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Hi Xinjie,
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<div>I’m not sure what could be causing your issue at this point. It appears to be a problem with your install. Hopefully somebody else might have an idea and can provide their insight.</div>
<div><br>
</div>
<div>My next best suggestion would be to try vGATE and see if your issue occurs there. You could also try setting your material as G4_WATER instead. A more involved approach to determining the issue would involve recompiling GATE with your build type set to
RelWithDebIbfo, then run your code in a debugger such as gdb.<br>
<br>
Regards,<br>
<div dir="ltr">Matthew</div>
<div dir="ltr"><br>
<blockquote type="cite">On Jan 20, 2021, at 11:35 AM, Xinjie Cao <xinjie.cao@stonybrook.edu> wrote:<br>
<br>
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<span style="font-weight:bold;font-size:12px;">CAUTION:</span> The Sender of this email is not from within Dalhousie.</div>
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<div>
<div dir="ltr">Hi Matthew,
<div><br>
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<div>I am using GATE v8.2 and geant4.10.05.p01. Our cluster workstations are with CentOS 7 operating system.</div>
<div><br>
</div>
<div>Best,</div>
<div>Xinjie</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, Jan 19, 2021 at 12:35 PM Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca" target="_blank">matthew.strugari@dal.ca</a>> wrote:<br>
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<p class="MsoNormal"><span lang="EN-US" style="color:black">Hi Xinjie,</span><span style="color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black"> </span><span style="color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black">What version of GATE and Geant4 are you using and what is your operating system? I find no relevant errors when running the simulation with phantom1 as Water.</span><span style="color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black"> </span><span style="color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black">Aside from that, your code could be updated to use the <a href="https://opengate.readthedocs.io/en/latest/setting_up_the_physics.html?highlight=physics%20list#new-physics-list-mechanism" target="_blank"><span style="color:rgb(0,0,106)">new
physics list mechanism</span></a> by replacing your physics section with “/gate/physics/addPhysicsList emstandard_opt4”. Your source definition also contains a few deprecation warnings.</span><span style="color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black"> </span><span style="color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black">Cheers,</span><span style="color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:black">Matthew</span><span style="color:black"><u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
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<p class="MsoNormal" style="margin-bottom:12pt"><b><span style="font-size:12pt;color:black">From:
</span></b><span style="font-size:12pt;color:black">Xinjie Cao <<a href="mailto:xinjie.cao@stonybrook.edu" target="_blank">xinjie.cao@stonybrook.edu</a>><br>
<b>Date: </b>Tuesday, January 19, 2021 at 11:41<br>
<b>To: </b>Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca" target="_blank">matthew.strugari@dal.ca</a>><br>
<b>Subject: </b>Re: [Gate-users] Weird Phantom Warning<u></u><u></u></span></p>
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<p class="MsoNormal" style="line-height:12pt"><b><span style="font-size:9pt;font-family:Arial,sans-serif;color:white">CAUTION:</span></b><span style="font-size:9pt;font-family:Arial,sans-serif;color:white"> The Sender of this email is not from within Dalhousie.<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="color:white">Hi Matthew, </span><u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<div>
<p class="MsoNormal">I did the test as you recommended, there is still an error/warning with only phantom1 as water (no daughter). Also, I checked my GATE material database and I didn't find anything wrong. Here is the database file and a simplified macro,
feel free to try it and let me know if you have any questions or insight. Thank you for you kindly help!<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Best,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Xinjie<u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<div>
<p class="MsoNormal">On Tue, Jan 19, 2021 at 10:11 AM Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca" target="_blank">matthew.strugari@dal.ca</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal">Hi Xenjie, <u></u><u></u></p>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12pt">What happens when you define only phantom1 as water with no daughters? Check the definition of water in your materials database to make sure it’s not a problem there. If that doesn’t give any insight, could you
