Hojjat Mahani | 10 Mar 06:57 2014
Picon

Total detected photons in detector

Dear GATErs,

Having generated ASCII-output, how can one calculate total detected photons within the crystal (continuous or pixelated)?
Currently, I am summing up those singles having same VolumeID, but, the results are not meaningful and seem to be incorrect probably due to my procedure. 

As far as I know (please correct me), some of users prefer to use deposited-energy in the crystal (or in pixels with pixelated-scanners case) as detected photons instead of counting single-by-single in each pixel.

Any idea would be highly appreciated.
 
Hojjat Mahani


<div><div>
<div><span>Dear GATErs,</span></div>
<div><br></div>
<div><span>Having generated ASCII-output, how can one calculate total detected photons within the crystal (continuous or pixelated)?</span></div>
<div><span>Currently, I am summing up
 those singles having same VolumeID, but, the results are not meaningful and seem to be incorrect probably due to my procedure.&nbsp;</span></div>
<div><span><br></span></div>
<div><span>As far as I know (please correct me), some of users prefer to use deposited-energy in the crystal (or in pixels with pixelated-scanners case) as detected photons instead of counting single-by-single in each pixel.</span></div>
<div><span><br></span></div>
<div><span>Any idea would be highly appreciated.</span></div>
<div></div>
<div>&nbsp;</div>
<div>Hojjat Mahani</div>
<div><br></div>
<div><br></div>
</div></div>
Yunfeng Guo | 9 Mar 12:43 2014
Picon

SetCutInRegion in Siemens Biograph TruePoint PET/CT

Hello! 
I'm a Gate newer, now I'm doing simulation of Siemens Biograph TruePoint PET/CT, but I don't konw how to set SetCutInRegion in Phantom and LSO ?  1cm or 1 mm or other else ?  Is there some rules to set this value when do other PET simulations ? 

Best Regards,
Yunfeng 
<div><div dir="ltr">Hello!&nbsp;<div>I'm a Gate newer, now I'm doing simulation of&nbsp;Siemens Biograph TruePoint PET/CT, but I don't konw how to set&nbsp;SetCutInRegion in Phantom and LSO ? &nbsp;1cm or 1 mm or other else ? &nbsp;Is there some rules to set this value when do other PET simulations ?&nbsp;</div>
<div><br></div>
<div>Best Regards,</div>
<div>Yunfeng&nbsp;</div>
</div></div>
Tahereh Niknejad | 9 Mar 04:11 2014
Picon

Number of coincidences

Hi,
 
Does anyone know why the total number of coincidences is less than the sum of the trues, randoms and scatters?
 
 
if ( eventID1 != eventID2 ) Nbr_Coinc_Random++;
            
if ( eventID1 == eventID2 && comptonPhantom1 == 0 && comptonPhantom2 == 0 ) Nbr_Coinc_Trues++;
  
if ( comptonPhantom1 > 0 || comptonPhantom2 > 0) Nbr_Coinc_Scatter++;
 
Regards,
Tahereh
<div><div dir="ltr">
<div>Hi,</div>
<div>&nbsp;</div>
<div>Does anyone know why the total number of coincidences is less than the sum of the trues, randoms and scatters?</div>
<div>&nbsp;</div>
<div>&nbsp;</div>
<div>if ( eventID1 != eventID2 ) Nbr_Coinc_Random++;<br>

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<br> if ( eventID1 == eventID2 &amp;&amp; comptonPhantom1 == 0 &amp;&amp; comptonPhantom2 == 0 ) Nbr_Coinc_Trues++;<br>&nbsp;&nbsp;<br>if ( comptonPhantom1 &gt; 0 || comptonPhantom2 &gt; 0) Nbr_Coinc_Scatter++;</div>
<div>

&nbsp;</div>
<div>Regards,</div>
<div>Tahereh</div>
</div></div>
Tahereh Niknejad | 9 Mar 03:31 2014
Picon

Re: Gate-users Digest, Vol 94, Issue 15

Dear Chunhu,
 
It happened because the amount of yttrium in the Gate materials in very high.
for example for 10% yttrium you have to make change as below:
 
LYSO:   d=7.105 g/cm3; n=4 ; state=Solid
        +el: name=Lutetium ; f=0.714609801
        +el: name=Yttrium ; f=0.040381125
        +el: name=Silicon; f=0.063520871
        +el: name=Oxygen; f=0.181488203
 
 
Regards,
Tahereh


On Sun, Mar 9, 2014 at 3:33 AM, <gate-users-request <at> lists.opengatecollaboration.org> wrote:
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Today's Topics:

   1. Re: Unable to use phase space file from IAEA with Gate    6.2
      (Stathis Kamperis)
   2. Re: Unable to use phase space file from IAEA with Gate    6.2
      (Stathis Kamperis)
   3. About the performance comparison between LSO ans LYSO (???)


----------------------------------------------------------------------

Message: 1
Date: Sat, 8 Mar 2014 22:13:46 +0200
From: Stathis Kamperis <ekamperi <at> gmail.com>
To: gate-users <gate-users-ZwoEplunGu2uWGBtOU8ma0fXCdDtWGEhSoIsB4E12gc@public.gmane.org>
Subject: Re: [Gate-users] Unable to use phase space file from IAEA
        with Gate       6.2
Message-ID:
        <CACYCkUtbj8p9gE72CC2No7B0n03wXrF=3q9BaQ=edMbEfKae1Q-JsoAwUIsXosN+BqQ9rBEUg@public.gmane.org>
Content-Type: text/plain; charset=ISO-8859-1

I'm not sure why Gate can't parse the phase space file. I tried to
extract the information with Mathematica and it seems that the phase
space file is ok (not sure about the header though, especially where
the record contents are declared).

For example I get only 1,2,3 (gammas, e-, e+) for particles:

file =
  BinaryReadList[
   "~/Dropbox/foo",
   Join[
    Flatten <at>
     {"Byte", PadLeft[{}, 6, ToString <at> Real32], "Integer32", "Integer32"}],
   ByteOrdering -> -1];

h = HistogramList[file[[All, 1]]]
{{1, 2, 3, 4}, {1543049, 8306, 161}}

And the ratios seem to be in alignment with what is declared at the header:

First <at> Last <at> h/Total <at> Last <at> h // N
0.994543

125806703/126491813 // N
0.994584

I've only checked 50 MB worth of data but I doubt that there's a wrong
particle number in the rest (will check though).

So... has anyone ever successfully used the IAEA phase space files
with Gate 6.2 ?

Best regards,
Stathis




On Fri, Mar 7, 2014 at 11:40 PM, Stathis Kamperis <ekamperi-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
> Relevant:
>
> http://comments.gmane.org/gmane.comp.science.opengate.user/3115
>
> Best regards,
> Stathis
>
> On Fri, Mar 7, 2014 at 11:26 PM, Stathis Kamperis <ekamperi-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
>> Greetings everyone,
>>
>> I downloaded it from here:
>> https://www-nds.iaea.org/phsp/photon1/
>>
>> ELEKTA_PRECISE_6mv_part1.IAEAphsp and its associated header
>> ELEKTA_PRECISE_6mv_part1.IAEAheader
>>
>> When I try to use it from within Gate with:
>>
>> /gate/source/addSource mybeam phaseSpace
>> /gate/source/mybeam/addPhaseSpaceFile
>> /home/stathis/Downloads/ELEKTA_PRECISE_6mv_part1.IAEAphsp
>>
>> I get the following error:
>> /home/stathis/Downloads/gate_v6.2/source/physics/src/GateSourcePhaseSpace.cc
>> (l.252): Source phase space: particle not available in IAEA phase
>> space format.
>>
>> I checked the source code:
>> http://www.opengatecollaboration.org/lxr/source/6.2.0/source/physics/src/GateSourcePhaseSpace.cc#L231
>>
>> and it appears as if Gate can't recognize some particle type that the
>> header file is including. But,
>> https://www-nds.iaea.org/phsp/photon1/ELEKTA_PRECISE_6mv_part1.IAEAheader
>> has only photons, electrons, positrons that Gate should recognize.
>>
>> Any thoughts?
>>
>> Best regards,
>> Stathis


------------------------------

Message: 2
Date: Sat, 8 Mar 2014 22:34:36 +0200
From: Stathis Kamperis <ekamperi <at> gmail.com>
To: gate-users <gate-users-ZwoEplunGu2uWGBtOU8ma0fXCdDtWGEhSoIsB4E12gc@public.gmane.org>
Subject: Re: [Gate-users] Unable to use phase space file from IAEA
        with Gate       6.2
Message-ID:
        <CACYCkUuFkakuzc-WGG9+fpZsjreKK0oaw7MGgfFbwDZkeiB2HA-JsoAwUIsXosN+BqQ9rBEUg@public.gmane.org>
Content-Type: text/plain; charset=ISO-8859-1

