestedParametrisedVolume<br>
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<div>/gate/phantom/geometry/setImage data/Cropped_kidneyContour_binary.mhd<br>
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<div>/gate/phantom/geometry/TranslateTheImageAtThisIsoCenter 0 0 0 mm<br>
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<span>/gate/phantom/geometry/setRangeToMaterialFile data/KidneyAttenuationRange.dat</span></div>
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<br>
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I have also changed the attenuation range to overlap with values near 0 and 1 in case of any floating point errors to no avail. If anyone sees any mistakes in my phantom definition or has encountered similar issues, please let me know. I am not sure what to
do about this.</div>
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Regards,</div>
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Matthew<br>
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<div id="x_gmail-m_-5033725829893929921divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Gate-users <<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a>>
on behalf of Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca" target="_blank">matthew.strugari@dal.ca</a>><br>
<b>Sent:</b> February 28, 2020 12:43 PM<br>
<b>To:</b> <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">
gate-users@lists.opengatecollaboration.org</a> <<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>><br>
<b>Subject:</b> [Gate-users] Potential bug in units to materials conversion</font>
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Dear gate-users,</div>
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There appears to be an issue when defining the associated material for each voxel in an image. I have loaded a binary image with the units to materials conversion defined in a AttenuationRange.dat file:</div>
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<span>2<br>
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<div>0 0 worldDefaultAir<br>
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<span>1 1 Water</span></div>
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<span>I have also set the world material as worldDefaultAir resulting in a total of two defined materials throughout my entire simulation. When executing my macro, there is a message stating that 3 materials are in the image:</span></div>
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<span><span>[Volume-1] Number of different materials in the image data/Cropped_contour_binary.mhd : 3<br>
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<div>[Physic-1] <br>
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<div>[Physic-1] ----------------------------------------------------------<br>
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<div>[Physic-1] Ionization potential <br>
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<div>[Physic-1] - worldDefaultAir defaut value: I = 85.7031 eV <br>
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<div>[Physic-1] - Air defaut value: I = 85.6694 eV <br>
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<div>[Physic-1] - Water defaut value: I = 68.9984 eV <br>
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<span>[Physic-1] ----------------------------------------------------------</span><br>
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<span></span>Has anyone else noticed this issue? I don't know if it's possible to verify what voxels are assigned to what material. It would be nice to see the total number of voxels assigned to a given material at run time.</div>
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Best,<br>
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<p style="margin-top:0px; margin-bottom:0px"><span style="font-family:Calibri,Helvetica,sans-serif">Matthew</span></p>
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<p style="margin-top:0px; margin-bottom:0px"><span style="font-size:10.5pt; color:black; font-family:Calibri,Helvetica,sans-serif">--</span></p>
<span style="font-family:Calibri,Helvetica,sans-serif"></span>
<p style="margin-top:0px; margin-bottom:0px"><span style="font-size:10.5pt; color:black; font-family:Calibri,Helvetica,sans-serif">Matthew Strugari</span><span style="font-size:10.5pt; color:black"></span></p>
<span style="font-family:Calibri,Helvetica,sans-serif"></span><span style="font-size:10.5pt; color:black" lang="EN-US"><span style="font-family:Calibri,Helvetica,sans-serif">Biomedical Translational Imaging Centre -
</span><span style="background-color:rgb(255,255,255); color:black; font-family:Calibri,Helvetica,sans-serif">BIOTIC</span><span style="font-family:Calibri,Helvetica,sans-serif">,</span><br>
<span style="font-family:Calibri,Helvetica,sans-serif">5890 University Ave, </span><br>
<span style="font-family:Calibri,Helvetica,sans-serif">Halifax, NS, B3K 6R8</span></span><br>
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<div dir="ltr">David Sarrut, Phd<br>
Directeur de recherche CNRS<br>
CREATIS, UMR CNRS 5220, Inserm U1206
<div>Centre de lutte contre le cancer Léon Bérard<br>
28 rue Laënnec, 69373 Lyon cedex 08<br>
Tel : 04 78 78 51 51 / 06 74 72 05 42<br>
<a href="http://www.creatis.insa-lyon.fr/~dsarrut" target="_blank">http://www.creatis.insa-lyon.fr/~dsarrut</a><br>
_________________________________</div>
<div> "2 + 2 = 5, for extremely large values of 2"<br>
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