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

[Simon Stute]

Hi Tony,

1. The keyword auto change the seed automatically for the random engine
/gate/random/setEngineSeed auto   (it is based on the CPU time and Process
ID, which are both always different).

2. You can write an entire macro and then just type "Gate
my_main_macro.mac" from the command prompt, it will execute and stop the
simulation automatically. If you want plenty, you just write a bash (or
csh) script to launch the simulation for you (you can do loops and so).

Regards,
Simon


On Mon, Mar 17, 2014 at 8:09 AM, Tony <tucadaica at yahoo.com> wrote:

> 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 dosedeposited 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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