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Dear David,</div>
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Thanks for the quick reply and the quick fix. You are right, I just repeated the simulation with a thickness of 2 cm and the phantom shows up. Thank you!</div>
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Best,</div>
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Maggie</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> David Leibold <D.Leibold@tudelft.nl><br>
<b>Sent:</b> 26 August 2022 21:51<br>
<b>To:</b> Margarete Kattau <margarete.kattau@icr.ac.uk><br>
<b>Cc:</b> gate-users@lists.opengatecollaboration.org <gate-users@lists.opengatecollaboration.org><br>
<b>Subject:</b> Re: [Gate-users] Materials not showing up on GATE simulation</font>
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<span style="color:#9C6500; font-weight:bold">CAUTION:</span> This email originated from outside of the ICR. Do not click links or open attachments unless you recognize the sender's email address and know the content is safe.</div>
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<div>Dear Maggie,
<div class=""><br class="">
</div>
<div class="">I noticed that your phantom has a thickness of only 100 µm (if I’m not mistaken). With muscle tissue, you would see barely any attenuation; in fact, the attenuation is probably so low that you can’t see it in your projection images.</div>
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<div class="">The alternative materials you mention (uranium, gold, platinum and tungsten) are high Z (high atomic number) materials, therefore their attenuation is considerably higher than body-like materials (check e.g. the<a href="https://physics.nist.gov/PhysRefData/Xcom/html/xcom1.html" class="">
NIST database</a> for X-ray attenuation of e.g. uranium and water).</div>
<div class=""><br class="">
</div>
<div class="">I would advise you to increase the thickness of your phantom two a few centimetres, and then check whether you can see them in your projection images (note that a few centimetres of e.g. uranium would probably stop the X-ray beam completely).
Let us know whether that works.</div>
<div class=""><br class="">
</div>
<div class="">Best regards,</div>
<div class="">David</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 26 Aug2022, at 18:53, Margarete Kattau <<a href="mailto:margarete.kattau@icr.ac.uk" class="">margarete.kattau@icr.ac.uk</a>> wrote:</div>
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Dear fellow GATE-users,</div>
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I am facing issues with a simulation. My geometry consists of a planar X-ray source (120 kVp) irradiating a simple phantom consisting of a large disc (muscle) and three smaller inserts (air, bone and adipose tissue). The detector is positioned behind the phantom
(screenshot of geometry attached). The problem is that when I reconstruct the image based on the counts registered in the detector, I only see the source and no sign of the phantom (attached image.png). This is really odd, as I have previously run the same
mac script but with different materials (uranium, gold, platinum, tungsten) and the image looked as expected (attached image2.png).</div>
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I tried many things, such as only using uranium as a higher absorbing material for the large disc and keeping the smaller inserts as air, adipose and bone, which then makes the large disc appear, but the smaller discs are translucent (image3.png). Finally,
if I only use a bone disc without any inserts, I still see no disc, even though I should be able to see a difference in attenuation between bone and the surrounding air.</div>
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<span class="" style="background-color:rgb(255,255,255); display:inline!important">Please note that the images have different activity levels, but I don't expect that this to make such a big difference (</span><span class="" style="margin:0px; background-color:rgb(255,255,255); display:inline!important">~70e6
Bq for image.png and image2.png, ~7e6 Bq for image3.png, simulation time: 1 sec)</span><span class="" style="background-color:rgb(255,255,255); display:inline!important">. </span><br class="">