send a simplified macro with the minimum lines that reproduce your error?<u></u><u></u></p>
<div>
<p class="MsoNormal">Matthew<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><br>
<br>
<u></u><u></u></p>
<blockquote style="margin-top:5pt;margin-bottom:5pt">
<p class="MsoNormal" style="margin-bottom:12pt">On Jan 19, 2021, at 11:01 AM, Xinjie Cao <<a href="mailto:xinjie.cao@stonybrook.edu" target="_blank">xinjie.cao@stonybrook.edu</a>> wrote:<u></u><u></u></p>
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<div>
<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal" style="line-height:12pt"><b><span style="font-size:9pt;font-family:Arial,sans-serif;color:white">CAUTION:</span></b><span style="font-size:9pt;font-family:Arial,sans-serif;color:white"> The Sender of this email is not from within Dalhousie.<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="color:white">Hi Matthew, </span><u></u><u></u></p>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Same error, the error/warning disappears only when I change the phantom 3 material from water to air.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Best,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Xinjie<u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<div>
<p class="MsoNormal">On Tue, Jan 19, 2021 at 7:18 AM Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca" target="_blank">matthew.strugari@dal.ca</a>> wrote:<u></u><u></u></p>
</div>
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<p class="MsoNormal" style="margin-bottom:12pt">What happens when you define phantom 3 as the daughter of phantom 2? It’s still defined as the daughter of phantom 1.<u></u><u></u></p>
<div>
<p class="MsoNormal">Matthew<u></u><u></u></p>
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<div>
<p class="MsoNormal"><br>
<br>
<u></u><u></u></p>
<blockquote style="margin-top:5pt;margin-bottom:5pt">
<p class="MsoNormal" style="margin-bottom:12pt">On Jan 19, 2021, at 12:14 AM, Xinjie Cao <<a href="mailto:xinjie.cao@stonybrook.edu" target="_blank">xinjie.cao@stonybrook.edu</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal" style="line-height:12pt"><b><span style="font-size:9pt;font-family:Arial,sans-serif;color:white">CAUTION:</span></b><span style="font-size:9pt;font-family:Arial,sans-serif;color:white"> The Sender of this email is not from within Dalhousie.<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="color:white">Hi Matthew, </span><u></u><u></u></p>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">I tested another phantom configuration with some modification based on the before version. While the same error/warning showed again once I changed the phantom 3 material from the air to water, is there any rule about the material setting? <u></u><u></u></p>
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<div>
<p class="MsoNormal"><u></u> <u></u></p>
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<div>
<p class="MsoNormal">/gate/world/daughters/name phantom1<br>
/gate/world/daughters/insert cylinder<br>
/gate/phantom1/placement/setTranslation 0.0 0.0 0.0 mm<br>
/gate/phantom1/geometry/setRmax 101.5 mm<br>
/gate/phantom1/geometry/setHeight 700 mm<br>
/gate/phantom1/setMaterial Polyethylene<br>
/gate/phantom1/attachPhantomSD<br>
<br>
/gate/phantom1/daughters/name phantom2<br>
/gate/phantom1/daughters/insert cylinder<br>
/gate/phantom2/placement/setTranslation 0.0 -45.0 0.0 mm<br>
/gate/phantom2/geometry/setRmax 3.2 mm<br>
/gate/phantom2/geometry/setRmin 2.4 mm<br>
/gate/phantom2/geometry/setHeight 700 mm<br>
/gate/phantom2/setMaterial Air<br>
/gate/phantom2/attachPhantomSD<br>
<br>
/gate/phantom1/daughters/name phantom3<br>
/gate/phantom1/daughters/insert cylinder<br>
/gate/phantom3/placement/setTranslation 0.0 -45.0 0.0 mm<br>
/gate/phantom3/geometry/setRmax 1.6 mm<br>
/gate/phantom3/geometry/setHeight 700 mm<br>
/gate/phantom3/setMaterial Air<br>
/gate/phantom3/attachPhantomSD<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Best,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Xinjie<u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<div>
<p class="MsoNormal">On Mon, Jan 18, 2021 at 3:16 PM Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca" target="_blank">matthew.strugari@dal.ca</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal"><span lang="EN-US">You should always set the model dimensions to be exactly equal to the physical dimensions for accurate modelling. From there, check to make sure you do not have any overlapping geometries with the command “/geometry/test/run”
in your macro following “/gate/run/initialize”. If you do have overlapping geometries, GATE will tell you what is overlapping, where it’s overlapping, and by how much.