On Sat, Mar 8, 2014 at 10:13 PM, Stathis Kamperis <ekamperi-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
> I'm not sure why Gate can't parse the phase space file. I tried to
> extract the information with Mathematica and it seems that the phase
> space file is ok (not sure about the header though, especially where
> the record contents are declared).
>
> For example I get only 1,2,3 (gammas, e-, e+) for particles:
>
> file =
>   BinaryReadList[
>    "~/Dropbox/foo",
>    Join[
>     Flatten <at>
>      {"Byte", PadLeft[{}, 6, ToString <at> Real32], "Integer32", "Integer32"}],
>    ByteOrdering -> -1];
>
> h = HistogramList[file[[All, 1]]]
> {{1, 2, 3, 4}, {1543049, 8306, 161}}
>
> And the ratios seem to be in alignment with what is declared at the header:
>
> First <at> Last <at> h/Total <at> Last <at> h // N
> 0.994543
>
> 125806703/126491813 // N
> 0.994584
>
> I've only checked 50 MB worth of data but I doubt that there's a wrong
> particle number in the rest (will check though).
>

The whole phase space file is ok. I checked it with the following code snippet:

[stathis <at> fedora]~/Downloads% cat read.c
                                                     22:32:29
#include <assert.h>
#include <stdio.h>

struct rec {
        char particle;
        char pad[32];
} __attribute__((packed));

int
main(int argc, char *argv[])
{
        FILE *fp;
        struct rec r;
        int cnt, rv;

        fp = fopen(argv[1], "r");
        assert(fp);

        cnt = 0;
        do {
                ++cnt;

                rv = fread(&r, sizeof(struct rec), 1, fp);
                assert(rv > 0 || (rv == 0 && feof(fp)));

                if (r.particle != 1 && r.particle != 2 && r.particle != 3) {
                        printf("Wrong particle = %d at record = %d\n",
                            r.particle, cnt);
                }
        } while(!feof(fp) && !ferror(fp));

        fclose(fp);

        return 0;
}

[stathis <at> fedora]~/Downloads% gcc -Wall -ansi -pedantic read.c
[stathis <at> fedora]~/Downloads% ./a.out ELEKTA_PRECISE_6mv_part1.IAEAphsp
[stathis <at> fedora]~/Downloads%
[stathis <at> fedora]~/Downloads% echo $?
0
[stathis <at> fedora]~/Downloads%

> So... has anyone ever successfully used the IAEA phase space files
> with Gate 6.2 ?
>
> Best regards,
> Stathis
>
>
>
>
> On Fri, Mar 7, 2014 at 11:40 PM, Stathis Kamperis <ekamperi-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
>> Relevant:
>>
>> http://comments.gmane.org/gmane.comp.science.opengate.user/3115
>>
>> Best regards,
>> Stathis
>>
>> On Fri, Mar 7, 2014 at 11:26 PM, Stathis Kamperis <ekamperi-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
>>> Greetings everyone,
>>>
>>> I downloaded it from here:
>>> https://www-nds.iaea.org/phsp/photon1/
>>>
>>> ELEKTA_PRECISE_6mv_part1.IAEAphsp and its associated header
>>> ELEKTA_PRECISE_6mv_part1.IAEAheader
>>>
>>> When I try to use it from within Gate with:
>>>
>>> /gate/source/addSource mybeam phaseSpace
>>> /gate/source/mybeam/addPhaseSpaceFile
>>> /home/stathis/Downloads/ELEKTA_PRECISE_6mv_part1.IAEAphsp
>>>
>>> I get the following error:
>>> /home/stathis/Downloads/gate_v6.2/source/physics/src/GateSourcePhaseSpace.cc
>>> (l.252): Source phase space: particle not available in IAEA phase
>>> space format.
>>>
>>> I checked the source code:
>>> http://www.opengatecollaboration.org/lxr/source/6.2.0/source/physics/src/GateSourcePhaseSpace.cc#L231
>>>
>>> and it appears as if Gate can't recognize some particle type that the
>>> header file is including. But,
>>> https://www-nds.iaea.org/phsp/photon1/ELEKTA_PRECISE_6mv_part1.IAEAheader
>>> has only photons, electrons, positrons that Gate should recognize.
>>>
>>> Any thoughts?
>>>
>>> Best regards,
>>> Stathis


------------------------------

Message: 3
Date: Sun, 9 Mar 2014 10:07:39 +0800
From: ??? <arnoxiaolei86 <at> gmail.com>
To: "gate-users-ZwoEplunGu2uWGBtOU8ma0fXCdDtWGEhSoIsB4E12gc@public.gmane.org"
        <gate-users-ZwoEplunGu2uWGBtOU8ma0fXCdDtWGEhSoIsB4E12gc@public.gmane.org>
Subject: [Gate-users] About the performance comparison between LSO ans
        LYSO
Message-ID:
        <CAGMGNVN=Rx8YpX=Qg5Rq+yDbO+1YjY0tM47fDDHMYW1bRgVaFA <at> mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hello everyone:
       I did two experiments using GateV6.2, The conditions of these
two experiments are same with each other except the material of the
crystal (using LSO in first experiment and LYSO in secone one), but
the Coincidences number recorded in the first experiment is treble as
many as that recorded in the second experiment. What a bad performance
of LYSO! Can anyone tell me why? The macros are in the attachment.
Thanks a lot!--Chunhui Zhang
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------------------------------

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End of Gate-users Digest, Vol 94, Issue 15
******************************************

<div>
<div dir="ltr">
<div>Dear Chunhu,</div>
<div>&nbsp;</div>
<div>It happened because the amount of yttrium in the Gate materials in very high. </div>
<div>for example for 10% yttrium you have to make change as below:</div>
<div>&nbsp;</div>

<div>LYSO:&nbsp;&nbsp; d=7.105 g/cm3; n=4 ; state=Solid<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; +el: name=Lutetium ; f=0.714609801<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; +el: name=Yttrium ; f=0.040381125<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; +el: name=Silicon; f=0.063520871<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; +el: name=Oxygen; f=0.181488203</div>

