[Gate-users] Dose ditribution map when a point source moves along a human GI tract

[Tony]

Hi Simon,

I am following what you suggested, but I am getting stuck at some points. Could you please help me answer the following questions:

- When I perform one Gate simulation for each time position of the source, do I have to change the seed in /gate/random/setEngineSeed? As far as I know, when we use "jobsplitter", Gate will automatically generate different seed for different macros. But in my case, how would Gate know that the current simulation is the next stage of the previous simulation and change the seed accordingly?

- Are there any ways to automatically run different macros in GATE in sequence by a single command (or file)? Or do I have to manually type "/control/execute/position1.mac" (2,3,4...) one after one for each simulation?

Thank you,
Tony.





On Thursday, 13 March 2014 1:48 AM, Tony <tucadaica at yahoo.com> wrote:
 
Hi Simon,

This is a brilliant idea. Thanks a lot for your detailed answer. 

Firstly, I will need to get the NCAT package to compute the intestine position for the source for a given time. Then, I will try to do separated simulations and automatic code generation as you suggested.

Many many thanks again,
Tony.





On Wednesday, 12 March 2014 9:23 PM, Simon Stute <gate.stute at gmail.com> wrote:
 
Hi Tony,

This is not a simple thing that you want to do.

I would recommend to separate the problem of finding the intestine from the Gate simulations.
Start by writing a program to compute the intestine position for the source as you want, for a given time.
Then I would suggest to perform one Gate simulation for each time position of the source. Use the previously computed intestine source position to automatically generate the source macro for the simulations with respect to the chosen time slice. The rest of the macro should roughly stays the same from a position to another (change the output name and time info by automatic generation too).

I would do it that way if I had to do such an experiment. This is more simple to not correlate the 2 problems and this allows you to have more flexibilty to debug your simulations compared to using the GenericMove in one simulation.
At the end, just sum your dose maps.

Regards,
Simon




On Wed, Mar 12, 2014 at 7:42 AM, Tony <tucadaica at yahoo.com> wrote:

Could anybody please help with the above questions? Or is it possible to determine the position of the center of the cross section of the intestine at each slice/voxel, so that I can use the "Generic Move" in GATE to move the source in each time slice.
>
>
>Thank you in advance.
>
>
>
>
>On Monday, 10 March 2014 6:02 PM, Tony <tucadaica at yahoo.com> wrote:
> 
>Hi GATE users,
>
>
>I am trying to figure out if it would be possible to obtain
a 3D dose distribution map in a GATE simulation, in which a point source (geometric
source:  1mm-diameter sphere) moves along
a human gastro-intestinal tract. 
>
>
>
>I have read the GATE user guide carefully, especially the
section about voxelized phantom and dose collection. However, since I am quite
new to the field of medical physics, there were many parts I could not
understand clearly.
>
>
>As far as I know, I would need to use a voxelized phantom,
such as the “Extended 4D NCAT Phantom” in which the gastro-intestinal tract is
also included. Then, a 1mm-diameter sphere source needs to be defined and it should
be able to move along the intestine.  
>
>
>
>I have successfully run several GATE simulations in which a
geometric source moves in a basic trajectory inside a geometric phantom, but I
have never worked with a voxelized phantom and a complex movement of the source
before. 
>
>
>
>My questions are:
>1) Would it be possible to produce such a 3D dose
distribution map in GATE when a 1mm-diameter spherical source moves along the
intestinal tract (assuming the source has a constant speed, approximately 8 hours
to complete its journey, similar to food excretion)?
>
>
>2) Assume that I already got the Extended 4D NCAT Phantom,
how can I define the source movement so that the source can move along the
intestine of the phantom?
>
>
>3) Does the 3D dose distribution map show the total absorbed
dose deposited in every voxel of the NCAT phantom throughout 8 hour moving of
the source?
>
>
>Your help would be greatly appreciated. 
>Thank you,
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