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Hi Howard,
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<div class="">you are welcome. I didn’t help with your subscription issue, though, credits go to <a href="mailto:david.sarrut@creatis.insa-lyon.fr" class="">David Sarrut </a>for that.</div>
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<div class="">Kind regards,</div>
<div class="">David Leibold</div>
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<blockquote type="cite" class="">
<div class="">On 7 Jul2022, at 16:03, Howard <<a href="mailto:lomahu@gmail.com" class="">lomahu@gmail.com</a>> wrote:</div>
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<div dir="ltr" class="">HI David,
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<div class="">Thank you very much for your swift response to my question. It is very helpful. I will read the document carefully then and learn how to use the information stored in root files. I am also grateful to your help with my earlier question on the
subscription issue. </div>
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<div class="">Best,</div>
<div class="">Howard</div>
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<div dir="ltr" class="gmail_attr">On Thu, Jul 7, 2022 at 3:20 AM David Leibold <<a href="mailto:D.Leibold@tudelft.nl" class="">D.Leibold@tudelft.nl</a>> wrote:<br class="">
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<div style="overflow-wrap: break-word;" class="">Dear Howard,
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<div class="">you are using the imageCT output, and according to the <a href="https://urldefense.com/v3/__https://opengate.readthedocs.io/en/latest/data_output_management.html?highlight=imageCT*image-ct-output__;Iw!!PAKc-5URQlI!-arevwjGvGnlk0N06QSlf7YAK_z-IAknuLgEJ8hgubc6-IvsTOCCdqcGRjs5k_DiZ-XTcdQZsARpDZyKZA$" target="_blank" class="">docs</a>:</div>
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<div class="">"The <em class="">imageCT</em> output is a binary matrix of float numbers that stores the number of Singles per pixel and is produced for each time slice"</div>
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<div class="">Please note that this does reflect what a realistic detector would measure. A common CBCT detector outputs the deposited energy per pixel. To obtain this, you would need to access the root output and convert it to energy integrated projections
yourself.</div>
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<div class="">Kind regards,</div>
<div class="">David Leibold</div>
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<div class="">On 7 Jul2022, at 03:40, Howard <<a href="mailto:lomahu@gmail.com" target="_blank" class="">lomahu@gmail.com</a>> wrote:</div>
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<div class="">Hi GATE users,</div>
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<div class="">I have been using GATE to simulate CBCT. One question I have been thinking to ask is: what does each detector pixel (set as the crystal sensitive detector) record, photon energy or photo number?
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<div class="">Let's say the output of each run (one projection angle) is set as:</div>
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<div class=""># Specific CT Image output<br class="">
/gate/output/imageCT/enable<br class="">
/gate/output/imageCT/setFileName output_dir/proj<br class="">
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<div class="">What if I use ROOT output format?<br class="">
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<div class=""># Generic ROOT output<br class="">
#/gate/output/root/enable<br class="">
#/gate/output/root/setFileName output_dir/results<br class="">
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<div class="">My detector macro is set as follows for your reference.<br class="">
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<div class="">#### General informations about the scanner<br class="">
# CT scanner for small animal imaging<br class="">
# 150 x 200 pixels in one module<br class="">
# Size of pixels : 0.4 x 0.3 x 3.0 mm3<br class="">
# Pixels are made up of silicon (no dead space between pixels)<br class="">
# This scanner is designed to be fixed (the phantom will rotate instead).<br class="">
# Let's position it perpendicular to the Z axis at a radial distance of 80 mm.<br class="">
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## CTscanner system (this is the encompassing volume)<br class="">
# This first volume containing the scanner should have the same hard-coded name<br class="">
# as the one predefined in GATE (here CTscanner)<br class="">
# Create it as a box that can contain all pixels<br class="">
# Set it 80 mm away from the center of the world along the Z axis<br class="">
# Set material Air, and visualize it as a white wire frame<br class="">
/gate/world/daughters/name CTscanner<br class="">