<div>&nbsp;</div>
<div>&nbsp;</div>
<div>Regards,</div>
<div>Tahereh</div>
</div>
<div class="gmail_extra">
<br><br><div class="gmail_quote">On Sun, Mar 9, 2014 at 3:33 AM,  <span dir="ltr">&lt;<a href="mailto:gate-users-request <at> lists.opengatecollaboration.org" target="_blank">gate-users-request <at> lists.opengatecollaboration.org</a>&gt;</span> wrote:<br><blockquote class="gmail_quote">Send Gate-users mailing list submissions to<br>
&nbsp; &nbsp; &nbsp; &nbsp; <a href="mailto:gate-users@...g">gate-users@...</a><br><br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
&nbsp; &nbsp; &nbsp; &nbsp; <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a><br>
or, via email, send a message with subject or body 'help' to<br>
&nbsp; &nbsp; &nbsp; &nbsp; <a href="mailto:gate-users-request@...ation.org">gate-users-request@...</a><br><br>
You can reach the person managing the list at<br>
&nbsp; &nbsp; &nbsp; &nbsp; <a href="mailto:gate-users-owner@...ion.org">gate-users-owner@...</a><br><br>
When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of Gate-users digest..."<br><br><br>
Today's Topics:<br><br>
&nbsp; &nbsp;1. Re: Unable to use phase space file from IAEA with Gate &nbsp; &nbsp;6.2<br>
&nbsp; &nbsp; &nbsp; (Stathis Kamperis)<br>
&nbsp; &nbsp;2. Re: Unable to use phase space file from IAEA with Gate &nbsp; &nbsp;6.2<br>
&nbsp; &nbsp; &nbsp; (Stathis Kamperis)<br>
&nbsp; &nbsp;3. About the performance comparison between LSO ans LYSO (???)<br><br><br>
----------------------------------------------------------------------<br><br>
Message: 1<br>
Date: Sat, 8 Mar 2014 22:13:46 +0200<br>
From: Stathis Kamperis &lt;<a href="mailto:ekamperi@...">ekamperi <at> gmail.com</a>&gt;<br>
To: gate-users &lt;<a href="mailto:gate-users@....org">gate-users@...</a>&gt;<br>
Subject: Re: [Gate-users] Unable to use phase space file from IAEA<br>
&nbsp; &nbsp; &nbsp; &nbsp; with Gate &nbsp; &nbsp; &nbsp; 6.2<br>
Message-ID:<br>
&nbsp; &nbsp; &nbsp; &nbsp; &lt;CACYCkUtbj8p9gE72CC2No7B0n03wXrF=3q9BaQ=<a href="mailto:edMbEfKae1Q@...">edMbEfKae1Q@...</a>&gt;<br>
Content-Type: text/plain; charset=ISO-8859-1<br><br>
I'm not sure why Gate can't parse the phase space file. I tried to<br>
extract the information with Mathematica and it seems that the phase<br>
space file is ok (not sure about the header though, especially where<br>
the record contents are declared).<br><br>
For example I get only 1,2,3 (gammas, e-, e+) for particles:<br><br>
file =<br>
&nbsp; BinaryReadList[<br>
&nbsp; &nbsp;"~/Dropbox/foo",<br>
&nbsp; &nbsp;Join[<br>
&nbsp; &nbsp; Flatten <at> <br>
&nbsp; &nbsp; &nbsp;{"Byte", PadLeft[{}, 6, ToString <at> Real32], "Integer32", "Integer32"}],<br>
&nbsp; &nbsp;ByteOrdering -&gt; -1];<br><br>
h = HistogramList[file[[All, 1]]]<br>
{{1, 2, 3, 4}, {1543049, 8306, 161}}<br><br>
And the ratios seem to be in alignment with what is declared at the header:<br><br>
First <at> Last <at> h/Total <at> Last <at> h // N<br>
0.994543<br><br>
125806703/126491813 // N<br>
0.994584<br><br>
I've only checked 50 MB worth of data but I doubt that there's a wrong<br>
particle number in the rest (will check though).<br><br>
So... has anyone ever successfully used the IAEA phase space files<br>
with Gate 6.2 ?<br><br>
Best regards,<br>
Stathis<br><br><br><br><br>
On Fri, Mar 7, 2014 at 11:40 PM, Stathis Kamperis &lt;<a href="mailto:ekamperi@...">ekamperi@...</a>&gt; wrote:<br>
&gt; Relevant:<br>
&gt;<br>
&gt; <a href="http://comments.gmane.org/gmane.comp.science.opengate.user/3115" target="_blank">http://comments.gmane.org/gmane.comp.science.opengate.user/3115</a><br>
&gt;<br>
&gt; Best regards,<br>
&gt; Stathis<br>
&gt;<br>
&gt; On Fri, Mar 7, 2014 at 11:26 PM, Stathis Kamperis &lt;<a href="mailto:ekamperi@...">ekamperi@...</a>&gt; wrote:<br>
&gt;&gt; Greetings everyone,<br>
&gt;&gt;<br>
&gt;&gt; I downloaded it from here:<br>
&gt;&gt; <a href="https://www-nds.iaea.org/phsp/photon1/" target="_blank">https://www-nds.iaea.org/phsp/photon1/</a><br>
&gt;&gt;<br>
&gt;&gt; ELEKTA_PRECISE_6mv_part1.IAEAphsp and its associated header<br>
&gt;&gt; ELEKTA_PRECISE_6mv_part1.IAEAheader<br>
&gt;&gt;<br>
&gt;&gt; When I try to use it from within Gate with:<br>
&gt;&gt;<br>
&gt;&gt; /gate/source/addSource mybeam phaseSpace<br>
&gt;&gt; /gate/source/mybeam/addPhaseSpaceFile<br>
&gt;&gt; /home/stathis/Downloads/ELEKTA_PRECISE_6mv_part1.IAEAphsp<br>
&gt;&gt;<br>
&gt;&gt; I get the following error:<br>
&gt;&gt; /home/stathis/Downloads/gate_v6.2/source/physics/src/GateSourcePhaseSpace.cc<br>
&gt;&gt; (l.252): Source phase space: particle not available in IAEA phase<br>
&gt;&gt; space format.<br>
&gt;&gt;<br>
&gt;&gt; I checked the source code:<br>
&gt;&gt; <a href="http://www.opengatecollaboration.org/lxr/source/6.2.0/source/physics/src/GateSourcePhaseSpace.cc#L231" target="_blank">http://www.opengatecollaboration.org/lxr/source/6.2.0/source/physics/src/GateSourcePhaseSpace.cc#L231</a><br>

&gt;&gt;<br>
&gt;&gt; and it appears as if Gate can't recognize some particle type that the<br>
&gt;&gt; header file is including. But,<br>
&gt;&gt; <a href="https://www-nds.iaea.org/phsp/photon1/ELEKTA_PRECISE_6mv_part1.IAEAheader" target="_blank">https://www-nds.iaea.org/phsp/photon1/ELEKTA_PRECISE_6mv_part1.IAEAheader</a><br>
&gt;&gt; has only photons, electrons, positrons that Gate should recognize.<br>
&gt;&gt;<br>
&gt;&gt; Any thoughts?<br>
&gt;&gt;<br>
&gt;&gt; Best regards,<br>
&gt;&gt; Stathis<br><br><br>
------------------------------<br><br>
Message: 2<br>
Date: Sat, 8 Mar 2014 22:34:36 +0200<br>
From: Stathis Kamperis &lt;<a href="mailto:ekamperi@...">ekamperi <at> gmail.com</a>&gt;<br>
To: gate-users &lt;<a href="mailto:gate-users@....org">gate-users@...</a>&gt;<br>
Subject: Re: [Gate-users] Unable to use phase space file from IAEA<br>
&nbsp; &nbsp; &nbsp; &nbsp; with Gate &nbsp; &nbsp; &nbsp; 6.2<br>
Message-ID:<br>
&nbsp; &nbsp; &nbsp; &nbsp; &lt;<a href="mailto:CACYCkUuFkakuzc-WGG9%2BfpZsjreKK0oaw7MGgfFbwDZkeiB2HA@...">CACYCkUuFkakuzc-WGG9+fpZsjreKK0oaw7MGgfFbwDZkeiB2HA@...</a>&gt;<br>
Content-Type: text/plain; charset=ISO-8859-1<br><br>
On Sat, Mar 8, 2014 at 10:13 PM, Stathis Kamperis &lt;<a href="mailto:ekamperi@...">ekamperi@...</a>&gt; wrote:<br>
&gt; I'm not sure why Gate can't parse the phase space file. I tried to<br>
&gt; extract the information with Mathematica and it seems that the phase<br>
&gt; space file is ok (not sure about the header though, especially where<br>
&gt; the record contents are declared).<br>
&gt;<br>
&gt; For example I get only 1,2,3 (gammas, e-, e+) for particles:<br>
&gt;<br>
&gt; file =<br>
&gt; &nbsp; BinaryReadList[<br>
&gt; &nbsp; &nbsp;"~/Dropbox/foo",<br>
&gt; &nbsp; &nbsp;Join[<br>
&gt; &nbsp; &nbsp; Flatten <at> <br>
&gt; &nbsp; &nbsp; &nbsp;{"Byte", PadLeft[{}, 6, ToString <at> Real32], "Integer32", "Integer32"}],<br>
&gt; &nbsp; &nbsp;ByteOrdering -&gt; -1];<br>
&gt;<br>
&gt; h = HistogramList[file[[All, 1]]]<br>
&gt; {{1, 2, 3, 4}, {1543049, 8306, 161}}<br>
&gt;<br>
&gt; And the ratios seem to be in alignment with what is declared at the header:<br>
&gt;<br>
&gt; First <at> Last <at> h/Total <at> Last <at> h // N<br>
&gt; 0.994543<br>
&gt;<br>
&gt; 125806703/126491813 // N<br>
&gt; 0.994584<br>
&gt;<br>
&gt; I've only checked 50 MB worth of data but I doubt that there's a wrong<br>
&gt; particle number in the rest (will check though).<br>
&gt;<br><br>
The whole phase space file is ok. I checked it with the following code snippet:<br><br>
[stathis <at> fedora]~/Downloads% cat read.c<br>
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;22:32:29<br>
#include &lt;assert.h&gt;<br>
#include &lt;stdio.h&gt;<br><br>
struct rec {<br>
&nbsp; &nbsp; &nbsp; &nbsp; char particle;<br>
&nbsp; &nbsp; &nbsp; &nbsp; char pad[32];<br>
} __attribute__((packed));<br><br>
int<br>
main(int argc, char *argv[])<br>
{<br>
&nbsp; &nbsp; &nbsp; &nbsp; FILE *fp;<br>
&nbsp; &nbsp; &nbsp; &nbsp; struct rec r;<br>
&nbsp; &nbsp; &nbsp; &nbsp; int cnt, rv;<br><br>
&nbsp; &nbsp; &nbsp; &nbsp; fp = fopen(argv[1], "r");<br>
&nbsp; &nbsp; &nbsp; &nbsp; assert(fp);<br><br>
&nbsp; &nbsp; &nbsp; &nbsp; cnt = 0;<br>
&nbsp; &nbsp; &nbsp; &nbsp; do {<br>
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; ++cnt;<br><br>
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; rv = fread(&amp;r, sizeof(struct rec), 1, fp);<br>
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; assert(rv &gt; 0 || (rv == 0 &amp;&amp; feof(fp)));<br><br>
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; if (r.particle != 1 &amp;&amp; r.particle != 2 &amp;&amp; r.particle != 3) {<br>
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; printf("Wrong particle = %d at record = %d\n",<br>
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; r.particle, cnt);<br>
&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; }<br>
&nbsp; &nbsp; &nbsp; &nbsp; } while(!feof(fp) &amp;&amp; !ferror(fp));<br><br>
&nbsp; &nbsp; &nbsp; &nbsp; fclose(fp);<br><br>
&nbsp; &nbsp; &nbsp; &nbsp; return 0;<br>
}<br><br>
[stathis <at> fedora]~/Downloads% gcc -Wall -ansi -pedantic read.c<br>
[stathis <at> fedora]~/Downloads% ./a.out ELEKTA_PRECISE_6mv_part1.IAEAphsp<br>
[stathis <at> fedora]~/Downloads%<br>
[stathis <at> fedora]~/Downloads% echo $?<br>
0<br>
[stathis <at> fedora]~/Downloads%<br><br>
&gt; So... has anyone ever successfully used the IAEA phase space files<br>
&gt; with Gate 6.2 ?<br>
&gt;<br>
&gt; Best regards,<br>
&gt; Stathis<br>
&gt;<br>
&gt;<br>
&gt;<br>
&gt;<br>
&gt; On Fri, Mar 7, 2014 at 11:40 PM, Stathis Kamperis &lt;<a href="mailto:ekamperi@...">ekamperi@...</a>&gt; wrote:<br>
&gt;&gt; Relevant:<br>
&gt;&gt;<br>
&gt;&gt; <a href="http://comments.gmane.org/gmane.comp.science.opengate.user/3115" target="_blank">http://comments.gmane.org/gmane.comp.science.opengate.user/3115</a><br>
&gt;&gt;<br>
&gt;&gt; Best regards,<br>
&gt;&gt; Stathis<br>
&gt;&gt;<br>
&gt;&gt; On Fri, Mar 7, 2014 at 11:26 PM, Stathis Kamperis &lt;<a href="mailto:ekamperi@...">ekamperi@...</a>&gt; wrote:<br>
&gt;&gt;&gt; Greetings everyone,<br>
&gt;&gt;&gt;<br>
&gt;&gt;&gt; I downloaded it from here:<br>
&gt;&gt;&gt; <a href="https://www-nds.iaea.org/phsp/photon1/" target="_blank">https://www-nds.iaea.org/phsp/photon1/</a><br>
&gt;&gt;&gt;<br>
&gt;&gt;&gt; ELEKTA_PRECISE_6mv_part1.IAEAphsp and its associated header<br>
&gt;&gt;&gt; ELEKTA_PRECISE_6mv_part1.IAEAheader<br>
&gt;&gt;&gt;<br>
&gt;&gt;&gt; When I try to use it from within Gate with:<br>
&gt;&gt;&gt;<br>
&gt;&gt;&gt; /gate/source/addSource mybeam phaseSpace<br>
&gt;&gt;&gt; /gate/source/mybeam/addPhaseSpaceFile<br>
&gt;&gt;&gt; /home/stathis/Downloads/ELEKTA_PRECISE_6mv_part1.IAEAphsp<br>
&gt;&gt;&gt;<br>
&gt;&gt;&gt; I get the following error:<br>
&gt;&gt;&gt; /home/stathis/Downloads/gate_v6.2/source/physics/src/GateSourcePhaseSpace.cc<br>
&gt;&gt;&gt; (l.252): Source phase space: particle not available in IAEA phase<br>
&gt;&gt;&gt; space format.<br>
&gt;&gt;&gt;<br>
&gt;&gt;&gt; I checked the source code:<br>
&gt;&gt;&gt; <a href="http://www.opengatecollaboration.org/lxr/source/6.2.0/source/physics/src/GateSourcePhaseSpace.cc#L231" target="_blank">http://www.opengatecollaboration.org/lxr/source/6.2.0/source/physics/src/GateSourcePhaseSpace.cc#L231</a><br>

