[Gate-users] Defining an activity distribution with background

Satyajit Ghosh satyajitghosh.email at gmail.com
Fri Nov 15 22:09:31 CET 2019 

Hi Cassandra,

              Thank you for your mail.

              I have tried the 'forbid' command, as you suggested. To start
with I have been attempting the simple case of a cold region inside hot
source -

##########################################################

/gate/world/daughters/name cold_area
/gate/world/daughters/insert cylinder
/gate/cold_area/setMaterial Air
/gate/cold_area/vis/forceWireframe
/gate/cold_area/vis/setColor green
/gate/cold_area/geometry/setRmax 50.0 mm
/gate/cold_area/geometry/setRmin 0.0 mm
/gate/cold_area/geometry/setHeight 52. mm
/gate/cold_area/placement/setTranslation 0. 0. 0. cm

/gate/run/initialize # placed here according to the manual

/gate/source/addSource mother_S
/gate/source/mother_S/setActivity 10.0 muCi
/gate/source/mother_S/gps/particle gamma
/gate/source/mother_S/setType backtoback
/gate/source/mother_S/gps/energytype Mono
/gate/source/mother_S/gps/monoenergy 0.511 MeV
/gate/source/mother_S/setForcedUnstableFlag true
/gate/source/mother_S/setForcedHalfLife 50 s
/gate/source/mother_S/gps/type Volume
/gate/source/mother_S/gps/shape Cylinder
/gate/source/mother_S/gps/radius 90. mm
/gate/source/mother_S/gps/halfz 26.0 mm
/gate/source/mother_S/gps/centre 0. 0. 0. cm
*/gate/source/mother_S/gps/Forbid cold_area_phys        *# extra '_phys' is
attached because in terminal cold_area is termed as cold_area_phys
/gate/source/mother_S/dump 1
/gate/source/mother_S/visualize 5000 blue 10

##########################################################.

 The code runs without error, but the *source point visualization with ROOT*
(file attached) and *STIR reconstructed image* (file attached) shows
*activity in the forbidden area.*
 The Bin_GATE_v1.0.c code shows *same number of coincidences in two root
files* with 'forbid' command commented and uncommented.

 Interestingly, the* 'forbid' command indeed pings its presence *when I
have defined the cold cylinder radius to be *equal* to mother source
cylinder radius in this way -

##########################################################

[G4-cerr]
-------- EEEE ------- G4Exception-START -------- EEEE -------
*** G4Exception : GenerateOne
      issued by : GateSPSPosDistribution::GenerateOne
1000000 primaries were always generated in forbidden volumes !
 It seems that all sources are forbidden.
*** Fatal Exception *** core dump ***
-------- EEEE -------- G4Exception-END --------- EEEE -------

##########################################################

Is there any *MISTAKE* that I have made in implementation code? Finally,
like to mention that I am using *GATE 8.0* in case there is any issue of*
bug*.

Thanking you,

Satyajit Ghosh
Phd student
Department of Physics
IIT Bombay, Mumbai
INDIA
16-Nov.-2019

On Thu, Nov 14, 2019 at 9:34 AM Cassandra Miller <
cassandramiller at phas.ubc.ca> wrote:

> Hi Satyajit,
>
> Have you tried defining a cold source? You can use the "forbid" command,
> for example:
>
> /gate/world/daughters/name cold_area
> /gate/world/daughters/insert cylinder
> /gate/cold_area/vis/forceWireframe
> /gate/cold_area/vis/setColor green
> /gate/cold_area/geometry/setRmax 3.0 cm
> /gate/cold_area/geometry/setHeight 1. cm
>
> /gate/source/addSource number1
> /gate/source/number1/setActivity 100000. becquerel
> /gate/source/number1/gps/particle gamma
> /gate/source/number1/setType backtoback
> /gate/source/number1/gps/type Volume
> /gate/source/number1/gps/shape Cylinder
> /gate/source/number1/gps/radius 5. cm
> /gate/source/number1/gps/halfz 0.5 cm
> /gate/source/number1/gps/centre 0. 0. 0. cm
> /gate/source/number1/gps/monoenergy 511. keV
> /gate/source/number1/gps/angtype iso
> */gate/source/number1/gps/Forbid cold_area *
> /gate/source/number1/dump 1
>
> It might work if when you define your background, you forbid the area
> where the hot rods are, and then you define your hot rods separately as you
> are already doing. I'm not sure if it will fix your problem but it's worth
> a shot. Then you also can define the rods with whatever activity you want,
> without having to take into account the background.
>
> Best,
> Cassandra Miller
> PhD Student
> Quantitative Tomography Lab & Medical Imaging Research Group
> Department of Physics & Astronomy, University of British Columbia
>
>
> On 2019-11-13 8:54 a.m., Satyajit Ghosh wrote:
>
> Dear GATE users,
>
>                I am trying to define an activity distribution of four
> circular hot rods with a backgrodeund (of ratio 1:2 wrt hot region) using
> analytic definition of source (not voxelized definition). I know that the
> 'setActivity' command basically assigns a certain amount of activity inside
> a the defined volume. Naturally the background volume is needed to be
> defined as universal volume containing four volumes for hot rods. After
> assigning the appropriate activity values in 5 volumes (4 hot rods and one
> background), I am not getting desired hot to background ratio in STIR
> reconstructed image of GATE data. Please note that I have set the activity
> of individual hot rods considering contribution from background activity. *I
> believe the reason of not getting desired result can be the fact that one
> can't define overlapping source volumes. Is this correct?* If not then
> how do I define an activity distribution with a background using analytic
> definition of source.
>
> Satyajit Ghosh
> Phd student
> Physics Department
> IIT Bombay, Mumbai
> 13-Nov.2019
> --
> *Satyajit Ghosh*
> *PhD Student*
>
> *Nuclear Spectroscopy and Molecular Imaging Lab, *
> *Physics Department, IIT Bombay,*
> *Mumbai-400076, INDIA*
>
> _______________________________________________
> Gate-users mailing listGate-users at lists.opengatecollaboration.orghttp://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>
>

-- 
*Satyajit Ghosh*
*PhD Student*

*Nuclear Spectroscopy and Molecular Imaging Lab,*
*Physics Department, IIT Bombay,*
*Mumbai-400076, INDIA*
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