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Has anyone ever experienced similar issues or knows how to solve this? Many thanks in advance!</div>
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Best,</div>
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Maggie</div>
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P.S.:</div>
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This is my mac script:</div>
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#==============================================================================================
<div class=""># Visualization</div>
<div class="">#==============================================================================================</div>
<div class=""><br class="">
</div>
<div class="">#/control/execute mac/visu.mac</div>
<div class=""><br class="">
</div>
<div class="">#==============================================================================================</div>
<div class=""># Materials</div>
<div class="">#==============================================================================================</div>
<div class=""><br class="">
</div>
<div class="">/gate/geometry/setMaterialDatabase data/GateMaterials.db</div>
<div class=""><br class="">
</div>
<div class="">#==============================================================================================</div>
<div class=""># Geometry<span class="x_Apple-converted-space"> </span></div>
<div class="">#==============================================================================================</div>
<div class=""><br class="">
</div>
<div class="">/gate/world/setMaterial Air</div>
<div class="">/gate/world/geometry/setXLength 5 m</div>
<div class="">/gate/world/geometry/setYLength 5 m</div>
<div class="">/gate/world/geometry/setZLength 5 m</div>
<div class=""><br class="">
</div>
<div class="">/gate/world/daughters/name scanner</div>
<div class="">/gate/world/daughters/insert box</div>
<div class="">/gate/scanner/geometry/setXLength 53. mm</div>
<div class="">/gate/scanner/geometry/setYLength 40. mm</div>
<div class="">/gate/scanner/geometry/setZLength 2. mm</div>
<div class=""><br class="">
</div>
<div class="">/gate/scanner/daughters/name detector</div>
<div class="">/gate/scanner/daughters/insert box</div>
<div class="">/gate/detector/geometry/setXLength 0.220 mm</div>
<div class="">/gate/detector/geometry/setYLength 0.220 mm</div>
<div class="">/gate/detector/geometry/setZLength 1. mm</div>
<div class="">/gate/detector/setMaterial CdTe</div>
<div class="">/gate/detector/repeaters/insert cubicArray</div>
<div class="">/gate/detector/cubicArray/setRepeatNumberX 240</div>
<div class="">/gate/detector/cubicArray/setRepeatNumberY 180</div>
<div class="">/gate/detector/cubicArray/setRepeatVector 0.220 0.220 0. mm </div>
<div class="">/gate/detector/vis/setVisible 1<span class="x_Apple-converted-space"> </span></div>
<div class="">/gate/detector/vis/setColor yellow</div>
<div class="">/gate/detector/vis/forceSolid</div>
<div class=""><br class="">
</div>
<div class="">/gate/world/daughters/name musclePhantom</div>
<div class="">/gate/world/daughters/insert cylinder<span class="x_Apple-converted-space"> </span></div>
<div class="">/gate/musclePhantom/geometry/setRmin 0. mm</div>
<div class="">/gate/musclePhantom/geometry/setRmax 15.84 mm</div>
<div class="">/gate/musclePhantom/geometry/setHeight 0.1 mm</div>
<div class="">/gate/musclePhantom/placement/setTranslation 0. 0. 5. cm</div>
<div class="">/gate/musclePhantom/setMaterial Muscle</div>
<div class="">/gate/musclePhantom/vis/setVisible 1</div>
<div class="">/gate/musclePhantom/vis/setColor red</div>
<div class="">/gate/musclePhantom/vis/forceWireframe</div>
<div class=""><br class="">
</div>
<div class="">/gate/musclePhantom/daughters/name airDisc</div>
<div class="">/gate/musclePhantom/daughters/insert cylinder</div>
<div class="">/gate/airDisc/geometry/setRmin 0. mm</div>
<div class="">/gate/airDisc/geometry/setRmax 4. mm</div>
<div class="">/gate/airDisc/geometry/setHeight 0.1 mm</div>
<div class="">/gate/airDisc/placement/setTranslation 0. 10.42 0. mm</div>
<div class="">/gate/airDisc/setMaterial Air</div>
<div class="">/gate/airDisc/vis/setVisible 1</div>
<div class="">/gate/airDisc/vis/setColor cyan</div>
<div class="">/gate/airDisc/vis/forceSolid</div>
<div class=""><br class="">
</div>