&gt;&gt;&gt;<br>
&gt;&gt;&gt; and it appears as if Gate can't recognize some particle type that the<br>
&gt;&gt;&gt; header file is including. But,<br>
&gt;&gt;&gt; <a href="https://www-nds.iaea.org/phsp/photon1/ELEKTA_PRECISE_6mv_part1.IAEAheader" target="_blank">https://www-nds.iaea.org/phsp/photon1/ELEKTA_PRECISE_6mv_part1.IAEAheader</a><br>
&gt;&gt;&gt; has only photons, electrons, positrons that Gate should recognize.<br>
&gt;&gt;&gt;<br>
&gt;&gt;&gt; Any thoughts?<br>
&gt;&gt;&gt;<br>
&gt;&gt;&gt; Best regards,<br>
&gt;&gt;&gt; Stathis<br><br><br>
------------------------------<br><br>
Message: 3<br>
Date: Sun, 9 Mar 2014 10:07:39 +0800<br>
From: ??? &lt;<a href="mailto:arnoxiaolei86@...">arnoxiaolei86 <at> gmail.com</a>&gt;<br>
To: "<a href="mailto:gate-users@...">gate-users@...</a>"<br>
&nbsp; &nbsp; &nbsp; &nbsp; &lt;<a href="mailto:gate-users@...n.org">gate-users@...</a>&gt;<br>
Subject: [Gate-users] About the performance comparison between LSO ans<br>
&nbsp; &nbsp; &nbsp; &nbsp; LYSO<br>
Message-ID:<br>
&nbsp; &nbsp; &nbsp; &nbsp; &lt;CAGMGNVN=Rx8YpX=<a href="mailto:Qg5Rq%2ByDbO%2B1YjY0tM47fDDHMYW1bRgVaFA@...">Qg5Rq+yDbO+1YjY0tM47fDDHMYW1bRgVaFA <at> mail.gmail.com</a>&gt;<br>
Content-Type: text/plain; charset="iso-8859-1"<br><br>
Hello everyone:<br>
&nbsp; &nbsp; &nbsp; &nbsp;I did two experiments using GateV6.2, The conditions of these<br>
two experiments are same with each other except the material of the<br>
crystal (using LSO in first experiment and LYSO in secone one), but<br>
the Coincidences number recorded in the first experiment is treble as<br>
many as that recorded in the second experiment. What a bad performance<br>
of LYSO! Can anyone tell me why? The macros are in the attachment.<br>
Thanks a lot!--Chunhui Zhang<br>
-------------- next part --------------<br>
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------------------------------<br><br>
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End of Gate-users Digest, Vol 94, Issue 15<br>
******************************************<br>
</blockquote>
</div>
<br>
</div>
</div>
张春晖 | 9 Mar 03:07 2014
Picon

About the performance comparison between LSO ans LYSO

Hello everyone:
       I did two experiments using GateV6.2, The conditions of these
two experiments are same with each other except the material of the
crystal (using LSO in first experiment and LYSO in secone one), but
the Coincidences number recorded in the first experiment is treble as
many as that recorded in the second experiment. What a bad performance
of LYSO! Can anyone tell me why? The macros are in the attachment.
Thanks a lot!--Chunhui Zhang
Attachment (PET.zip): application/zip, 149 KiB
Hello everyone:
       I did two experiments using GateV6.2, The conditions of these
two experiments are same with each other except the material of the
crystal (using LSO in first experiment and LYSO in secone one), but
the Coincidences number recorded in the first experiment is treble as
many as that recorded in the second experiment. What a bad performance
of LYSO! Can anyone tell me why? The macros are in the attachment.
Thanks a lot!--Chunhui Zhang
Stathis Kamperis | 7 Mar 22:26 2014
Picon

Unable to use phase space file from IAEA with Gate 6.2

Greetings everyone,

I downloaded it from here:
https://www-nds.iaea.org/phsp/photon1/

ELEKTA_PRECISE_6mv_part1.IAEAphsp and its associated header
ELEKTA_PRECISE_6mv_part1.IAEAheader

When I try to use it from within Gate with:

/gate/source/addSource mybeam phaseSpace
/gate/source/mybeam/addPhaseSpaceFile
/home/stathis/Downloads/ELEKTA_PRECISE_6mv_part1.IAEAphsp

I get the following error:
/home/stathis/Downloads/gate_v6.2/source/physics/src/GateSourcePhaseSpace.cc
(l.252): Source phase space: particle not available in IAEA phase
space format.

I checked the source code:
http://www.opengatecollaboration.org/lxr/source/6.2.0/source/physics/src/GateSourcePhaseSpace.cc#L231

and it appears as if Gate can't recognize some particle type that the
header file is including. But,
https://www-nds.iaea.org/phsp/photon1/ELEKTA_PRECISE_6mv_part1.IAEAheader
has only photons, electrons, positrons that Gate should recognize.

Any thoughts?

Best regards,
Stathis
Berker, Yannick | 6 Mar 14:02 2014
Picon

Re: No comptonPhantom or RayleighPhantom entries for voxelized phantom

Hi Tom,

which version of GATE are you using? I had my problems with early versions of GATE 6 (like 6.0 or 6.1), and I have managed to get seemingly correct values with GATE 6.2.

