<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" style="display:none;"> P {margin-top:0;margin-bottom:0;} </style>
</head>
<body dir="ltr">
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Hi everyone,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
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.
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
I use the following lines to define my voxelized phantom:<br>
</div>
<blockquote style="margin-top: 0px; margin-bottom: 0px;">
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span>/gate/world/daughters/name phantom<br>
</span>
<div>/gate/world/daughters/insert ImageNestedParametrisedVolume<br>
</div>
<div>/gate/phantom/geometry/setImage data/Cropped_kidneyContour_binary.mhd<br>
</div>
<div>/gate/phantom/geometry/TranslateTheImageAtThisIsoCenter 0 0 0 mm<br>
</div>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span>/gate/phantom/geometry/setRangeToMaterialFile data/KidneyAttenuationRange.dat</span></div>
</blockquote>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
<span></span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
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>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Regards,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Matthew<br>
</div>
<div>
<div id="appendonsend"></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Gate-users <gate-users-bounces@lists.opengatecollaboration.org> on behalf of Matthew Strugari <matthew.strugari@dal.ca><br>
<b>Sent:</b> February 28, 2020 12:43 PM<br>
<b>To:</b> gate-users@lists.opengatecollaboration.org <gate-users@lists.opengatecollaboration.org><br>
<b>Subject:</b> [Gate-users] Potential bug in units to materials conversion</font>
<div> </div>
</div>
<div dir="ltr">
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
Dear gate-users,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
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>
<blockquote style="margin-top:0px; margin-bottom:0px">
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<span>2<br>
</span>
<div>0 0 worldDefaultAir<br>
</div>
<span>1 1 Water</span></div>
</blockquote>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<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>
<blockquote style="margin-top:0px; margin-bottom:0px">
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<span><span>[Volume-1] Number of different materials in the image data/Cropped_contour_binary.mhd : 3<br>
</span>
<div>[Physic-1] <br>
</div>
<div>[Physic-1] ----------------------------------------------------------<br>
</div>
<div>[Physic-1] Ionization potential <br>
</div>
<div>[Physic-1] - worldDefaultAir defaut value: I = 85.7031 eV <br>
</div>
<div>[Physic-1] - Air defaut value: I = 85.6694 eV <br>
</div>
<div>[Physic-1] - Water defaut value: I = 68.9984 eV <br>
</div>
<span>[Physic-1] ----------------------------------------------------------</span><br>
</span></div>
</blockquote>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<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>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
Best,<br>
</div>
<div id="x_Signature">
<div id="x_divtagdefaultwrapper" dir="ltr" style="font-size:12pt; color:#000000; background-color:#ffffff; font-family:Calibri,Arial,Helvetica,sans-serif">
<p style="margin-top: 0px; margin-bottom: 0px;margin-top:0px; margin-bottom:0px">
<span style="font-family:Calibri,Helvetica,sans-serif">Matthew</span></p>
<span style="font-family:Calibri,Helvetica,sans-serif"></span>
<p style="margin-top: 0px; margin-bottom: 0px;margin-top:0px; margin-bottom:0px">
</p>
<span style="font-family:Calibri,Helvetica,sans-serif"></span>
<p class="x_x_MsoNormal" style="margin-top: 0px; margin-bottom: 0px;margin-top:0px; margin-bottom:0px">
<span style="font-size:10.5pt; color:black; font-family:Calibri,Helvetica,sans-serif"><br>
</span></p>
<span style="font-family:Calibri,Helvetica,sans-serif"></span>
<p class="x_x_MsoNormal" style="margin-top: 0px; margin-bottom: 0px;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 class="x_x_MsoNormal" style="margin-top: 0px; margin-bottom: 0px;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 class="x_markcp47xw9my" 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>
<p style="margin-top: 0px; margin-bottom: 0px;margin-top:0px; margin-bottom:0px">
</p>
</div>
</div>
</div>
</div>
</body>
</html>