</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US">In some cases of exact dimensions, I found that abutting geometries required trimming by 1um to avoid overlap warnings, but they are just warnings and should not restrict the simulation from running. I trimmed them for
peace of mind.</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US">Best,</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US">Matthew</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US"> </span><u></u><u></u></p>
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<p class="MsoNormal" style="margin-bottom:12pt"><b><span style="font-size:12pt;color:black">From:
</span></b><span style="font-size:12pt;color:black">Xinjie Cao <<a href="mailto:xinjie.cao@stonybrook.edu" target="_blank">xinjie.cao@stonybrook.edu</a>><br>
<b>Date: </b>Monday, January 18, 2021 at 15:40<br>
<b>To: </b>Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca" target="_blank">matthew.strugari@dal.ca</a>><br>
<b>Cc: </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>Re: [Gate-users] Weird Phantom Warning</span><u></u><u></u></p>
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<p class="MsoNormal" style="line-height:12pt"><b><span style="font-size:9pt;font-family:Arial,sans-serif;color:white">CAUTION:</span></b><span style="font-size:9pt;font-family:Arial,sans-serif;color:white"> The Sender of this email is not from within Dalhousie.</span><u></u><u></u></p>
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<p class="MsoNormal"><span style="color:white">Hi Matthew, </span><u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<div>
<p class="MsoNormal">Thanks! I think I get your point now. One more question about the detailed size of the daughter volume. As for the example you presented in the last email, If the mother cylinder is with a 3.2 mm radius, what is the actual radius should
I define for the following daughter cylinder? Rmax is 3.2 or 3.199 (some number that is very close to 3.2) considering the overlap? Or it doesn't matter?<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">Best,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Xinjie<u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
<div>
<div>
<p class="MsoNormal">On Mon, Jan 18, 2021 at 1:59 PM Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca" target="_blank">matthew.strugari@dal.ca</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal"><span lang="EN-US">Hi Xinjie,</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US">In any geometry definition, it is important to follow these three rules when
<a href="https://opengate.readthedocs.io/en/latest/defining_a_geometry.html?highlight=daughter#building-a-volume" target="_blank">
building a volume</a>:</span><u></u><u></u></p>
<ul type="disc">
<li class="MsoNormal"><span lang="EN-US">A volume which is located inside another must be its daughter</span><u></u><u></u></li><li class="MsoNormal"><span lang="EN-US">A daughter must be fully included in its mother</span><u></u><u></u></li><li class="MsoNormal"><span lang="EN-US">Volumes must not overlap.</span><u></u><u></u></li></ul>
<p class="MsoNormal"><span lang="EN-US">This may require you to get creative with daughter definitions in order to obtain a final geometry representing your physical setup.
</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US">Your geometry does not satisfy these points based on the issues that I previously outlined. If part of your geometry requires polyethylene with a height of 800mm, I would start by defining that size as your mother volume.
You can add on a daughter volume if you need a specific 100 mm region to be replaced with air.