 

First, I recall that for Rayleigh (not Compton) interactions, there was a bug in GATE 6.0 and 6.1 that was fixed in 6.2. In 6.0 and 6.1, an interaction from a “PenelopeRayleighScattering” (6.0/6.1) or “RayleighScattering” (6.1) process would not be counted as a Rayleigh interaction in the ROOT output since the code checks for a process name with “LowEnRayleigh” in it – this is due to these lines here:

http://www.opengatecollaboration.org/lxr/source/6.0.0/source/digits_hits/src/GateAnalysis.cc#L278

http://www.opengatecollaboration.org/lxr/source/6.1.0/source/digits_hits/src/GateAnalysis.cc#L281

 

Here, is it fixed:

http://www.opengatecollaboration.org/lxr/source/6.2.0/source/digits_hits/src/GateAnalysis.cc#L292

 

Here are some physics processes which could have been affected by that bug:

http://www.opengatecollaboration.org/lxr/source/6.0.0/source/physics/src/GateRayleighPenelopePB.cc

http://www.opengatecollaboration.org/lxr/source/6.1.0/source/physics/src/GateRayleighPenelopePB.cc

http://www.opengatecollaboration.org/lxr/source/6.1.0/source/physics/src/GateRayleighPB.cc

 

If you are already using GATE 6.2, the problem (or at least one solution) might be that you can attach the PhantomSD to the subvolumes which are created from your voxelized phantom. My current code contains this:

 

/gate/patientAT_AG_SI1_31/attachPhantomSD

[…, 4 more]

/gate/patientAT_AG_SI5_36/attachPhantomSD

/gate/patientAir_0/attachPhantomSD

/gate/patientAir_1/attachPhantomSD

/gate/patientConnectiveTissue_40/attachPhantomSD

/gate/patientLung_10/attachPhantomSD

[…, 27 more]

/gate/patientLung_9/attachPhantomSD

/gate/patientMarrow_Bone01_41/attachPhantomSD

[…, 13 more]

/gate/patientMarrow_Bone08_55/attachPhantomSD

/gate/patientSoftTissus_37/attachPhantomSD

/gate/patientSoftTissus_38/attachPhantomSD

/gate/patientSoftTissus_39/attachPhantomSD

/gate/patientworldDefaultAir/attachPhantomSD

 

The complete list depends on your phantom – you should include all subvolumes, but you may only include existing ones. I think the list of volumes generated is part of the GATE output, so you can grab this from your current simulation, prepend “/gate/patient” (or whatever your generating volume name is), append “/attachPhantomSD” and save this as the phantomSD.mac specific to that voxelized input and the volume-generation parameters. Should any of these change without yout re-generating the mac file, in the best case you lose one of the volumes you had in your the mac file before and your script returns an error message. In the worst case, you will get inaccurate results without noticing, for example, when only additional volumes are generated and you miss scatter interactions in those without getting any error message.

 

Best regards

 

Yannick

 

From: Tom Buitenhuis [mailto:h.j.t.buitenhuis-39IHFo8E5E0@public.gmane.org]
Sent: Thursday, March 06, 2014 12:27 PM
To: Berker, Yannick; gate-users-ZwoEplunGu2uWGBtOU8ma0fXCdDtWGEhSoIsB4E12gc@public.gmane.org
Subject: No comptonPhantom or RayleighPhantom entries for voxelized phantom

 

Dear GATE users,

 

I am having the same problem as Yannick Berker described on 2011-10-21. I use the ImageNestedParametrisedVolume phantom for a PET simulation. The sources are described using interfiles. Everything seems to be working correctly, i.e. the sources and phantom are in the right place and coincidences are detected. The effect of phantom attenuation is also clearly visible.

 

The problem that I’m having, is that in the ROOT coincidences tree there is no comptonPhantom and RayleighPhantom data. I cannot add the VoxelPhantomSD to the ImageNestedParametrisedVolume, because I get an error message saying the command is unavailable. I can add the ordinary PhantomSD, but this does not seem to add the comptonPhantom or RayleighPhantom information to the coincidence tree. The comptonCrystal and RayleighCrystal entries are correct, so I think the physics processes are registered and working correctly. 

 

I need the comptonPhantom and RayleighPhantom information to get scatter information on coincidences.

 

Did anyone else come across this problem, and if so, how did you solve it? Or can anyone point me in the direction of a solution?

 

Regards,

 

Tom Buitenhuis

 

PhD student

KVI - Center for Advanced Radiation Technology

University of Groningen

The Netherlands



Dear GATE users,

 

I have some issues using the HounsfieldMaterialGenerator to simulate a PET scan of a patient. The

simulation itself is running fine, but I am lacking two features that I am used to from other simulations,

which are scatter information and color visualization. I mainly used the example from

http://www.creatis.insa-lyon.fr/gate/Example2/ to generate the following phantom:

 

/gate/HounsfieldMaterialGenerator/SetMaterialTable                  CT/Schneider2000MaterialsTable.txt

/gate/HounsfieldMaterialGenerator/SetDensityTable                   CT/Schneider2000DensitiesTable.txt

/gate/HounsfieldMaterialGenerator/SetDensityTolerance               0.03 g/cm3

/gate/HounsfieldMaterialGenerator/SetOutputMaterialDatabaseFilename CT/p971-HUmaterials.db

/gate/HounsfieldMaterialGenerator/SetOutputHUMaterialFilename       CT/p971-HU2mat.txt

/gate/HounsfieldMaterialGenerator/Generate

/gate/world/daughters/name                                          patient

/gate/world/daughters/insert                                        ImageRegionalizedVolume

/gate/geometry/setMaterialDatabase                                  CT/p971-HUmaterials.db

/gate/patient/geometry/SetHUToMaterialFile                          CT/p971-HU2mat.txt

/gate/patient/geometry/SetImage                                     CT/p971s3.hdr

...

 

The ROOT output shows me that the volume is placed correctly, and the distribution of detected

coincidences also shows the effect of photon attenuation by the phantom. However, I cannot attach a

VoxelPhantomSD to the patient - I receive an error message telling me that this command is unavailable:

[G4-cerr] ***** COMMAND NOT FOUND </gate/patient/attachVoxelPhantomSD> *****

Attaching an ordinary PhantomSD seems to work, but only generates 0 entries in ComptonPhantom and

RayleighPhantom. I also tried using a ImageNestedParametrisedVolume, with no effect. ComptonCrystal

entries, however, seem to be correct (>= 0).

 

Apart from that, how can I visualize the voxelized phantom using colors? I was not able to add color

attributes (like "true 0.5 0.5 0.5 1.0") to p971-HU2mat.txt manually, since this resulted in the

following error message:

src/GateVImageVolume.cc (l.332): No Hounsfield material defined in the file

CT/p971s3_ToSim_OneBP_HU2mat_Colors.txt. Abort

 

Does anyone have knowledge in this area, or can point to some helpful documentation on this topic? The GATE

User's Guide has a few, but only incomplete examples for the case of voxelized phantoms and sources.

 

Best regards,

 

Yannick Berker

 

The information contained in this message may be confidential and legally protected under applicable

law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are

hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly

prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return

e-mail and destroy all copies of the original message.

 