/gate/world/daughters/insert box<br class="">
/gate/CTscanner/geometry/setXLength 60. mm<br class="">
/gate/CTscanner/geometry/setYLength 60. mm<br class="">
/gate/CTscanner/geometry/setZLength 3. mm<br class="">
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/gate/CTscanner/placement/setTranslation 0. 0. 80. mm # original position<br class="">
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#/gate/CTscanner/placement/setTranslation 0. -80. 0. mm # for parallel computing, 6/10/2022<br class="">
#/gate/CTscanner/placement/setRotationAxis 1 0 0 # for parallel computing, 6/10/2022<br class="">
#/gate/CTscanner/placement/setRotationAngle -90. deg # for parallel computing, 6/10/2022<br class="">
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/gate/CTscanner/setMaterial Air<br class="">
/gate/CTscanner/vis/forceWireframe<br class="">
/gate/CTscanner/vis/setColor white<br class="">
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## The first component of the CTscanner is the module<br class="">
# CTSCANNER # ----> # MODULE #<br class="">
# Here we will use only one module, so just create it identical to the encompassing volume<br class="">
/gate/CTscanner/daughters/name module<br class="">
/gate/CTscanner/daughters/insert box<br class="">
/gate/module/geometry/setXLength 60. mm<br class="">
/gate/module/geometry/setYLength 60. mm</div>
<div class="">/gate/module/geometry/setZLength 3. mm<br class="">
/gate/module/setMaterial Air<br class="">
/gate/module/vis/forceWireframe<br class="">
/gate/module/vis/setColor white<br class="">
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## The second component of the CTscanner is the cluster (located inside the module)<br class="">
# There are 3 possible clusters: cluster_0, cluster_1 and cluster_2<br class="">
# MODULE # ----> # CLUSTER_0 #<br class="">
# Here we will use only one type of clusters, so again just create it identical to the mother volume<br class="">
/gate/module/daughters/name cluster<br class="">
/gate/module/daughters/insert box<br class="">
/gate/cluster/geometry/setXLength 60. mm<br class="">
/gate/cluster/geometry/setYLength 60. mm<br class="">
/gate/cluster/geometry/setZLength 3. mm<br class="">
/gate/cluster/setMaterial Air<br class="">
/gate/cluster/vis/forceWireframe<br class="">
/gate/cluster/vis/setColor white<br class="">
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## The third component of the CTscanner is the pixel (located inside the cluster)<br class="">
# There are 3 possible pixels, one by cluster: pixel_0 (in cluster_0), pixel_1 (in cluster_1) and pixel_2 (in cluster_2)<br class="">
# MODULE # ----> # CLUSTER_0 # ----> # PIXEL_0 #<br class="">
# Here we will use only one type of pixels<br class="">
# The pixel size is 0.4 x 0.3 x 3 mm3<br class="">
# Visualize it as a solid object, color of your choice<br class="">
/gate/cluster/daughters/name pixel<br class="">
/gate/cluster/daughters/insert box<br class="">
/gate/pixel/geometry/setXLength 0.4 mm<br class="">
/gate/pixel/geometry/setYLength 0.3 mm<br class="">
/gate/pixel/geometry/setZLength 3. mm<br class="">
/gate/pixel/setMaterial Silicon<br class="">
/gate/pixel/vis/forceSolid<br class="">
/gate/pixel/vis/setColor red<br class="">
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# Now we can repeat the pixel inside the cluster<br class="">
# We want 150 x 200 pixels<br class="">
# Note: the repeated objects will be automatically centered on the original position of the single volume<br class="">
# Set the correct number of repeated volumes and the repeat vector<br class="">
/gate/pixel/repeaters/insert cubicArray<br class="">
/gate/pixel/cubicArray/setRepeatNumberX 150<br class="">
/gate/pixel/cubicArray/setRepeatNumberY 200<br class="">
/gate/pixel/cubicArray/setRepeatNumberZ 1<br class="">
/gate/pixel/cubicArray/setRepeatVector 0.4 0.3 0. mm</div>
<div class="">## Attach to hard-coded CTscanner system (here only cluster_0 and pixel_0 are used)<br class="">
# These commands allow GATE to make a link between the arbitrary volumes you defined and the predefined components of<br class="">
# the system in use (here the CTscanner). It is used to make a link with the output modules associated to the system<br class="">
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/gate/systems/CTscanner/module/attach module<br class="">
/gate/systems/CTscanner/cluster_0/attach cluster<br class="">
/gate/systems/CTscanner/pixel_0/attach pixel<br class="">
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## Attach the pixel as the crystal sensitive detector<br class="">
# This command is used to specify which arbitrary volume is used as the sensitive volume.<br class="">
# All interactions occuring in this volume can be recorded and analyzed.<br class="">
/gate/pixel/attachCrystalSD<br class="">
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<div class="">Any feedback is greatly appreciated!</div>
<div class="">Howard<br class="">
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