</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US">Consider, for example, that you define a mother polyethylene cylinder with a radius of 3.2 mm. Next, you define a daughter cylinder of air with a radius r of 2.4 <= r(mm) < 3.2 and within that daughter, you define a daughter
cylinder of water with a radius of 0 <= r(mm) < 1.6. The remaining volume between 1.6 <= r(mm) < 2.4 will remain as polyethylene (i.e. there’s no need to redefine a daughter of polyethylene with those dimensions). Try to use that approach when defining your
nested phantoms.</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US">Hth,</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US">Matthew</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US"> </span><u></u><u></u></p>
<div style="border-right:none;border-bottom:none;border-left:none;border-top:1pt solid rgb(181,196,223);padding:3pt 0cm 0cm">
<p class="MsoNormal" style="margin-bottom:12pt"><b><span style="font-size:12pt;color:black">From:
</span></b><span style="font-size:12pt;color:black">Xinjie Cao <<a href="mailto:xinjie.cao@stonybrook.edu" target="_blank">xinjie.cao@stonybrook.edu</a>><br>
<b>Date: </b>Monday, January 18, 2021 at 13:08<br>
<b>To: </b>Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca" target="_blank">matthew.strugari@dal.ca</a>><br>
<b>Cc: </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>Re: [Gate-users] Weird Phantom Warning</span><u></u><u></u></p>
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<p class="MsoNormal" style="line-height:12pt"><b><span style="font-size:9pt;font-family:Arial,sans-serif;color:white">CAUTION:</span></b><span style="font-size:9pt;font-family:Arial,sans-serif;color:white"> The Sender of this email is not from within Dalhousie.</span><u></u><u></u></p>
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<p class="MsoNormal"><span style="color:white">Hi Matthew, </span><u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">Thanks for your remind, how about setting the phantom 3 as the world daughter too to avoid that violation? Because that 800 mm length is according to the NEMA standard, so I am guessing better keep it if it could be solved.<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">For the phantom 3 configuration, I think it is necessary. There is actually an air gap between the inner plastic tube and the outer 200 mm diameter plastic shell according to the standard I believe.<u></u><u></u></p>
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<p class="MsoNormal">Best,<u></u><u></u></p>
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<p class="MsoNormal">Xinjie<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">On Mon, Jan 18, 2021 at 11:58 AM Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca" target="_blank">matthew.strugari@dal.ca</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal"><span lang="EN-US">Hi Xinjie,</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US">It looks like you have issues with overlapping geometries. You could try nesting phantom4 within phantom3 and nest phantom3 within phantom2. Also, is the height of phantom3 correct at 800mm? This does not fit within your
parent volume of phantom1.</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US">Alternatively, is phantom3 even required? It looks like you’re reinserting polystyrene after voiding the region with air in phantom2. This could be avoided by setting Rmin to 2.4mm in phantom2.</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US"> </span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US">Regards,</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US">Matthew</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US"> </span><u></u><u></u></p>
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<p class="MsoNormal" style="margin-bottom:12pt"><b><span style="font-size:12pt;color:black">From:
</span></b><span style="font-size:12pt;color:black">Gate-users <<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a>> on behalf of Xinjie Cao <<a href="mailto:xinjie.cao@stonybrook.edu" target="_blank">xinjie.cao@stonybrook.edu</a>><br>
<b>Date: </b>Monday, January 18, 2021 at 12:38<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] Weird Phantom Warning</span><u></u><u></u></p>
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<p class="MsoNormal" style="line-height:12pt"><b><span style="font-size:9pt;font-family:Arial,sans-serif;color:white">CAUTION:</span></b><span style="font-size:9pt;font-family:Arial,sans-serif;color:white"> The Sender of this email is not from within Dalhousie.</span><u></u><u></u></p>
