[Gate-users] Problem in Projection calculation in simulating SPECT/Gamma Camera

Fri Jan 31 19:27:32 CET 2020

Hi Hussain,

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.

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.

Regards,
Matthew

________________________________
From: Khalid Hussain <khalidhussain1134 at gmail.com>
Sent: January 31, 2020 10:07 AM
To: Matthew Strugari <matthew.strugari at dal.ca>
Cc: gate-users at lists.opengatecollaboration.org <gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] Problem in Projection calculation in simulating SPECT/Gamma Camera

Dear Matthew,

Please see the geometry described below;

#############
# W O R L D #
#############
# SPECT Camera geometry
/gate/world/geometry/setXLength 100 cm
/gate/world/geometry/setYLength 100 cm
/gate/world/geometry/setZLength 100 cm

# S C A N N E R   H E A D

/gate/world/daughters/name SPECThead
/gate/world/daughters/insert box
/gate/SPECThead/geometry/setXLength 61.1 cm
/gate/SPECThead/geometry/setYLength 46.5 cm
/gate/SPECThead/geometry/setZLength 14.005 cm
/gate/SPECThead/placement/setTranslation 0. 0. 15 cm
/gate/SPECThead/setMaterial Air
/gate/SPECThead/vis/setColor magenta
/gate/SPECThead/vis/forceWireframe

/gate/SPECThead/repeaters/insert ring
/gate/SPECThead/ring/setRepeatNumber 2
/gate/SPECThead/ring/setPoint1 0. 1. 0. mm
/gate/SPECThead/ring/setPoint2 0. 0. 0. mm

# S H I E L D I N G
/gate/SPECThead/daughters/name shielding
/gate/SPECThead/daughters/insert box
/gate/shielding/geometry/setXLength 61.1  cm
/gate/shielding/geometry/setYLength 46.5 cm
/gate/shielding/geometry/setZLength 14.005 cm
/gate/shielding/placement/setTranslation 0. 0. 0.0 cm
/gate/shielding/setMaterial Lead
/gate/shielding/attachPhantomSD
/gate/shielding/vis/forceWireframe
/gate/shielding/vis/setColor red

############################
# LOW ENERGY HIGH RESOLUTION COLLIMATOR #
############################

# C O L L I M A T O R

/gate/SPECThead/daughters/name collimator
/gate/SPECThead/daughters/insert box
/gate/collimator/geometry/setXLength 59.1 cm
/gate/collimator/geometry/setYLength 44.5 cm
/gate/collimator/geometry/setZLength 2.405 cm
/gate/collimator/placement/setTranslation 0. 0. -5.0025 cm
/gate/collimator/setMaterial Lead
/gate/collimator/attachPhantomSD
/gate/collimator/vis/forceWireframe
/gate/collimator/vis/setColor blue

# H O L E S

/gate/collimator/daughters/name hole
/gate/collimator/daughters/insert hexagone
/gate/hole/geometry/setHeight 24.05 mm
/gate/hole/geometry/setRadius  0.555 mm
/gate/hole/placement/setRotationAxis 1 0  0
/gate/hole/placement/setRotationAngle 0 deg
/gate/hole/setMaterial Air
/gate/hole/vis/forceWireframe
/gate/hole/vis/setColor white

# FILL THE WHOLE COLLIMATOR WITH SEPTA-HOLE

/gate/hole/repeaters/insert cubicArray
/gate/hole/cubicArray/setRepeatNumberX 465
/gate/hole/cubicArray/setRepeatNumberY 350
/gate/hole/cubicArray/setRepeatNumberZ 1
/gate/hole/cubicArray/setRepeatVector 1.27 1.27 0.0 mm

# C R Y S T A L

/gate/SPECThead/daughters/name crystal
/gate/SPECThead/daughters/insert box
/gate/crystal/geometry/setXLength 59.1 cm
/gate/crystal/geometry/setYLength 44.5 cm
/gate/crystal/geometry/setZLength 9.525 mm
/gate/crystal/placement/setTranslation   0. 0. -2.07375 cm
/gate/crystal/setMaterial NaI
/gate/crystal/attachCrystalSD
/gate/crystal/vis/forceWireframe
/gate/crystal/vis/setColor yellow

/gate/systems/SPECThead/crystal/attach crystal
/gate/systems/SPECThead/describe

/gate/crystal/attachCrystalSD

# B A C K C O M P A R T M E N T

/gate/SPECThead/daughters/name backcompartment
/gate/SPECThead/daughters/insert box
/gate/backcompartment/geometry/setXLength 59.1 cm
/gate/backcompartment/geometry/setYLength 44.5 cm
/gate/backcompartment/geometry/setZLength 6.6 cm
/gate/backcompartment/placement/setTranslation  0. 0. 1.7025 cm
/gate/backcompartment/setMaterial Air
/gate/backcompartment/attachPhantomSD
/gate/backcompartment/vis/forceWireframe
/gate/backcompartment/vis/setColor green

I cannot find the problem, Please guide me.

Thank you for you cooperation.

The entire mac files are also attached below.

