<div dir="ltr">Hi Cassandra,<br><br> Thank you for your mail.<br><br> I have tried the 'forbid' command, as you suggested. To start with I have been attempting the simple case of a cold region inside hot source - <br><br>##########################################################<br><br>/gate/world/daughters/name cold_area<br>/gate/world/daughters/insert cylinder<br>/gate/cold_area/setMaterial Air<br>/gate/cold_area/vis/forceWireframe<br>/gate/cold_area/vis/setColor green<br>/gate/cold_area/geometry/setRmax 50.0 mm<br>/gate/cold_area/geometry/setRmin 0.0 mm<br>/gate/cold_area/geometry/setHeight 52. mm<br>/gate/cold_area/placement/setTranslation 0. 0. 0. cm<br><br>/gate/run/initialize # placed here according to the manual<br><br>/gate/source/addSource mother_S<br>/gate/source/mother_S/setActivity 10.0 muCi<br>/gate/source/mother_S/gps/particle gamma<br>/gate/source/mother_S/setType backtoback<br>/gate/source/mother_S/gps/energytype Mono<br>/gate/source/mother_S/gps/monoenergy 0.511 MeV<br>/gate/source/mother_S/setForcedUnstableFlag true<br>/gate/source/mother_S/setForcedHalfLife 50 s<br>/gate/source/mother_S/gps/type Volume<br>/gate/source/mother_S/gps/shape Cylinder<br>/gate/source/mother_S/gps/radius 90. mm<br>/gate/source/mother_S/gps/halfz 26.0 mm<br>/gate/source/mother_S/gps/centre 0. 0. 0. cm<br><b>/gate/source/mother_S/gps/Forbid cold_area_phys </b># extra '_phys' is attached because in terminal cold_area is termed as cold_area_phys<br>/gate/source/mother_S/dump 1<br>/gate/source/mother_S/visualize 5000 blue 10<br><br>##########################################################.<br><br> The code runs without error, but the <b>source point visualization with ROOT</b> (file attached) and <b>STIR reconstructed image</b> (file attached) shows <b>activity in the forbidden area.<br></b><br> The Bin_GATE_v1.0.c code shows <b>same number of coincidences in two root files</b> with 'forbid' command commented and uncommented.<br><br> Interestingly, the<b> 'forbid' command indeed pings its presence </b>when I have defined the cold cylinder radius to be <b>equal</b> to mother source cylinder radius in this way - <br><br>##########################################################<br><br>[G4-cerr] <br>-------- EEEE ------- G4Exception-START -------- EEEE -------<br>*** G4Exception : GenerateOne<br> issued by : GateSPSPosDistribution::GenerateOne<br>1000000 primaries were always generated in forbidden volumes !<br> It seems that all sources are forbidden.<br>*** Fatal Exception *** core dump ***<br>-------- EEEE -------- G4Exception-END --------- EEEE -------<br><br>########################################################## <br><br>Is there any <b>MISTAKE</b> that I have made in implementation code? Finally, like to mention that I am using <b>GATE 8.0</b> in case there is any issue of<b> bug</b>.<br><br>Thanking you,<br><br>Satyajit Ghosh<div>Phd student</div><div>Department of Physics </div><div>IIT Bombay, Mumbai</div><div>INDIA</div><div>16-Nov.-2019<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Nov 14, 2019 at 9:34 AM Cassandra Miller <<a href="mailto:cassandramiller@phas.ubc.ca">cassandramiller@phas.ubc.ca</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF">
<p>Hi Satyajit,</p>
<p>Have you tried defining a cold source? You can use the "forbid"
command, for example:</p>
<p>/gate/world/daughters/name cold_area
<br>
/gate/world/daughters/insert cylinder
<br>
/gate/cold_area/vis/forceWireframe<br>
/gate/cold_area/vis/setColor green
<br>
/gate/cold_area/geometry/setRmax 3.0 cm
<br>
/gate/cold_area/geometry/setHeight 1. cm </p>
<p>/gate/source/addSource number1<br>
/gate/source/number1/setActivity 100000. becquerel<br>
/gate/source/number1/gps/particle gamma
<br>
/gate/source/number1/setType backtoback
<br>
/gate/source/number1/gps/type Volume
<br>
/gate/source/number1/gps/shape Cylinder
<br>
/gate/source/number1/gps/radius 5. cm
<br>
/gate/source/number1/gps/halfz 0.5 cm
<br>
/gate/source/number1/gps/centre 0. 0. 0. cm<br>
/gate/source/number1/gps/monoenergy 511. keV
<br>
/gate/source/number1/gps/angtype iso
<br>
<b>/gate/source/number1/gps/Forbid cold_area
</b><br>
/gate/source/number1/dump 1
<br>
</p>
<p>It might work if when you define your background, you forbid the
area where the hot rods are, and then you define your hot rods
separately as you are already doing. I'm not sure if it will fix
your problem but it's worth a shot. Then you also can define the
rods with whatever activity you want, without having to take into
account the background.<br>
<br>
</p>
<p>Best,<br>
Cassandra Miller<br>
PhD Student<br>
Quantitative Tomography Lab & Medical Imaging Research Group<br>
Department of Physics & Astronomy, University of British
Columbia<br>
</p>
<p><br>
</p>
<div>On 2019-11-13 8:54 a.m., Satyajit Ghosh
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Dear GATE users,
<div><br>
</div>
<div> I am trying to define an activity
distribution of four circular hot rods with a backgrodeund (of
ratio 1:2 wrt hot region) using analytic definition of source
(not voxelized definition). I know that the 'setActivity'
command basically assigns a certain amount of activity inside
a the defined volume. Naturally the background volume is
needed to be defined as universal volume containing four
volumes for hot rods. After assigning the appropriate activity
values in 5 volumes (4 hot rods and one background), I am not
getting desired hot to background ratio in STIR reconstructed
image of GATE data. Please note that I have set the activity
of individual hot rods considering contribution from
background activity. <b>I believe the reason of not getting
desired result can be the fact that one can't define
overlapping source volumes. Is this correct?</b> If not then
how do I define an activity distribution with a background
using analytic definition of source.</div>
<div><br>
</div>
<div>Satyajit Ghosh</div>
<div>Phd student</div>
<div>Physics Department</div>
<div>IIT Bombay, Mumbai</div>
<div>13-Nov.2019<br>
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<div dir="ltr"><font face="arial,
sans-serif"><b>Satyajit Ghosh</b></font></div>
<div dir="ltr">
<div><font face="arial, sans-serif"><b>PhD
Student</b></font></div>
<div><font face="arial, sans-serif"><b>Nuclear
Spectroscopy and Molecular
Imaging Lab,<br>
</b></font>
<div><font face="arial,
sans-serif"><b>Physics
Department, IIT Bombay,</b></font></div>
</div>
<div><font face="arial, sans-serif"><b>Mumbai-400076,
INDIA</b></font></div>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><font face="arial, sans-serif"><b>Satyajit Ghosh</b></font></div><div dir="ltr"><div><font face="arial, sans-serif"><b>PhD Student</b></font></div><div><font face="arial, sans-serif"><b>Nuclear Spectroscopy and Molecular Imaging Lab,<br></b></font><div><font face="arial, sans-serif"><b>Physics Department, IIT Bombay,</b></font></div></div><div><font face="arial, sans-serif"><b>Mumbai-400076, INDIA</b></font></div></div></div><div dir="ltr"><font face="arial, sans-serif"><b></b></font></div></div></div></div></div></div></div></div></div></div></div></div>