AHN, Sunghwan | 11 Jul 13:30 2014
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(no subject)

<div></div>
동근 | 11 Jul 03:42 2014
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visualization the phantom

hi

 

I hope to use the thorax phantom but dose not visualization

I had only just seen the gray box so the front part is not distinguished and can not recognize localization.

I attached the image for your reference.


Thanks

 

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

/gate/world/daughters/name                        thorax

/gate/world/daughters/insert                        ImageNestedParametrisedVolume

/gate/geometry/setMaterialDatabase              /home/gate/Desktop/thorax phantom/data/Thorax-HUmaterials.db

/gate/thorax/geometry/SetHUToMaterialFile     /home/gate/Desktop/thorax phantom/data/Thorax-HU2mat.txt

/gate/thorax/geometry/SetImage                     /home/gate/Desktop/thorax phantom/data/resampledTHORAX.hdr

 

 

 




<div>
<div>
<table border="0" width="100%" cellpadding="0" cellspacing="0"><tr><td valign="top">
<div class="tx-hanmail-content-wrapper">
<p>hi</p>
<p>&nbsp;</p>
<p class="HStyle0">I hope to use the thorax phantom but dose not visualization</p>
<p class="HStyle0">I had only just seen the gray box so the front part is not distinguished and can not recognize localization.</p>
<p class="HStyle0">I attached the image for your reference.</p>
<p class="HStyle0"><br></p>
<p class="HStyle0">Thanks</p>
<p class="HStyle0">&nbsp;</p>
<p class="HStyle0">#####################################################</p>
<p class="HStyle0">/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; thorax</p>
<p class="HStyle0">/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; ImageNestedParametrisedVolume</p>
<p class="HStyle0">/gate/geometry/setMaterialDatabase&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;/home/gate/Desktop/thorax phantom/data/Thorax-HUmaterials.db</p>
<p class="HStyle0">/gate/thorax/geometry/SetHUToMaterialFile&nbsp;&nbsp;&nbsp; &nbsp;/home/gate/Desktop/thorax phantom/data/Thorax-HU2mat.txt</p>
<p class="HStyle0">/gate/thorax/geometry/SetImage&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;/home/gate/Desktop/thorax phantom/data/resampledTHORAX.hdr</p>
<p class="HStyle0">&nbsp;</p>
<p class="HStyle0">&nbsp;</p>
<p class="HStyle0"></p>
<p class="HStyle0">&nbsp;</p>
<p class="HStyle0"><br></p>
</div>
</td></tr></table>
</div>
<br><br><a href="mailto:bluejdg <at> hanmail.net"></a>
</div>
jehangir khan | 10 Jul 16:15 2014
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Re: Gate-users Digest, Vol 98, Issue 18

> Dear Gate users!
>
> Can anybody share information or experience for vGate installation on clusters.
> I have installed VGate successfully on My main cluster. My question is , do I need to install vGate   On each clusters respectively?  After that install NFS , and MPI for sharing folder ?
> I shall appreciate for response or suggestion
> Best Regards
> Jehangir

On Thu, Jul 10, 2014 at 2:49 PM, <gate-users-request-ZwoEplunGu2uWGBtOU8ma0fXCdDtWGEhSoIsB4E12gc@public.gmane.org> wrote:
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Today's Topics:

   1. Re: Orientation of mhd file (Albert Hirtl)


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

Message: 1
Date: Thu, 10 Jul 2014 15:37:26 +0200
From: Albert Hirtl <albert.hirtl-1Exk/Z/VcF+XamxT8X54fw@public.gmane.org>
To: J?r?me Suhard <jerome-VWaMH2iSGBRQFI55V6+gNQ@public.gmane.org>
Cc: gate-users <gate-users-ZwoEplunGu2zQB+pC5nmwQ@public.gmane.orgngatecollaboration.org>
Subject: Re: [Gate-users] Orientation of mhd file
Message-ID: <53BE9716.7080306 <at> meduniwien.ac.at>
Content-Type: text/plain; charset="utf-8"; Format="flowed"

Hi,

Ok thanks for your help and the clarification.

By the way, is there a method to visualize voxelized sources which are
read in from an interfile? At least I wasn't able to visualize it in
order to check whether it is located where it should be.

My workaround would be to read it in as phantom an check the position.
However, in the manual it says, that I have to shift the source by half
in -x and -y direction. Is there a better way to check the position?