<div>
<div class="WordSection1">
<p class="MsoNormal"><span>Hi Tom,<p></p></span></p>
<p class="MsoNormal"><span>which version of GATE are you using? I had my problems with early versions of GATE 6 (like 6.0 or 6.1), and I have managed to get seemingly correct values with
 GATE 6.2.<p></p></span></p>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
<p class="MsoNormal"><span>First, I recall that for Rayleigh (not Compton) interactions, there was a bug in GATE 6.0 and 6.1 that was fixed in 6.2. In 6.0 and 6.1, an interaction from
 a &ldquo;PenelopeRayleighScattering&rdquo; (6.0/6.1) or &ldquo;RayleighScattering&rdquo; (6.1) process would not be counted as a Rayleigh interaction in the ROOT output since the code checks for a process name with &ldquo;LowEnRayleigh&rdquo; in it &ndash; this is due to these lines here:<p></p></span></p>
<p class="MsoNormal"><span><a href="http://www.opengatecollaboration.org/lxr/source/6.0.0/source/digits_hits/src/GateAnalysis.cc#L278">http://www.opengatecollaboration.org/lxr/source/6.0.0/source/digits_hits/src/GateAnalysis.cc#L278</a><p></p></span></p>
<p class="MsoNormal"><span><a href="http://www.opengatecollaboration.org/lxr/source/6.1.0/source/digits_hits/src/GateAnalysis.cc#L281">http://www.opengatecollaboration.org/lxr/source/6.1.0/source/digits_hits/src/GateAnalysis.cc#L281</a><p></p></span></p>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
<p class="MsoNormal"><span>Here, is it fixed:<p></p></span></p>
<p class="MsoNormal"><span><a href="http://www.opengatecollaboration.org/lxr/source/6.2.0/source/digits_hits/src/GateAnalysis.cc#L292">http://www.opengatecollaboration.org/lxr/source/6.2.0/source/digits_hits/src/GateAnalysis.cc#L292</a><p></p></span></p>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
<p class="MsoNormal"><span>Here are some physics processes which could have been affected by that bug:<p></p></span></p>
<p class="MsoNormal"><span><a href="http://www.opengatecollaboration.org/lxr/source/6.0.0/source/physics/src/GateRayleighPenelopePB.cc">http://www.opengatecollaboration.org/lxr/source/6.0.0/source/physics/src/GateRayleighPenelopePB.cc</a><p></p></span></p>
<p class="MsoNormal"><span><a href="http://www.opengatecollaboration.org/lxr/source/6.1.0/source/physics/src/GateRayleighPenelopePB.cc">http://www.opengatecollaboration.org/lxr/source/6.1.0/source/physics/src/GateRayleighPenelopePB.cc</a><p></p></span></p>
<p class="MsoNormal"><span><a href="http://www.opengatecollaboration.org/lxr/source/6.1.0/source/physics/src/GateRayleighPB.cc">http://www.opengatecollaboration.org/lxr/source/6.1.0/source/physics/src/GateRayleighPB.cc</a><p></p></span></p>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
<p class="MsoNormal"><span>If you are already using GATE 6.2, the problem (or at least one solution) might be that you can attach the PhantomSD to the subvolumes which are created from
 your voxelized phantom. My current code contains this:<p></p></span></p>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
<p class="MsoNormal"><span>/gate/patientAT_AG_SI1_31/attachPhantomSD<p></p></span></p>
<p class="MsoNormal"><span>[&hellip;, 4 more]<p></p></span></p>
<p class="MsoNormal"><span>/gate/patientAT_AG_SI5_36/attachPhantomSD<p></p></span></p>
<p class="MsoNormal"><span>/gate/patientAir_0/attachPhantomSD<p></p></span></p>
<p class="MsoNormal"><span>/gate/patientAir_1/attachPhantomSD<p></p></span></p>
<p class="MsoNormal"><span>/gate/patientConnectiveTissue_40/attachPhantomSD<p></p></span></p>
<p class="MsoNormal"><span>/gate/patientLung_10/attachPhantomSD<p></p></span></p>
<p class="MsoNormal"><span>[&hellip;, 27 more]<p></p></span></p>
<p class="MsoNormal"><span>/gate/patientLung_9/attachPhantomSD<p></p></span></p>
<p class="MsoNormal"><span>/gate/patientMarrow_Bone01_41/attachPhantomSD<p></p></span></p>
<p class="MsoNormal"><span>[&hellip;, 13 more]<p></p></span></p>
<p class="MsoNormal"><span>/gate/patientMarrow_Bone08_55/attachPhantomSD<p></p></span></p>
<p class="MsoNormal"><span>/gate/patientSoftTissus_37/attachPhantomSD<p></p></span></p>
<p class="MsoNormal"><span>/gate/patientSoftTissus_38/attachPhantomSD<p></p></span></p>
<p class="MsoNormal"><span>/gate/patientSoftTissus_39/attachPhantomSD<p></p></span></p>
<p class="MsoNormal"><span>/gate/patientworldDefaultAir/attachPhantomSD<p></p></span></p>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
<p class="MsoNormal"><span>The complete list depends on your phantom &ndash; you should include all subvolumes, but you may only include existing ones. I think the list of volumes generated
 is part of the GATE output, so you can grab this from your current simulation, prepend &ldquo;/gate/patient&rdquo; (or whatever your generating volume name is), append &ldquo;/attachPhantomSD&rdquo; and save this as the phantomSD.mac
specific to that voxelized input and the volume-generation parameters. Should any of these change without yout re-generating the mac file, in the best case you lose one of the volumes you had in your the mac file before and your script returns an error
 message. In the worst case, you will get inaccurate results without noticing, for example, when only additional volumes are generated and you miss scatter interactions in those without getting any error message.<p></p></span></p>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
<p class="MsoNormal"><span>Best regards<p></p></span></p>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
<p class="MsoNormal"><span>Yannick<p></p></span></p>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
<div>
<div>
<p class="MsoNormal"><span>From:</span><span> Tom Buitenhuis [mailto:h.j.t.buitenhuis@...]
<br>Sent: Thursday, March 06, 2014 12:27 PM<br>To: Berker, Yannick; gate-users@...<br>Subject: No comptonPhantom or RayleighPhantom entries for voxelized phantom<p></p></span></p>
</div>
</div>
<p class="MsoNormal"><p>&nbsp;</p></p>
<div>
<p class="MsoNormal">Dear GATE users,<p></p></p>
</div>
<div>
<p class="MsoNormal"><p>&nbsp;</p></p>
</div>
<div>
<p class="MsoNormal">I am having the same problem as Yannick Berker described on 2011-10-21. I use the ImageNestedParametrisedVolume phantom for a PET simulation. The sources are described using interfiles. Everything seems to be working correctly, i.e. the
 sources and phantom are in the right place and coincidences are detected. The effect of phantom attenuation is also clearly visible.<p></p></p>
</div>
<div>
<p class="MsoNormal"><p>&nbsp;</p></p>
</div>
<div>
<p class="MsoNormal">The problem that I&rsquo;m having, is that in the ROOT coincidences tree there is no comptonPhantom and RayleighPhantom data. I cannot add the VoxelPhantomSD to the ImageNestedParametrisedVolume, because I get an error message saying the command
 is unavailable. I can add the ordinary PhantomSD, but this does not seem to add the comptonPhantom or RayleighPhantom information to the coincidence tree. The comptonCrystal and RayleighCrystal entries are correct, so I think the physics processes are registered
 and working correctly.&nbsp;<p></p></p>
</div>
<div>
<p class="MsoNormal"><p>&nbsp;</p></p>
</div>
<div>
<p class="MsoNormal">I need the comptonPhantom and RayleighPhantom information to get scatter information on coincidences.<p></p></p>
</div>
<div>
<p class="MsoNormal"><p>&nbsp;</p></p>
</div>
<div>
<p class="MsoNormal">Did anyone else come across this problem, and if so, how did you solve it? Or can anyone point me in the direction of a solution?<p></p></p>
</div>
<div>
<p class="MsoNormal"><p>&nbsp;</p></p>
</div>
<div>
<p class="MsoNormal">Regards,<p></p></p>
</div>
<div>
<p class="MsoNormal"><p>&nbsp;</p></p>
</div>
<div>
<p class="MsoNormal">Tom Buitenhuis<p></p></p>
</div>
<div>
<p class="MsoNormal"><p>&nbsp;</p></p>
</div>
<div>
<p class="MsoNormal">PhD student<p></p></p>
</div>
<div>
<p class="MsoNormal">KVI - Center for Advanced Radiation Technology<p></p></p>
</div>
<div>
<p class="MsoNormal">University of Groningen<p></p></p>
</div>
<div>
<p class="MsoNormal">The Netherlands<p></p></p>
</div>
<p class="MsoNormal"><br><br><p></p></p>
<blockquote>
<div>
Dear GATE users,<p></p>
<p>&nbsp;</p>
I have some issues using the HounsfieldMaterialGenerator to simulate a PET scan of a patient. The<p></p>
simulation itself is running fine, but I am lacking two features that I am used to from other simulations,<p></p>
which are scatter information and color visualization. I mainly used the example from<p></p>
<a href="http://www.creatis.insa-lyon.fr/gate/Example2/" target="_top"><span>http://www.creatis.insa-lyon.fr/gate/Example2/</span></a> to generate the following phantom:<p></p>
<p>&nbsp;</p>
/gate/HounsfieldMaterialGenerator/SetMaterialTable&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; CT/Schneider2000MaterialsTable.txt<p></p>
/gate/HounsfieldMaterialGenerator/SetDensityTable&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;CT/Schneider2000DensitiesTable.txt<p></p>
/gate/HounsfieldMaterialGenerator/SetDensityTolerance&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.03 g/cm3<p></p>
/gate/HounsfieldMaterialGenerator/SetOutputMaterialDatabaseFilename CT/p971-HUmaterials.db<p></p>
/gate/HounsfieldMaterialGenerator/SetOutputHUMaterialFilename&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; CT/p971-HU2mat.txt<p></p>
/gate/HounsfieldMaterialGenerator/Generate<p></p>
/gate/world/daughters/name&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; patient<p></p>
/gate/world/daughters/insert&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ImageRegionalizedVolume<p></p>
/gate/geometry/setMaterialDatabase&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; CT/p971-HUmaterials.db<p></p>
/gate/patient/geometry/SetHUToMaterialFile&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; CT/p971-HU2mat.txt<p></p>
/gate/patient/geometry/SetImage&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; CT/p971s3.hdr<p></p>
...<p></p>
<p>&nbsp;</p>
The ROOT output shows me that the volume is placed correctly, and the distribution of detected<p></p>
coincidences also shows the effect of photon attenuation by the phantom. However, I cannot attach a<p></p>
<span>VoxelPhantomSD</span> to the patient - I receive an error message telling me that this command is unavailable:<p></p>
[G4-cerr] ***** COMMAND NOT FOUND &lt;/gate/patient/attach<span>VoxelPhantomSD</span>&gt; *****≤p></p>
Attaching an ordinary PhantomSD seems to work, but only generates 0 entries in ComptonPhantom and<p></p>
RayleighPhantom. I also tried using a ImageNestedParametrisedVolume, with no effect. ComptonCrystal<p></p>
entries, however, seem to be correct (&gt;= 0).<p></p>
<p>&nbsp;</p>
Apart from that, how can I visualize the voxelized phantom using colors? I was not able to add color<p></p>
attributes (like "true 0.5 0.5 0.5 1.0") to p971-HU2mat.txt manually, since this resulted in the<p></p>
following error message:<p></p>
src/<a href="http://GateVImageVolume.cc">GateVImageVolume.cc</a> (l.332): No Hounsfield material defined in the file<p></p>
CT/p971s3_ToSim_OneBP_HU2mat_Colors.txt. Abort<p></p>
<p>&nbsp;</p>
Does anyone have knowledge in this area, or can point to some helpful documentation on this topic? The GATE<p></p>
User's Guide has a few, but only incomplete examples for the case of voxelized phantoms and sources.<p></p>
<p>&nbsp;</p>
Best regards,<p></p>
<p>&nbsp;</p>
Yannick Berker<p></p>
<p>&nbsp;</p>
The information contained in this message may be confidential and legally protected under applicable<p></p>
law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are<p></p>
hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly<p></p>
prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return<p></p>
e-mail and destroy all copies of the original message.<p></p>
</div>
</blockquote>
<div>
<p class="MsoNormal"><p>&nbsp;</p></p>
</div>
</div>
</div>
Grevillot Loic | 6 Mar 13:23 2014
Picon

Re: output-Edep / output-Dose

Hi Mike,

 

Please post your questions on the list, so that anyone can benefit and participate.