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<p class="MsoNormal"><span style="color:white">Dear GATE users, </span><u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">I am simulating the count rate performance of some PET scanners, while I found an interesting warning/error when I made a change to the phantom configuration.<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal"><b>With the following simplified phantom configuration, both single thread or cluster tool can run the macro well:</b><u></u><u></u></p>
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<p class="MsoNormal">#==========================<br>
# P H A N T O M<br>
#==========================<br>
<br>
/gate/world/daughters/name phantom1<br>
/gate/world/daughters/insert cylinder<br>
/gate/phantom1/placement/setTranslation 0.0 0.0 0.0 mm<br>
/gate/phantom1/geometry/setRmax 101.5 mm<br>
/gate/phantom1/geometry/setHeight 700 mm<br>
/gate/phantom1/setMaterial Polyethylene<br>
/gate/phantom1/attachPhantomSD<br>
<br>
/gate/phantom1/daughters/name phantom2<br>
/gate/phantom1/daughters/insert cylinder<br>
/gate/phantom2/placement/setTranslation 0.0 -45.0 0.0 mm<br>
/gate/phantom2/geometry/setRmax 3.2 mm<br>
/gate/phantom2/geometry/setHeight 700 mm<br>
/gate/phantom2/setMaterial Air<br>
/gate/phantom2/attachPhantomSD<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal"><b>While when I added two more daughter phantoms inside the previous outer shell volume as followed</b>,<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">#===========================<br>
# P H A N T O M<br>
#===========================<br>
<br>
/gate/world/daughters/name phantom1<br>
/gate/world/daughters/insert cylinder<br>
/gate/phantom1/placement/setTranslation 0.0 0.0 0.0 mm<br>
/gate/phantom1/geometry/setRmax 101.5 mm<br>
/gate/phantom1/geometry/setHeight 700 mm<br>
/gate/phantom1/setMaterial Polyethylene<br>
/gate/phantom1/attachPhantomSD<br>
<br>
/gate/phantom1/daughters/name phantom2<br>
/gate/phantom1/daughters/insert cylinder<br>
/gate/phantom2/placement/setTranslation 0.0 -45.0 0.0 mm<br>
/gate/phantom2/geometry/setRmax 3.2 mm<br>
/gate/phantom2/geometry/setHeight 700 mm<br>
/gate/phantom2/setMaterial Air<br>
/gate/phantom2/attachPhantomSD<br>
<br>
/gate/phantom1/daughters/name phantom3<br>
/gate/phantom1/daughters/insert cylinder<br>
/gate/phantom3/placement/setTranslation 0.0 -45.0 0.0 mm<br>
/gate/phantom3/geometry/setRmax 2.4 mm<br>
/gate/phantom3/geometry/setRmin 1.6 mm<br>
/gate/phantom3/geometry/setHeight 800 mm<br>
/gate/phantom3/setMaterial Polyethylene<br>
/gate/phantom3/attachPhantomSD<br>
<br>
/gate/phantom1/daughters/name phantom4<br>
/gate/phantom1/daughters/insert cylinder<br>
/gate/phantom4/placement/setTranslation 0.0 -45.0 0.0 mm<br>
/gate/phantom4/geometry/setRmax 1.6 mm<br>
/gate/phantom4/geometry/setHeight 700 mm<br>
/gate/phantom4/setMaterial Water<br>
/gate/phantom4/attachPhantomSD<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal"><b>the GATE feedbacked a warning/error like this,</b><u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">*** Break *** segmentation violation<br>
<br>
===========================================================<br>
There was a crash.<br>
This is the entire stack trace of all threads:<br>
===========================================================<br>
#0 0x00007f563c6d146c in waitpid () at /lib64/libc.so.6<br>
#1 0x00007f563c64ef62 in do_system () at /lib64/libc.so.6<br>
#2 0x00007f564b4c70c4 in TUnixSystem::StackTrace() () at /home/goldan/GATE/root/lib/libCore.so.6.18<br>
#3 0x00007f564b4c97fc in TUnixSystem::DispatchSignals(ESignals) () at /home/goldan/GATE/root/lib/libCore.so.6.18<br>
#4 0x00007f56471f4630 in <signal handler called> () at /lib64/libpthread.so.0<br>
#5 0x0000000000000040 in ()<br>
#6 0x00000000008e2658 in GateMaterialDatabase::~GateMaterialDatabase() ()<br>
#7 0x000000000087a8e6 in GateDetectorConstruction::~GateDetectorConstruction() ()<br>
#8 0x00007f564423a1e6 in G4RunManager::DeleteUserInitializations() (this=this<br>
entry=0x32997c0) at /home/goldan/GATE/geant4.10.05.p01/source/run/src/G4RunManager.cc:236<br>
#9 0x00007f564423ae75 in G4RunManager::~G4RunManager() (this=0x32997c0, __in_chrg=<optimized out>) at /home/goldan/GATE/geant4.10.05.p01/source/run/src/G4RunManager.cc:211<br>
#10 0x0000000000830e19 in GateRunManager::~GateRunManager() ()<br>
#11 0x000000000050198f in main ()<br>
===========================================================<br>
<br>
<br>
The lines below might hint at the cause of the crash.<br>
You may get help by asking at the ROOT forum <a href="http://root.cern.ch/forum" target="_blank">
http://root.cern.ch/forum</a><br>
Only if you are really convinced it is a bug in ROOT then please submit a<br>
report at <a href="http://root.cern.ch/bugs" target="_blank">http://root.cern.ch/bugs</a> Please post the ENTIRE stack trace<br>
