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Hi Hussain,</div>
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Your most recent attachment was missing the readout module in the digitizer. I was able to produce output from your simulation after adding "/gate/digitizer/Singles/insert readout" to your output.mac file. For an initial test, I commented out the shielding,
collimator, and backcompartment components in your geometry.mac file, leaving only the SPECThead and crystal definitions. This produced output with a low number of particles. Keep in mind that if the aforementioned components are enabled (i.e. the collimator),
you will require significantly more primaries to produce registered hits due to attenuation.<br>
</div>
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<br>
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On a side note, I would recommend using /vis/disable at the start of your main.mac when you're not interested in visualization. I would also recommend using the new physics list mechanism by replacing your current physics list with "/gate/physics/addPhysicsList
emstandard_opt4" or whichever builder is most appropriate for your application. The previous method is deprecated. Implementing these changes will remove the warnings you are seeing in your terminal output. As always, the documentation is your friend.</div>
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<br>
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Regards,</div>
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Matthew<br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Khalid Hussain <khalidhussain1134@gmail.com><br>
<b>Sent:</b> January 31, 2020 10:07 AM<br>
<b>To:</b> Matthew Strugari <matthew.strugari@dal.ca><br>
<b>Cc:</b> gate-users@lists.opengatecollaboration.org <gate-users@lists.opengatecollaboration.org><br>
<b>Subject:</b> Re: [Gate-users] Problem in Projection calculation in simulating SPECT/Gamma Camera</font>
<div> </div>
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<div>
<div dir="ltr">Dear Matthew,
<div> </div>
<div>Please see the geometry described below;</div>
<div><br>
</div>
<div><font color="#00ff00">#############<br>
# W O R L D #<br>
#############<br>
# SPECT Camera geometry <br>
/gate/world/geometry/setXLength 100 cm<br>
/gate/world/geometry/setYLength 100 cm<br>
/gate/world/geometry/setZLength 100 cm<br>
<br>
# S C A N N E R H E A D<br>
<br>
/gate/world/daughters/name SPECThead<br>
/gate/world/daughters/insert box<br>
/gate/SPECThead/geometry/setXLength 61.1 cm <br>
/gate/SPECThead/geometry/setYLength 46.5 cm<br>
/gate/SPECThead/geometry/setZLength 14.005 cm<br>
/gate/SPECThead/placement/setTranslation 0. 0. 15 cm<br>
/gate/SPECThead/setMaterial Air<br>
/gate/SPECThead/vis/setColor magenta<br>
/gate/SPECThead/vis/forceWireframe<br>
<br>
/gate/SPECThead/repeaters/insert ring<br>
/gate/SPECThead/ring/setRepeatNumber 2<br>
/gate/SPECThead/ring/setPoint1 0. 1. 0. mm<br>
/gate/SPECThead/ring/setPoint2 0. 0. 0. mm<br>
<br>
<br>
# S H I E L D I N G<br>
/gate/SPECThead/daughters/name shielding<br>
/gate/SPECThead/daughters/insert box<br>
/gate/shielding/geometry/setXLength 61.1 cm<br>
/gate/shielding/geometry/setYLength 46.5 cm<br>
/gate/shielding/geometry/setZLength 14.005 cm<br>
/gate/shielding/placement/setTranslation 0. 0. 0.0 cm<br>
/gate/shielding/setMaterial Lead<br>
/gate/shielding/attachPhantomSD<br>