 

 

From: Mike Tabriz [mailto:mtabriz <at> yahoo.com]
Sent: Donnerstag, 6. März 2014 02:10
To: Grevillot Loic
Subject: Re: [Gate-users] output-Edep / output-Dose

 

Hi Loic,

I did try attaching the dose actor to phantom but still not luck. I was just wondering if you had tried running the macro by any chance and whether I am on the right track. Do you think I would perhaps need to read in the geometry separately for the dose actor to work?

 

Thank you,

Mike

 

On Wednesday, March 5, 2014 1:35 AM, Grevillot Loic <loic.grevillot <at> medaustron.at> wrote:

Dear Mike,

 

Please try to attach the dose actor to “phantom” instead of “world”.

 

Kind regards,

 

Loïc Grevillot

 

 

 

From: gate-users-bounces <at> lists.opengatecollaboration.org [mailto:gate-users-bounces <at> lists.opengatecollaboration.org] On Behalf Of Mike Tabriz
Sent: Dienstag, 4. März 2014 16:13
To: gate-users <at> lists.opengatecollaboration.org
Subject: [Gate-users] output-Edep / output-Dose

 

Dear Gate users,

 

I have written several working macros in simulating dose distributions in a 3D voxelized human phantom. Now, I am trying to validate the code by creating a simple geometry which is no more than a sphere filled with water and a radioactive point source at the center.

 

Everything appears to be fine when I run the code and I get all the output images in hdr/img format, as expected. When I open the output-Edep or output-Dose files using ImageJ, however, I get a large file filled only with zero values in the matrix. In other words, all of matrix characteristics are as assigned in the Actors macro (size, dimensions etc.) but I cannot find any signals (positive values) anywhere. No dose is collected!

 

My guess is that the code requires the geometry to be read in as an image with .hdr format and that the sphere created by the code itself is not adequate when you use doseActor (?) I would appreciate your opinion in this area and whether you think there is an easier way of designing this simulation without having to create a sphere separately, converting it into Analyze format and then reading it into the code. I am enclosing some of the relevant information with this e-mail. Thank you.

 

 

 

Sincerely,

Mike

 

Disclaimer:
Please notice our E-Mail Disclaimer http://www.medaustron.at/email-disclaimer/  

 

 

Disclaimer:
Please notice our E-Mail Disclaimer http://www.medaustron.at/email-disclaimer/

 


<div>
<div class="WordSection1">
<p class="MsoNormal"><span>Hi Mike,<p></p></span></p>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
<p class="MsoNormal"><span>Please post your questions on the list, so that anyone can benefit and participate.<p></p></span></p>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
<div>
<div>
<p class="MsoNormal"><span>From:</span><span> Mike Tabriz [mailto:mtabriz <at> yahoo.com]
<br>Sent: Donnerstag, 6. M&auml;rz 2014 02:10<br>To: Grevillot Loic<br>Subject: Re: [Gate-users] output-Edep / output-Dose<p></p></span></p>
</div>
</div>
<p class="MsoNormal"><p>&nbsp;</p></p>
<div>
<div>
<p class="MsoNormal"><span>Hi Loic,<p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span>I did try attaching the dose actor to phantom but still not luck. I was just wondering if you had tried running the macro by any chance and whether
 I am on the right track. Do you think I would perhaps need to read in the geometry separately for the dose actor to work?<p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span>&nbsp;<p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span>Thank you,<p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span>Mike<p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
<div>
<div>
<div>
<p class="MsoNormal"><span>On Wednesday, March 5, 2014 1:35 AM, Grevillot Loic &lt;<a href="mailto:loic.grevillot <at> medaustron.at">loic.grevillot <at> medaustron.at</a>&gt; wrote:</span><span><p></p></span></p>
</div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span>Dear Mike,</span><span><p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span>Please try to attach the dose actor to &ldquo;phantom&rdquo; instead of &ldquo;world&rdquo;.</span><span><p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="DE">Kind regards,</span><span><p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="DE-AT">&nbsp;</span><span><p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span lang="DE-AT">Lo&iuml;c Grevillot</span><span><p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span>From:</span><span>
<a href="mailto:gate-users-bounces <at> lists.opengatecollaboration.org">gate-users-bounces <at> lists.opengatecollaboration.org</a> [<a href="mailto:gate-users-bounces <at> lists.opengatecollaboration.org">mailto:gate-users-bounces <at> lists.opengatecollaboration.org</a>]
On Behalf Of Mike Tabriz<br>Sent: Dienstag, 4. M&auml;rz 2014 16:13<br>To: <a href="mailto:gate-users <at> lists.opengatecollaboration.org">gate-users <at> lists.opengatecollaboration.org</a><br>Subject: [Gate-users] output-Edep / output-Dose</span><span><p></p></span></p>
</div>
</div>
</div>
<div>
<p class="MsoNormal"><span>&nbsp;<p></p></span></p>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span>Dear Gate users,<p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>I have written several working macros in simulating dose distributions in a 3D voxelized human phantom. Now, I am trying to validate the code by creating
 a simple geometry which is no more than a sphere filled with water and a radioactive point source at the center.<p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>Everything appears to be&nbsp;fine when I run the code and I get all the output images in hdr/img format, as expected. When I open the output-Edep or output-Dose
 files using ImageJ, however, I get a large file filled&nbsp;only with zero values in the matrix. In other words, all of matrix characteristics are as assigned in the Actors&nbsp;macro (size, dimensions etc.) but I cannot find any signals (positive values) anywhere.
 No dose is collected!<p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>My guess is that the code requires the geometry to be read in as an image with .hdr format and that the sphere created by the code itself is not adequate
 when you use doseActor (?) I would appreciate your opinion in this area and whether you think there is an easier way of designing this simulation without having to create a sphere separately, converting it into Analyze format and then reading it into the code.
 I am enclosing some of the relevant information with this e-mail. Thank you.<p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>Sincerely,<p></p></span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>Mike<p></p></span></p>
</div>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span>&nbsp;</span><span><p></p></span></p>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<p class="MsoNormal"><span lang="EN-GB">Disclaimer:</span><span><br></span><span lang="EN-GB">Please notice our E-Mail Disclaimer&nbsp;<a href="http://www.medaustron.at/email-disclaimer/" target="_blank"><span>http://www.medaustron.at/email-disclaimer/</span></a></span><span>
 &nbsp;<p></p></span></p>
</div>
</div>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
</div>
</div>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="WordSection1">
<p class="MsoNormal"><span><p></p></span><span lang="EN-GB">Disclaimer:</span><br><span lang="EN-GB">Please notice our E-Mail Disclaimer&nbsp;<a href="http://www.medaustron.at/email-disclaimer/"><span>http://www.medaustron.at/email-disclaimer/</span></a></span><span><p></p></span><p>&nbsp;</p></p>
</div>
<br>
</div>
Tom Buitenhuis | 6 Mar 12:37 2014
Picon

No comptonPhantom or RayleighPhantom entries for voxelized phantom

Dear GATE users,

I am having the same problem as Yannick Berker described on 2011-10-21. I use the ImageNestedParametrisedVolume phantom for a PET simulation. The sources are described using interfiles. Everything seems to be working correctly, i.e. the sources and phantom are in the right place and coincidences are detected. The effect of phantom attenuation is also clearly visible.

The problem that I’m having, is that in the ROOT coincidences tree there is no comptonPhantom and RayleighPhantom data. I cannot add the VoxelPhantomSD to the ImageNestedParametrisedVolume, because I get an error message saying the command is unavailable. I can add the ordinary PhantomSD, but this does not seem to add the comptonPhantom or RayleighPhantom information to the coincidence tree. The comptonCrystal and RayleighCrystal entries are correct, so I think the physics processes are registered and working correctly. 

I need the comptonPhantom and RayleighPhantom information to get scatter information on coincidences.

Did anyone else come across this problem, and if so, how did you solve it? Or can anyone point me in the direction of a solution?