<div class="">/gate/musclePhantom/daughters/name boneDisc</div>
<div class="">/gate/musclePhantom/daughters/insert cylinder</div>
<div class="">/gate/boneDisc/geometry/setRmin 0. mm</div>
<div class="">/gate/boneDisc/geometry/setRmax 4. mm</div>
<div class="">/gate/boneDisc/geometry/setHeight 0.1 mm</div>
<div class="">/gate/boneDisc/placement/setTranslation 0. 0. 0. mm</div>
<div class="">/gate/boneDisc/setMaterial Bone</div>
<div class="">/gate/boneDisc/vis/setVisible 1</div>
<div class="">/gate/boneDisc/vis/setColor white</div>
<div class="">/gate/boneDisc/vis/forceSolid</div>
<div class=""><br class="">
</div>
<div class="">/gate/musclePhantom/daughters/name fatDisc</div>
<div class="">/gate/musclePhantom/daughters/insert cylinder</div>
<div class="">/gate/fatDisc/geometry/setRmin 0. mm</div>
<div class="">/gate/fatDisc/geometry/setRmax 4. mm</div>
<div class="">/gate/fatDisc/geometry/setHeight 0.1 mm</div>
<div class="">/gate/fatDisc/placement/setTranslation 0. -10.42 0. mm</div>
<div class="">/gate/fatDisc/setMaterial Adipose</div>
<div class="">/gate/fatDisc/vis/setVisible 1</div>
<div class="">/gate/fatDisc/vis/setColor yellow</div>
<div class="">/gate/fatDisc/vis/forceSolid</div>
<div class=""><br class="">
</div>
<div class="">#============================================================================================</div>
<div class=""># Physics</div>
<div class="">#============================================================================================</div>
<div class=""><br class="">
</div>
<div class="">/gate/physics/addPhysicsList emstandard_opt4</div>
<div class=""><br class="">
</div>
<div class="">#==============================================================================================</div>
<div class=""># Outputs & Actors</div>
<div class="">#==============================================================================================</div>
<div class=""><br class="">
</div>
<div class="">/gate/systems/scanner/level1/attach detector</div>
<div class="">/gate/detector/attachCrystalSD</div>
<div class=""><br class="">
</div>
<div class="">/gate/output/tree/enable</div>
<div class="">/gate/output/tree/addFileName output/tree.root</div>
<div class="">/gate/output/tree/hits/enable</div>
<div class=""><br class="">
</div>
<div class="">#==============================================================================================</div>
<div class=""># Initialisation</div>
<div class="">#==============================================================================================</div>
<div class=""><br class="">
</div>
<div class="">/gate/run/initialize</div>
<div class=""><br class="">
</div>
<div class="">#==============================================================================================</div>
<div class=""># Source</div>
<div class="">#==============================================================================================</div>
<div class=""><br class="">
</div>
<div class=""># X-ray spectrum</div>
<div class="">/gate/source/addSource interpolationSpectrum gps</div>
<div class="">/gate/source/interpolationSpectrum/gps/particle gamma</div>
<div class="">/gate/source/interpolationSpectrum/gps/energytype UserSpectrum</div>
<div class="">/gate/source/interpolationSpectrum/gps/setSpectrumFile ../Xray_spectrum120kVp_new_MeV.txt</div>
<div class="">/gate/source/interpolationSpectrum/gps/position 0. 0. 10. cm</div>
<div class="">/gate/source/interpolationSpectrum/gps/type Plane</div>
<div class="">/gate/source/interpolationSpectrum/gps/shape Circle</div>
<div class="">/gate/source/interpolationSpectrum/gps/radius 21.78 mm</div>
<div class="">/gate/source/interpolationSpectrum/setActivity 7.36e6 becquerel </div>
<div class=""><br class="">
</div>
<div class="">#==============================================================================================</div>
<div class=""># Main program</div>
<div class="">#==============================================================================================</div>
<div class="">/gate/random/setEngineSeed 523678<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">/gate/application/setTimeSlice 0.1 s</div>
<div class="">/gate/application/setTimeStart 0. s</div>
<div class="">/gate/application/setTimeStop 1. s</div>
/gate/application/start<br class="">
</div>
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