/gate/shielding/vis/forceWireframe<br>
/gate/shielding/vis/setColor red<br>
<br>
<br>
############################<br>
# LOW ENERGY HIGH RESOLUTION COLLIMATOR #<br>
############################<br>
<br>
# C O L L I M A T O R<br>
<br>
/gate/SPECThead/daughters/name collimator<br>
/gate/SPECThead/daughters/insert box <br>
/gate/collimator/geometry/setXLength 59.1 cm<br>
/gate/collimator/geometry/setYLength 44.5 cm<br>
/gate/collimator/geometry/setZLength 2.405 cm<br>
/gate/collimator/placement/setTranslation 0. 0. -5.0025 cm<br>
/gate/collimator/setMaterial Lead<br>
/gate/collimator/attachPhantomSD<br>
/gate/collimator/vis/forceWireframe<br>
/gate/collimator/vis/setColor blue<br>
<br>
<br>
# H O L E S<br>
<br>
/gate/collimator/daughters/name hole<br>
/gate/collimator/daughters/insert hexagone<br>
/gate/hole/geometry/setHeight 24.05 mm<br>
/gate/hole/geometry/setRadius 0.555 mm<br>
/gate/hole/placement/setRotationAxis 1 0 0<br>
/gate/hole/placement/setRotationAngle 0 deg<br>
/gate/hole/setMaterial Air<br>
/gate/hole/vis/forceWireframe<br>
/gate/hole/vis/setColor white <br>
<br>
<br>
# FILL THE WHOLE COLLIMATOR WITH SEPTA-HOLE<br>
<br>
/gate/hole/repeaters/insert cubicArray<br>
/gate/hole/cubicArray/setRepeatNumberX 465<br>
/gate/hole/cubicArray/setRepeatNumberY 350 <br>
/gate/hole/cubicArray/setRepeatNumberZ 1<br>
/gate/hole/cubicArray/setRepeatVector 1.27 1.27 0.0 mm<br>
<br>
<br>
# C R Y S T A L<br>
<br>
/gate/SPECThead/daughters/name crystal<br>
/gate/SPECThead/daughters/insert box<br>
/gate/crystal/geometry/setXLength 59.1 cm<br>
/gate/crystal/geometry/setYLength 44.5 cm<br>
/gate/crystal/geometry/setZLength 9.525 mm<br>
/gate/crystal/placement/setTranslation 0. 0. -2.07375 cm<br>
/gate/crystal/setMaterial NaI<br>
/gate/crystal/attachCrystalSD<br>
/gate/crystal/vis/forceWireframe<br>
/gate/crystal/vis/setColor yellow<br>
<br>
/gate/systems/SPECThead/crystal/attach crystal<br>
/gate/systems/SPECThead/describe<br>
<br>
/gate/crystal/attachCrystalSD<br>
<br>
# B A C K C O M P A R T M E N T<br>
<br>
/gate/SPECThead/daughters/name backcompartment<br>
/gate/SPECThead/daughters/insert box<br>
/gate/backcompartment/geometry/setXLength 59.1 cm<br>
/gate/backcompartment/geometry/setYLength 44.5 cm<br>
/gate/backcompartment/geometry/setZLength 6.6 cm<br>
/gate/backcompartment/placement/setTranslation 0. 0. 1.7025 cm<br>
/gate/backcompartment/setMaterial Air<br>
/gate/backcompartment/attachPhantomSD<br>
/gate/backcompartment/vis/forceWireframe<br>
/gate/backcompartment/vis/setColor green</font><br clear="all">
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<div dir="ltr"><br>
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<div dir="ltr">I cannot find the problem, Please guide me.</div>
<div dir="ltr"><br>
</div>
<div dir="ltr">Thank you for you cooperation.</div>
<div dir="ltr"><br>
</div>
<div dir="ltr">The entire mac files are also attached below.<br>
<div><br>
</div>
<div>
<div>Regards</div>
<div>Hussain</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
</div>
<br>
<div class="x_gmail_quote">
<div dir="ltr" class="x_gmail_attr">On Mon, Jan 27, 2020 at 3:24 PM Khalid Hussain <<a href="mailto:khalidhussain1134@gmail.com">khalidhussain1134@gmail.com</a>> wrote:<br>
</div>
<blockquote class="x_gmail_quote" style="margin:0px 0px 0px 0.8ex; border-left:1px solid rgb(204,204,204); padding-left:1ex">
<div dir="ltr">Dear Matthew,
<div><br>
</div>