from above as an attachment in addition to anything else<br>
that might help us fixing this issue.<br>
===========================================================<br>
#5 0x0000000000000040 in ()<br>
#6 0x00000000008e2658 in GateMaterialDatabase::~GateMaterialDatabase() ()<br>
#7 0x000000000087a8e6 in GateDetectorConstruction::~GateDetectorConstruction() ()<br>
#8 0x00007f564423a1e6 in G4RunManager::DeleteUserInitializations() (this=this<br>
entry=0x32997c0) at /home/goldan/GATE/geant4.10.05.p01/source/run/src/G4RunManager.cc:236<br>
#9 0x00007f564423ae75 in G4RunManager::~G4RunManager() (this=0x32997c0, __in_chrg=<optimized out>) at /home/goldan/GATE/geant4.10.05.p01/source/run/src/G4RunManager.cc:211<br>
#10 0x0000000000830e19 in GateRunManager::~GateRunManager() ()<br>
#11 0x000000000050198f in main ()<br>
===========================================================<br>
<br>
<br>
WARNING - Attempt to delete the physical volume store while geometry closed !<br>
WARNING - Attempt to delete the logical volume store while geometry closed !<br>
WARNING - Attempt to delete the solid store while geometry closed !<br>
WARNING - Attempt to delete the region store while geometry closed !<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal"><b>The cluster tool could run the macro with added phantom configuration well with no warning/error, so I am not sure where the wrong with it or whether it has an</b>
<b>influence on the simulation result. I probably have seen </b>a<b> similar issue when I used CASToR for reconstruction so I am guessing it is related to ROOT?</b><u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal"><b>Did anyone ever meet this issue before? Any reply will be highly appreciated! Thanks!</b><u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">Best,<u></u><u></u></p>
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<p class="MsoNormal">Xinjie<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal"><br clear="all">
<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">-- <u></u><u></u></p>
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<p class="MsoNormal"><b><span style="color:black">....................................................</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:10pt;font-family:"Arial Black",sans-serif;color:rgb(153,0,0)">Xinjie Cao</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">M.E. / Ph.D. Candidate</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Research Project Assistant</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Department of Electrical and Computer Engineering & Radiology </span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Novel Medical Imaging Technologies Lab</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Health Science Center Level 8</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Stony Brook, NY 11794-8460 </span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Tel: +1 (631)202-9445</span></b><u></u><u></u></p>
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<p class="MsoNormal"><a href="https://you.stonybrook.edu/goldan/people/" target="_blank">you.stonybrook.edu/goldan/people/</a><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">email:
</span></b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif"><a href="mailto:xinjie.cao@stonybrook.edu" target="_blank"><b>xinjie.cao@stonybroo</b>k.edu</a></span><u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif"> </span><img border="0" width="200" height="28" style="width: 2.0833in; height: 0.2916in;" id="gmail-m_-3091569250842001824gmail-m_-8219071829138791603gmail-m_-4321371104164278345gmail-m_-3599849425980688379gmail-m_-3439672209627971201gmail-m_2229372970447384328gmail-m_8784737044276392042_x005f_x0000_i1026" src="https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ" data-unique-identifier="">
<img border="0" width="200" height="33" style="width: 2.0833in; height: 0.3437in;" id="gmail-m_-3091569250842001824gmail-m_-8219071829138791603gmail-m_-4321371104164278345gmail-m_-3599849425980688379gmail-m_-3439672209627971201gmail-m_2229372970447384328gmail-m_8784737044276392042_x005f_x0000_i1025" src="https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download" data-unique-identifier=""><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="color:black">....................................................</span></b><u></u><u></u></p>
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<p class="MsoNormal">It is prohibited to distribute or publish the files attached to any other people unless you get permission from the writer himself. All rights reserved.<u></u><u></u></p>