Regards
Hussain

On Mon, Jan 27, 2020 at 3:24 PM Khalid Hussain <khalidhussain1134 at gmail.com<mailto:khalidhussain1134 at gmail.com>> wrote:
Dear Matthew,

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.

Thank you

Regards
Hussain

On Mon, Jan 27, 2020 at 2:53 AM Matthew Strugari <matthew.strugari at dal.ca<mailto:matthew.strugari at dal.ca>> wrote:
Hi Hussain,

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.

Regards,
Matthew

On Jan 26, 2020, at 1:37 PM, Khalid Hussain <khalidhussain1134 at gmail.com<mailto:khalidhussain1134 at gmail.com>> wrote:

Dear Matthew,

Thank you for your reply.
I added the readout module which I missed previously, but still the situation seems to be same.
# D I G I T I Z E R
/gate/digitizer/Singles/insert adder
/gate/digitizer/Singles/insert readout
/gate/digitizer/Singles/insert blurring
/gate/digitizer/Singles/blurring/setResolution 0.10
/gate/digitizer/Singles/blurring/setEnergyOfReference 140. keV
/gate/digitizer/Singles/insert spblurring
/gate/digitizer/Singles/spblurring/setSpresolution 2.0 mm
/gate/digitizer/Singles/spblurring/verbose 0
/gate/digitizer/Singles/insert thresholder
/gate/digitizer/Singles/thresholder/setThreshold 126. keV
/gate/digitizer/Singles/insert upholder
/gate/digitizer/Singles/upholder/setUphold 154. keV

# O U T P U T
/gate/output/root/enable
/gate/output/root/setFileName output/benchSPECT
/gate/output/root/setRootSinglesAdderFlag 1
/gate/output/root/setRootSinglesBlurringFlag 1
/gate/output/root/setRootSinglesSpblurringFlag 1
/gate/output/root/setRootSinglesThresholderFlag 1
/gate/output/root/setRootSinglesUpholderFlag 1

# P R O J E C T I O N
/gate/output/projection/enable
/gate/output/projection/setFileName output/myProjection
/gate/output/projection/pixelSizeX 0.48 cm
/gate/output/projection/pixelSizeY 0.48 cm
/gate/output/projection/pixelNumberX 59
/gate/output/projection/pixelNumberY 44
/gate/output/projection/projectionPlane XY
 The projection image is still black, no source image is reflected.
<image.png>

Further more, still I cannot see any information in .root file hit and single and others.

Please guide?

Thank you
Regards
Hussain

On Mon, Jan 27, 2020 at 12:35 AM Matthew Strugari <matthew.strugari at dal.ca<mailto:matthew.strugari at dal.ca>> wrote:
Hi Hussain,

From first glance, it looks like you’re missing the readout module in the digitizer. Try that out and let me know.

Cheers,
Matthew

On Jan 26, 2020, at 6:03 AM, Khalid Hussain <khalidhussain1134 at gmail.com<mailto:khalidhussain1134 at gmail.com>> wrote:

Dear Gate Users,

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.

I want to see the projection of photons detected by the NaI detector.

For Projection I used the following code

# D I G I T I Z E R
#####

/gate/digitizer/Singles/insert adder
/gate/digitizer/Singles/insert blurring
/gate/digitizer/Singles/blurring/setResolution 0.10
/gate/digitizer/Singles/blurring/setEnergyOfReference 140. keV
/gate/digitizer/Singles/insert spblurring
/gate/digitizer/Singles/spblurring/setSpresolution 2.0 mm
/gate/digitizer/Singles/spblurring/verbose 0
/gate/digitizer/Singles/insert thresholder
/gate/digitizer/Singles/thresholder/setThreshold 126. keV
/gate/digitizer/Singles/insert upholder
/gate/digitizer/Singles/upholder/setUphold 154. keV

# O U T P U T
#####

/gate/output/root/enable
/gate/output/root/setFileName output/benchSPECT
/gate/output/root/setRootSinglesAdderFlag 1
/gate/output/root/setRootSinglesBlurringFlag 1
/gate/output/root/setRootSinglesSpblurringFlag 1
/gate/output/root/setRootSinglesThresholderFlag 1
/gate/output/root/setRootSinglesUpholderFlag 1

# P R O J E C T I O N
#####
/gate/output/projection/enable
/gate/output/projection/setFileName output/myProjection
/gate/output/projection/pixelSizeX 0.48 cm
/gate/output/projection/pixelSizeY 0.48 cm
#/gate/output/projection/pixelNumberX 128
#/gate/output/projection/pixelNumberY 128
/gate/output/projection/projectionPlane XY

I want to analyse the projection, and interested to calculate projection/image specification.
Please see and guide where I am wrong, thanks for your cooperation.

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.
Regards
Hussain
<myProjection.sin>
<myProjection.hdr>
<benchSPECT.root>
_______________________________________________
Gate-users mailing list
Gate-users at lists.opengatecollaboration.org<mailto:Gate-users at lists.opengatecollaboration.org>
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200131/1c35c76e/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: spect-test_working.zip
Type: application/zip
Size: 993956 bytes
Desc: spect-test_working.zip
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200131/1c35c76e/attachment-0001.zip>