<div>The files are attached. In this geometry , there is a shielding around the collimator and detector. May be this approach is wrong. You can find detail in the attached files.</div>
<div><br>
</div>
<div>Thank you<br clear="all">
<div>
<div dir="ltr">
<div dir="ltr">
<div>
<div dir="ltr"><br>
<div><br>
</div>
<div>
<div>Regards</div>
<div>Hussain</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
</div>
<br>
<div class="x_gmail_quote">
<div dir="ltr" class="x_gmail_attr">On Mon, Jan 27, 2020 at 2:53 AM Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca" target="_blank">matthew.strugari@dal.ca</a>> wrote:<br>
</div>
<blockquote class="x_gmail_quote" style="margin:0px 0px 0px 0.8ex; border-left:1px solid rgb(204,204,204); padding-left:1ex">
<div dir="auto">Hi Hussain,
<div><br>
</div>
<div>Could you possibly include your .mac file? Two things to check would be to make sure to have defined attachCrystalSD with your scintillator, and make sure your scintillator is defined as a daughter of SPECThead.</div>
<div><br>
</div>
<div>Regards,</div>
<div>Matthew</div>
<div>
<div dir="ltr"><br>
<blockquote type="cite">On Jan 26, 2020, at 1:37 PM, Khalid Hussain <<a href="mailto:khalidhussain1134@gmail.com" target="_blank">khalidhussain1134@gmail.com</a>> wrote:<br>
<br>
</blockquote>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">Dear Matthew,
<div><br>
<div>Thank you for your reply.</div>
<div>I added the readout module which I missed previously, but still the situation seems to be same.</div>
<div><font color="#ff9900"># D I G I T I Z E R<br>
/gate/digitizer/Singles/insert adder</font></div>
<div><font color="#ff9900">/gate/digitizer/Singles/insert readout <br>
/gate/digitizer/Singles/insert blurring<br>
/gate/digitizer/Singles/blurring/setResolution 0.10<br>
/gate/digitizer/Singles/blurring/setEnergyOfReference 140. keV<br>
/gate/digitizer/Singles/insert spblurring<br>
/gate/digitizer/Singles/spblurring/setSpresolution 2.0 mm<br>
/gate/digitizer/Singles/spblurring/verbose 0<br>
/gate/digitizer/Singles/insert thresholder<br>
/gate/digitizer/Singles/thresholder/setThreshold 126. keV<br>
/gate/digitizer/Singles/insert upholder<br>
/gate/digitizer/Singles/upholder/setUphold 154. keV<br>
<br>
# O U T P U T<br>
/gate/output/root/enable<br>
/gate/output/root/setFileName output/benchSPECT<br>
/gate/output/root/setRootSinglesAdderFlag 1<br>
/gate/output/root/setRootSinglesBlurringFlag 1 <br>
/gate/output/root/setRootSinglesSpblurringFlag 1<br>
/gate/output/root/setRootSinglesThresholderFlag 1<br>
/gate/output/root/setRootSinglesUpholderFlag 1</font></div>
<div><font color="#ff9900"><br>
# P R O J E C T I O N<br>
/gate/output/projection/enable<br>
/gate/output/projection/setFileName output/myProjection<br>
/gate/output/projection/pixelSizeX 0.48 cm<br>
/gate/output/projection/pixelSizeY 0.48 cm<br>
/gate/output/projection/pixelNumberX 59<br>
/gate/output/projection/pixelNumberY 44<br>
/gate/output/projection/projectionPlane XY</font><br>
</div>
<div> The projection image is still black, no source image is reflected.<br clear="all">
<div>
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<div dir="ltr">
<div dir="ltr">
<div>
<div><image.png></div>
<br>
</div>
<div><br>
</div>
<div>Further more, still I cannot see any information in .root file hit and single and others.</div>
<div><br>
</div>
<div>Please guide?</div>
<div><br>
</div>
<div>Thank you</div>
<div>
<div>Regards</div>
