<div dir="ltr"><div><div>Hi Tony,<br><br>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).<br>
<br></div>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).<br>
<br></div>Regards,<br>Simon<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Mar 17, 2014 at 8:09 AM, Tony <span dir="ltr"><<a href="mailto:tucadaica@yahoo.com" target="_blank">tucadaica@yahoo.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div style="font-size:14pt;font-family:times new roman,new york,times,serif">Hi Simon,<br><br>I am following what you suggested, but I am getting stuck at some points. Could you please help me answer the following questions:<br>
<br>- 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?<br>
<br>- 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?<br>
<br>Thank you,<br>Tony.<div><div class="h5"><br><div><span><br></span></div><div style="display:block"> <br> <br> <div style="font-family:times new roman,new york,times,serif;font-size:14pt"> <div style="font-family:times new roman,new york,times,serif;font-size:12pt">
<div dir="ltr"> <font face="Arial"> On Thursday, 13 March 2014 1:48 AM, Tony <<a href="mailto:tucadaica@yahoo.com" target="_blank">tucadaica@yahoo.com</a>> wrote:<br> </font> </div> <div><div><div><div style="font-size:14pt;font-family:times new roman,new york,times,serif">
Hi Simon,<br clear="none"><br clear="none">This is a brilliant idea. Thanks a lot for your detailed answer. <br clear="none"><br clear="none">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.<br clear="none">
<br clear="none">Many many thanks again,<br clear="none">Tony.<br clear="none"><div><span><br clear="none"></span></div><div><div style="display:block"> <br clear="none"> <br clear="none"> <div style="font-family:times new roman,new york,times,serif;font-size:14pt">
<div style="font-family:times new roman,new york,times,serif;font-size:12pt"> <div dir="ltr"> <font face="Arial"> On Wednesday, 12 March 2014 9:23 PM, Simon Stute <<a href="mailto:gate.stute@gmail.com" target="_blank">gate.stute@gmail.com</a>> wrote:<br clear="none">
</font> </div> <div><div><div><div dir="ltr"><div><div><div><div><div>Hi Tony,<br clear="none"><br clear="none">This is not a simple thing that you want to do.<br clear="none"></div><br clear="none">I would recommend to separate the problem of finding the intestine from the Gate simulations.<br clear="none">
Start by writing a program to compute the intestine position for the
source as you want, for a given time.<br clear="none">
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).<br clear="none">
<br clear="none"></div>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.<br clear="none">
</div>At the end, just sum your dose maps.<br clear="none"><br clear="none"></div>Regards,<br clear="none"></div>Simon<br clear="none"></div><div><br clear="none"><br clear="none"><div>On Wed, Mar 12, 2014 at 7:42 AM, Tony <span dir="ltr"><<a rel="nofollow" shape="rect" href="mailto:tucadaica@yahoo.com" target="_blank">tucadaica@yahoo.com</a>></span> wrote:<br clear="none">
<blockquote style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div style="font-size:14pt;font-family:times new roman,new york,times,serif"><div><span><font size="4">Could anybody please help with the above questions? Or is it possible </font></span><span><font size="4"><font size="4"><span>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.</span></font></font></span></div>
<div style="font-style:normal;font-size:18px;background-color:transparent;font-family:times new roman,new york,times,serif"><br clear="none"><span><font size="4"><font size="4"><span></span></font></font></span></div><div style="font-style:normal;font-size:18px;background-color:transparent;font-family:times new roman,new york,times,serif">
<span><font size="4"><font size="4"><span>Thank you in
advance.<br clear="none"></span></font></font></span></div><div style="display:block"> <br clear="none"> <br clear="none"> <div style="font-family:times new roman,new york,times,serif;font-size:14pt"> <div style="font-family:times new roman,new york,times,serif;font-size:12pt">
<div><div> <div dir="ltr"> <font face="Arial"> On Monday, 10 March 2014 6:02 PM, Tony <<a rel="nofollow" shape="rect" href="mailto:tucadaica@yahoo.com" target="_blank">tucadaica@yahoo.com</a>> wrote:<br clear="none">
</font> </div> </div></div>
<div><div><div><div><div><div style="font-size:12pt;font-family:times new roman,new york,times,serif"><div></div><div>
<div>Hi GATE users,</div><div><br clear="none"></div>
<div>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: <span> </span>1mm-diameter sphere) moves along
a human gastro-intestinal tract. <br clear="none"></div><div style="font-style:normal;font-size:16px;background-color:transparent;font-family:times new roman,new york,times,serif"><br clear="none"></div>
<div>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.</div><div><br clear="none"></div>
<div>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. <span><br clear="none"></span></div><div style="font-style:normal;font-size:16px;background-color:transparent;font-family:times new roman,new york,times,serif"><span><br clear="none">
</span></div>
<div>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. <br clear="none"></div><div><br clear="none"></div>
<div>My questions are:</div>
<div><span style="font-style:italic">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)?</span></div><div style="font-style:italic;font-size:16px;background-color:transparent;font-family:times new roman,new york,times,serif"><span style="font-style:italic"><br clear="none">
</span></div><span style="font-style:italic">
</span><div><span style="font-style:italic">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?</span></div><span style="font-style:italic">
</span><div><span style="font-style:italic"><br clear="none"></span></div><div style="font-style:italic;font-size:16px;background-color:transparent;font-family:times new roman,new york,times,serif"><span style="font-style:italic">3) Does the 3D dose distribution map show the <span style="text-decoration:underline">total absorbed
dose</span> deposited in every voxel of the NCAT phantom throughout 8 hour moving of
the source?</span></div>
<div><br clear="none"></div><div style="font-style:normal;font-size:16px;background-color:transparent;font-family:times new roman,new york,times,serif">Your help would be greatly appreciated. </div>
<div>Thank you,</div>
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