<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear Steven,<div class=""><br class=""></div><div class="">First, you are using correctly the stl to create a tesselated geometry of a heart.</div><div class=""><br class=""></div><div class="">But you are using a voxel source. A voxel source is intended for voxel geometries.</div><div class=""><br class=""></div><div class="">Instead here is what you should do:</div><div class="">- use a GPS source with, shape, volume, energy, etc… For example a simple cube</div><div class="">- attach it to the heart as you did (you can skip this if your heart will not move during the simulation)</div><div class="">- place it correctly with respect to the STL coordinates (check with visu like OGL)</div><div class="">- confine the source to heart: this final step is a trick to restrict the shape (cube) to the exact heart STL shape. So it is important that your simple shape (Cube, Sphere) is as close as possible but bigger than your heart.</div><div class=""><br class=""></div><div class="">For your second question, it could take a lot of time due to a side effect of your not correct source definition.</div><div class=""><br class=""></div><div class="">Best regards,</div><div class=""> Maxime Chauvin</div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 12 May 2020, at 06:24, Steven Marsh <<a href="mailto:steven.marsh@canterbury.ac.nz" class="">steven.marsh@canterbury.ac.nz</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0);"><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">Hi<o:p class=""></o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p class=""> </o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">Perhaps one of you can assist me…<o:p class=""></o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p class=""> </o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">My aim is to import, into my simulation, anatomy (in stl format – though I can change this if necessary) and fill the heart with Tc-99m. I want to assign a total amount of activity to the heart volume – i.e. ideally GATE will evenly spread the activity within the heart.<o:p class=""></o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p class=""> </o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">I have imported the anatomy - via the following:<o:p class=""></o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"> <o:p class=""></o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">/gate/phantom/daughters/name heart<o:p class=""></o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">/gate/phantom/daughters/insert tessellated<o:p class=""></o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">/gate/heart/geometry/setPathToSTLFile data/Heart.stl<o:p class=""></o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">/gate/heart/setMaterial Heart<o:p class=""></o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p class=""> </o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p class=""> </o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">And I have hopefully filled the heart with Tc-99m via the following:<o:p class=""></o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p class=""> </o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">/gate/source/addSource source voxel<o:p class=""></o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">/gate/source/source/gps/particle gamma<o:p class=""></o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">/gate/source/source/gps/type Volume<o:p class=""></o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">/gate/source/source/gps/angtype iso<o:p class=""></o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">/gate/source/source/gps/energytype UserSpectrum<o:p class=""></o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">/gate/source/source/gps/setSpectrumFile data/energy_spectrum_Tc99m.txt<o:p class=""></o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">/gate/source/source/setForcedHalfLife 21624.12 s #6.0 hrs<o:p class=""></o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">/gate/source/source/setActivity 0.001 MBq<o:p class=""></o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">/gate/source/source/attachTo heart<o:p class=""></o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p class=""> </o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">This (in addition to other code not given above) runs.<o:p class=""></o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p class=""> </o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">My questions are:<o:p class=""></o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p class=""> </o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">Firstly - is the above doing what I am hoping it will do? Will this spread 0.001MBq evenly throughout the heart volume? <o:p class=""></o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p class=""> </o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">Secondly - my code is running - though it is taking a very long time and is reporting it is up to run 4973100 with an elapsed time of 0.01 or so- does this relate to the release of primary photons - ie appx 5e6 photons have been released and tracked??<o:p class=""></o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p class=""> </o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">Any advice much appreciated<o:p class=""></o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;"><o:p class=""> </o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">Best wishes<o:p class=""></o:p></div><div class="" style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">Steve<o:p class=""></o:p></div></div><span class="" style="caret-color: rgb(0, 0, 0); float: none; display: inline !important;">_______________________________________________</span><br class="" style="caret-color: rgb(0, 0, 0);"><span class="" style="caret-color: rgb(0, 0, 0); float: none; display: inline !important;">Gate-users mailing list</span><br class="" style="caret-color: rgb(0, 0, 0);"><a href="mailto:Gate-users@lists.opengatecollaboration.org" class="" style="color: rgb(149, 79, 114);">Gate-users@lists.opengatecollaboration.org</a><br class="" style="caret-color: rgb(0, 0, 0);"><a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" class="" style="color: rgb(149, 79, 114);">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a></div></blockquote><div class=""><br class=""></div></div></div><div style=""><br class=""><blockquote type="cite" class=""><div class="">On 12 May 2020, at 06:24, Steven Marsh <<a href="mailto:steven.marsh@canterbury.ac.nz" class="">steven.marsh@canterbury.ac.nz</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Perhaps one of you can assist me…<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">My aim is to import, into my simulation, anatomy (in stl format – though I can change this if necessary) and fill the heart with Tc-99m. I want to assign a total amount of activity to the heart volume – i.e. ideally GATE will evenly spread the activity within the heart.<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I have imported the anatomy - via the following:<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <span class="Apple-converted-space"> </span><o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">/gate/phantom/daughters/name heart<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">/gate/phantom/daughters/insert tessellated<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">/gate/heart/geometry/setPathToSTLFile data/Heart.stl<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">/gate/heart/setMaterial Heart<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">And I have hopefully filled the heart with Tc-99m via the following:<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">/gate/source/addSource source voxel<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">/gate/source/source/gps/particle gamma<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">/gate/source/source/gps/type Volume<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">/gate/source/source/gps/angtype iso<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">/gate/source/source/gps/energytype UserSpectrum<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">/gate/source/source/gps/setSpectrumFile data/energy_spectrum_Tc99m.txt<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">/gate/source/source/setForcedHalfLife 21624.12 s #6.0 hrs<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">/gate/source/source/setActivity 0.001 MBq<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">/gate/source/source/attachTo heart<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">This (in addition to other code not given above) runs.<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">My questions are:<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Firstly - is the above doing what I am hoping it will do? Will this spread 0.001MBq evenly throughout the heart volume? <o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Secondly - my code is running - though it is taking a very long time and is reporting it is up to run 4973100 with an elapsed time of 0.01 or so- does this relate to the release of primary photons - ie appx 5e6 photons have been released and tracked??<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Any advice much appreciated<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Best wishes<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Steve<o:p class=""></o:p></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Gate-users mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><a href="mailto:Gate-users@lists.opengatecollaboration.org" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">Gate-users@lists.opengatecollaboration.org</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a></div></blockquote></div><br class=""></body></html>