<div>Hussain</div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
</div>
</div>
<br>
<div class="x_gmail_quote">
<div dir="ltr" class="x_gmail_attr">On Mon, Jan 27, 2020 at 12:35 AM Matthew Strugari <<a href="mailto:matthew.strugari@dal.ca" target="_blank">matthew.strugari@dal.ca</a>> wrote:<br>
</div>
<blockquote class="x_gmail_quote" style="margin:0px 0px 0px 0.8ex; border-left:1px solid rgb(204,204,204); padding-left:1ex">
<div dir="auto">Hi Hussain,
<div><br>
</div>
<div>From first glance, it looks like you’re missing the readout module in the digitizer. Try that out and let me know.</div>
<div><br>
</div>
<div>Cheers,<br>
<div dir="ltr">Matthew</div>
<div dir="ltr"><br>
<blockquote type="cite">On Jan 26, 2020, at 6:03 AM, Khalid Hussain <<a href="mailto:khalidhussain1134@gmail.com" target="_blank">khalidhussain1134@gmail.com</a>> wrote:<br>
<br>
</blockquote>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">Dear Gate Users,
<div><br>
</div>
<div>I am simulating dual head Gamma Camera with sphere source of volume 1 cm^3 (0.62 cm radius) in the center. I am using the Tc-99m as a source of radioactivity with activity 100 kBq.</div>
<div><br>
</div>
<div>I want to see the projection of photons detected by the NaI detector.</div>
<div><br>
</div>
<div>For Projection I used the following code </div>
<div><br>
</div>
<div><font color="#ff9900"># D I G I T I Z E R<br>
#####<br>
<br>
/gate/digitizer/Singles/insert adder<br>
/gate/digitizer/Singles/insert blurring<br>
/gate/digitizer/Singles/blurring/setResolution 0.10<br>
/gate/digitizer/Singles/blurring/setEnergyOfReference 140. keV<br>
/gate/digitizer/Singles/insert spblurring<br>
/gate/digitizer/Singles/spblurring/setSpresolution 2.0 mm<br>
/gate/digitizer/Singles/spblurring/verbose 0<br>
/gate/digitizer/Singles/insert thresholder<br>
/gate/digitizer/Singles/thresholder/setThreshold 126. keV<br>
/gate/digitizer/Singles/insert upholder<br>
/gate/digitizer/Singles/upholder/setUphold 154. keV<br>
<br>
<br>
<br>
# O U T P U T<br>
#####<br>
<br>
/gate/output/root/enable<br>
/gate/output/root/setFileName output/benchSPECT<br>
/gate/output/root/setRootSinglesAdderFlag 1<br>
/gate/output/root/setRootSinglesBlurringFlag 1 <br>
/gate/output/root/setRootSinglesSpblurringFlag 1<br>
/gate/output/root/setRootSinglesThresholderFlag 1<br>
/gate/output/root/setRootSinglesUpholderFlag 1<br>
<br>
# P R O J E C T I O N<br>
#####<br>
/gate/output/projection/enable<br>
/gate/output/projection/setFileName output/myProjection<br>
/gate/output/projection/pixelSizeX 0.48 cm<br>
/gate/output/projection/pixelSizeY 0.48 cm<br>
#/gate/output/projection/pixelNumberX 128<br>
#/gate/output/projection/pixelNumberY 128<br>
/gate/output/projection/projectionPlane XY</font><br>
</div>
<div>
<div dir="ltr">
<div dir="ltr">
<div dir="ltr"><br>
</div>
<div>I want to analyse the projection, and interested to calculate projection/image specification. </div>
<div dir="ltr">Please see and guide where I am wrong, thanks for your cooperation.<br>
<div><br>
</div>
<div>I viewed the projection.sin file in imagej, it has no information also the hits and singles have no as such useful information. Files are attached.</div>
<div>
<div>Regards</div>
<div>Hussain</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div><myProjection.sin></div>
<div><myProjection.hdr></div>
<div><benchSPECT.root></div>
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