Regards,

Tom Buitenhuis

PhD student
KVI - Center for Advanced Radiation Technology
University of Groningen
The Netherlands

Dear GATE users, I have some issues using the HounsfieldMaterialGenerator to simulate a PET scan of a patient. The simulation itself is running fine, but I am lacking two features that I am used to from other simulations, which are scatter information and color visualization. I mainly used the example from http://www.creatis.insa-lyon.fr/gate/Example2/ to generate the following phantom: /gate/HounsfieldMaterialGenerator/SetMaterialTable CT/Schneider2000MaterialsTable.txt /gate/HounsfieldMaterialGenerator/SetDensityTable CT/Schneider2000DensitiesTable.txt /gate/HounsfieldMaterialGenerator/SetDensityTolerance 0.03 g/cm3 /gate/HounsfieldMaterialGenerator/SetOutputMaterialDatabaseFilename CT/p971-HUmaterials.db /gate/HounsfieldMaterialGenerator/SetOutputHUMaterialFilename CT/p971-HU2mat.txt /gate/HounsfieldMaterialGenerator/Generate /gate/world/daughters/name patient /gate/world/daughters/insert ImageRegionalizedVolume /gate/geometry/setMaterialDatabase CT/p971-HUmaterials.db /gate/patient/geometry/SetHUToMaterialFile CT/p971-HU2mat.txt /gate/patient/geometry/SetImage CT/p971s3.hdr ... The ROOT output shows me that the volume is placed correctly, and the distribution of detected coincidences also shows the effect of photon attenuation by the phantom. However, I cannot attach a VoxelPhantomSD to the patient - I receive an error message telling me that this command is unavailable: [G4-cerr] ***** COMMAND NOT FOUND </gate/patient/attachVoxelPhantomSD> ***** Attaching an ordinary PhantomSD seems to work, but only generates 0 entries in ComptonPhantom and RayleighPhantom. I also tried using a ImageNestedParametrisedVolume, with no effect. ComptonCrystal entries, however, seem to be correct (>= 0). Apart from that, how can I visualize the voxelized phantom using colors? I was not able to add color attributes (like "true 0.5 0.5 0.5 1.0") to p971-HU2mat.txt manually, since this resulted in the following error message: src/GateVImageVolume.cc (l.332): No Hounsfield material defined in the file CT/p971s3_ToSim_OneBP_HU2mat_Colors.txt. Abort Does anyone have knowledge in this area, or can point to some helpful documentation on this topic? The GATE User's Guide has a few, but only incomplete examples for the case of voxelized phantoms and sources. Best regards, Yannick Berker The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message.


<div>
<div>Dear GATE users,<br><div><div>
<div><br></div>
<div>I am having the same problem as Yannick Berker described on 2011-10-21. I use the ImageNestedParametrisedVolume phantom for a PET simulation. The sources are described using interfiles. Everything seems to be working correctly, i.e. the sources and phantom are in the right place and coincidences are detected. The effect of phantom attenuation is also clearly visible.</div>
<div><br></div>
<div>The problem that I&rsquo;m having, is that in the ROOT coincidences tree there is no comptonPhantom and RayleighPhantom data. I cannot add the VoxelPhantomSD to the ImageNestedParametrisedVolume, because I get an error message saying the command is unavailable. I can add the ordinary PhantomSD, but this does not seem to add the comptonPhantom or RayleighPhantom information to the coincidence tree. The comptonCrystal and RayleighCrystal entries are correct, so I think the physics processes are registered and working correctly.&nbsp;</div>
<div><br></div>
<div>I need the comptonPhantom and RayleighPhantom information to get scatter information on coincidences.</div>
<div><br></div>
<div>Did anyone else come across this problem, and if so, how did you solve it? Or can anyone point me in the direction of a solution?</div>
<div><br></div>
<div>Regards,</div>
<div><br></div>
<div>Tom Buitenhuis</div>
<div><br></div>
<div>PhD student</div>
<div>KVI - Center for Advanced Radiation Technology</div>
<div>University of Groningen</div>
<div>The Netherlands</div>
<div></div>
<span></span><br><blockquote type="cite">Dear GATE users,

I have some issues using the HounsfieldMaterialGenerator to simulate a PET scan of a patient. The
simulation itself is running fine, but I am lacking two features that I am used to from other simulations,
which are scatter information and color visualization. I mainly used the example from
<a rel="nofollow" href="http://www.creatis.insa-lyon.fr/gate/Example2/" target="_top">http://www.creatis.insa-lyon.fr/gate/Example2/</a> to generate the following phantom:

/gate/HounsfieldMaterialGenerator/SetMaterialTable                  CT/Schneider2000MaterialsTable.txt
/gate/HounsfieldMaterialGenerator/SetDensityTable                   CT/Schneider2000DensitiesTable.txt
/gate/HounsfieldMaterialGenerator/SetDensityTolerance               0.03 g/cm3
/gate/HounsfieldMaterialGenerator/SetOutputMaterialDatabaseFilename CT/p971-HUmaterials.db
/gate/HounsfieldMaterialGenerator/SetOutputHUMaterialFilename       CT/p971-HU2mat.txt
/gate/HounsfieldMaterialGenerator/Generate
/gate/world/daughters/name                                          patient
/gate/world/daughters/insert                                        ImageRegionalizedVolume
/gate/geometry/setMaterialDatabase                                  CT/p971-HUmaterials.db
/gate/patient/geometry/SetHUToMaterialFile                          CT/p971-HU2mat.txt
/gate/patient/geometry/SetImage                                     CT/p971s3.hdr
...

The ROOT output shows me that the volume is placed correctly, and the distribution of detected
coincidences also shows the effect of photon attenuation by the phantom. However, I cannot attach a
VoxelPhantomSD to the patient - I receive an error message telling me that this command is unavailable:
[G4-cerr] ***** COMMAND NOT FOUND &lt;/gate/patient/attachVoxelPhantomSD&gt; *****
Attaching an ordinary PhantomSD seems to work, but only generates 0 entries in ComptonPhantom and
RayleighPhantom. I also tried using a ImageNestedParametrisedVolume, with no effect. ComptonCrystal
entries, however, seem to be correct (&gt;= 0).

Apart from that, how can I visualize the voxelized phantom using colors? I was not able to add color
attributes (like "true 0.5 0.5 0.5 1.0") to p971-HU2mat.txt manually, since this resulted in the
following error message:
src/<a href="http://gatevimagevolume.cc/">GateVImageVolume.cc</a> (l.332): No Hounsfield material defined in the file
CT/p971s3_ToSim_OneBP_HU2mat_Colors.txt. Abort

Does anyone have knowledge in this area, or can point to some helpful documentation on this topic? The GATE
User's Guide has a few, but only incomplete examples for the case of voxelized phantoms and sources.

Best regards,

Yannick Berker

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</blockquote>
<div><br></div>
</div></div>
</div>
<br>
</div>
Stephen Yip | 5 Mar 20:55 2014
Picon

From phantom to PET image

Hi,

I have a phantom image (with different radioactivity in different parts of anatomy) in binary format. I would love to obtain a PET projection of the phantom image. 

1. Can GATE read binary? Do I need to convert the image into another format?

2. How do I use insert the phantom in the written macro of a PET scanner? 

Thanks!
Stephen 
<div><div dir="ltr">Hi,<div><br></div>
<div>I have a phantom image (with different radioactivity in different parts of anatomy) in binary format. I would love to obtain a PET projection of the phantom image.&nbsp;</div>
<div><br></div>

<div>1. Can GATE read binary? Do I need to convert the image into another format?</div>
<div><br></div>
<div>2. How do I use insert the phantom in the written macro of a PET scanner?&nbsp;</div>
<div><br></div>
<div>Thanks!</div>
<div>
Stephen&nbsp;</div>
</div></div>
Wei ZHAO | 5 Mar 17:31 2014

a lot of NaN value in dose map of a voxelized phantom


Dear Gate user,

I have calculated the dose map for a voxelized phantom which was generated with a CT image. The image was transfered into GATE as .h33 and .i33 format. The dose maps was written in standard hdr/img format. But when I read the dose map in MATLAB, there are a lot of NaN in the body area and the dose value for air is fine. Did anyone know how to solve this problem? I will appreciate any feedback.

https://www.dropbox.com/s/2ht75fpvjfanw8w/doseMap.png

Thank you very much!
Best regards
Wei
<div><div>
<div><br></div>
<div>Dear Gate user,</div>
<div><br></div>
<div>I have calculated the dose map for a voxelized phantom which was generated with a CT image. The image was transfered into GATE as .h33 and .i33 format. The dose maps was written in standard hdr/img format. But when I read the dose map in MATLAB, there are a lot of NaN in the body area and the dose value for air is fine. Did anyone know how to solve this problem? I will appreciate any feedback.</div>
<div><br></div>
<a href="https://www.dropbox.com/s/2ht75fpvjfanw8w/doseMap.png" target="_blank">https://www.dropbox.com/s/2ht75fpvjfanw8w/doseMap.png</a><div><br></div>
<div>Thank you very much!</div>
<div>Best regards</div>
<div>Wei</div>
</div></div>

Gmane