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<p class="MsoNormal"><br clear="all">
<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">-- <u></u><u></u></p>
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<p class="MsoNormal"><b><span style="color:black">....................................................</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:10pt;font-family:"Arial Black",sans-serif;color:rgb(153,0,0)">Xinjie Cao</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">M.E. / Ph.D. Candidate</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Research Project Assistant</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Department of Electrical and Computer Engineering & Radiology </span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Novel Medical Imaging Technologies Lab</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Health Science Center Level 8</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Stony Brook, NY 11794-8460 </span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Tel: +1 (631)202-9445</span></b><u></u><u></u></p>
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<p class="MsoNormal"><a href="https://you.stonybrook.edu/goldan/people/" target="_blank">you.stonybrook.edu/goldan/people/</a><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">email:
</span></b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif"><a href="mailto:xinjie.cao@stonybrook.edu" target="_blank"><b>xinjie.cao@stonybroo</b>k.edu</a></span><u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<img border="0" width="200" height="33" style="width: 2.0833in; height: 0.3437in;" id="gmail-m_-3091569250842001824gmail-m_-8219071829138791603gmail-m_-4321371104164278345gmail-m_-3599849425980688379gmail-m_-3439672209627971201gmail-m_2229372970447384328_x005f_x0000_i1025" src="https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download" data-unique-identifier=""><u></u><u></u></p>
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<p class="MsoNormal">It is prohibited to distribute or publish the files attached to any other people unless you get permission from the writer himself. All rights reserved.<u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:10pt;font-family:"Arial Black",sans-serif;color:rgb(153,0,0)">Xinjie Cao</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">M.E. / Ph.D. Candidate</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Research Project Assistant</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Novel Medical Imaging Technologies Lab</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Health Science Center Level 8</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Stony Brook, NY 11794-8460 </span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Tel: +1 (631)202-9445</span></b><u></u><u></u></p>
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<p class="MsoNormal"><a href="https://you.stonybrook.edu/goldan/people/" target="_blank">you.stonybrook.edu/goldan/people/</a><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">email:
</span></b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif"><a href="mailto:xinjie.cao@stonybrook.edu" target="_blank"><b>xinjie.cao@stonybroo</b>k.edu</a></span><u></u><u></u></p>
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<img border="0" width="200" height="33" style="width: 2.0833in; height: 0.3437in;" id="gmail-m_-3091569250842001824gmail-m_-8219071829138791603gmail-m_-4321371104164278345_x0000_i1029" src="https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download" data-unique-identifier=""><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:10pt;font-family:"Arial Black",sans-serif;color:rgb(153,0,0)">Xinjie Cao</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">M.E. / Ph.D. Candidate</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Research Project Assistant</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Department of Electrical and Computer Engineering & Radiology </span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Novel Medical Imaging Technologies Lab</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Health Science Center Level 8</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Stony Brook, NY 11794-8460 </span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Tel: +1 (631)202-9445</span></b><u></u><u></u></p>
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<p class="MsoNormal"><a href="https://you.stonybrook.edu/goldan/people/" target="_blank">you.stonybrook.edu/goldan/people/</a><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">email:
</span></b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif"><a href="mailto:xinjie.cao@stonybrook.edu" target="_blank"><b>xinjie.cao@stonybroo</b>k.edu</a></span><u></u><u></u></p>
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<img border="0" width="200" height="33" style="width: 2.0833in; height: 0.3437in;" id="gmail-m_-3091569250842001824gmail-m_-8219071829138791603gmail-m_-4321371104164278345_x0000_i1027" src="https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download" data-unique-identifier=""><u></u><u></u></p>
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<p class="MsoNormal">It is prohibited to distribute or publish the files attached to any other people unless you get permission from the writer himself. All rights reserved.<u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:10pt;font-family:"Arial Black",sans-serif;color:rgb(153,0,0)">Xinjie Cao</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">M.E. / Ph.D. Candidate</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Research Project Assistant</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Department of Electrical and Computer Engineering & Radiology </span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Novel Medical Imaging Technologies Lab</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Health Science Center Level 8</span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Stony Brook, NY 11794-8460 </span></b><u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">Tel: +1 (631)202-9445</span></b><u></u><u></u></p>
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<p class="MsoNormal"><a href="https://you.stonybrook.edu/goldan/people/" target="_blank">you.stonybrook.edu/goldan/people/</a><u></u><u></u></p>
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<div>
<p class="MsoNormal"><b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif">email:
</span></b><span style="font-size:7.5pt;font-family:"Arial Black",sans-serif"><a href="mailto:xinjie.cao@stonybrook.edu" target="_blank"><b>xinjie.cao@stonybroo</b>k.edu</a></span><u></u><u></u></p>
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<img border="0" width="200" height="33" style="width: 2.0833in; height: 0.3437in;" id="gmail-m_-3091569250842001824gmail-m_-8219071829138791603gmail-m_-4321371104164278345_x0000_i1025" src="https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download" data-unique-identifier=""><u></u><u></u></p>
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<p class="MsoNormal">It is prohibited to distribute or publish the files attached to any other people unless you get permission from the writer himself. All rights reserved.<u></u><u></u></p>
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<div><b><font color="#000000">....................................................</font></b><br>
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<div><b><span style="color:rgb(153,0,0);font-family:"arial black",sans-serif;font-size:x-small">Xinjie Cao</span></b><br>
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<div><b><font size="1" face="arial black, sans-serif">M.E. / Ph.D. Candidate</font></b></div>
<div><b><font size="1" face="arial black, sans-serif">Research Project Assistant</font></b></div>
<div><b><font size="1" face="arial black, sans-serif">Department of Electrical and Computer Engineering & Radiology </font></b></div>
<div><b><font size="1" face="arial black, sans-serif">Novel Medical Imaging Technologies Lab</font></b></div>
<div><b><font size="1" face="arial black, sans-serif">Health Science Center Level 8</font></b></div>
<div><b><font size="1" face="arial black, sans-serif">Stony Brook, NY 11794-8460 </font></b></div>
<div><b><font size="1" face="arial black, sans-serif">Tel: +1 (631)202-9445</font></b></div>
<div><a href="https://you.stonybrook.edu/goldan/people/" target="_blank">you.stonybrook.edu/goldan/people/</a><b><font size="1" face="arial black, sans-serif"><br>
</font></b></div>
<div><font size="1" face="arial black, sans-serif"><b>email: </b><a href="mailto:xinjie.cao@stonybrook.edu" target="_blank"><b>xinjie.cao@stonybroo</b>k.edu</a></font></div>
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<div><font size="1" face="arial black, sans-serif"> </font><img src="https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ" width="200" height="28" data-unique-identifier="">
<img src="https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download" width="200" height="33" data-unique-identifier=""></div>
<div>
<div><b><font color="#000000">....................................................</font></b></div>
<div>It is prohibited to distribute or publish the files attached to any other people unless you get permission from the writer himself. All rights reserved.</div>
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