Cheers,
Albert

On 10/07/14 15:28, J?r?me Suhard wrote:
> Hi,
>
> I can reproduce it.
> Technically, my OpenGL custom commands are called one first time even
> in Stored mode. At this moment, it seems that the rotation was not yet
> applied.
> But with X11 in Stored mode, there is no "refresh" of the graphical
> scene thus leading to this artifact, you can remove it by forcing it with:
> /vis/viewer/refresh
>
> Best regards,
>
>
> 2014-07-10 9:25 GMT+02:00 Albert Hirtl <albert.hirtl <at> meduniwien.ac.at
> <mailto:albert.hirtl-1Exk/Z/VcF+XamxT8X54fw@public.gmane.org>>:
>
>     Dear Simon,
>
>     Thanks for the header. I thought it's best if I simply sent you
>     some screen shots from my system (attached). I hope the names make
>     clear what's in the image. Summarized one can say, that OGLIX does
>     what it should, OGLSX, however, at least on my system, does not
>     what I expect it to do.
>
>     The command
>
>     glxinfo | grep "OpenGL version"
>
>     gives
>
>     OpenGL version string: 2.1 Mesa 9.0-devel
>
>     I am running Scientific Linux 6.0.
>
>     Maybe everything is as it is expected to be? And simply I
>     misunderstand the properties of OGLSX?
>
>     Cheers,
>     Albert
>
>
>     On 09/07/14 16:59, Simon Rit wrote:
>>     Thanks for sharing the data with us. I tested on my computer and
>>     I have the expected behavior, i.e.,
>>     - the image is upside down because Y goes from bottom to the top
>>     on Gate and it's the opposite in VV,
>>     - if I set
>>     /gate/patient/placement/setRotationAngle 180 deg
>>     then it is back to its normal position
>>     - same thing if I use the enclosed mhd but it is now upside down
>>     in VV
>>     - if I do the last two points together, it's back to the original
>>     position.
>>     Is this not what you observe?
>>     Simon
>>
>>
>>     On Wed, Jul 9, 2014 at 3:55 PM, Albert Hirtl
>>     <albert.hirtl-1Exk/Z/VcF+XamxT8X54fw@public.gmane.org
>>     <mailto:albert.hirtl-1Exk/Z/VcF+XamxT8X54fw@public.gmane.org>> wrote:
>>
>>         Hi,
>>
>>         Please find attached my very basic macros and the header of
>>         my image file that I used to play around with the .mhd
>>         feature (as tar archive). I can not send the raw data, since
>>         even if I gzip them they are larger than 11 MB and my mail is
>>         rejected. Do you have a mailbox which accepts more than 11 MB?
>>
>>         Thanks again and cheers,
>>         Albert
>>
>>
>>
>>
>>         On 09/07/14 15:32, J?r?me Suhard wrote:
>>>         X stands for X11 (old static window)
>>>         Qt stands for ... Qt ( GUI with mouse support)
>>>
>>>         S(tored) mode: you just see a box
>>>         I(mmediate) mode: you see your image with Gate7
>>>
>>>         so OGLS or OGLI should not change orientation and/or rotation...
>>>
>>>         If you have time to send me your CT/macro, I'm still
>>>         interested by them
>>>
>>>
>>>         2014-07-09 15:24 GMT+02:00 Albert Hirtl
>>>         <albert.hirtl <at> meduniwien.ac.at
>>>         <mailto:albert.hirtl-1Exk/Z/VcF/AulCSGMW7Fw@public.gmane.orgat>>:
>>>
>>>             Hi,
>>>
>>>             Thanks for the prompt answer, it was already enough to
>>>             solve the problem:
>>>
>>>             I initially copied the following line from the
>>>             example_PHANTOM_SOURCE/Voxelized_Phantom_Source/mainMacro.mac
>>>
>>>             /vis/open OGLSX
>>>
>>>             Motivated by your answer I tried OGL*I*X and everything
>>>             is fine... Now all orientations are correct and
>>>             rotations work properly.
>>>
>>>             So, could OGLSX be a typo in the example?
>>>
>>>             Thanks a lot for you help!
>>>
>>>             Cheers,
>>>             Albert (a bit embarrassed :-[ )
>>>
>>>
>>>
>>>             On 09/07/14 15:09, J?r?me Suhard wrote:
>>>>             Hi,
>>>>
>>>>             2014-07-09 15:01 GMT+02:00 Albert Hirtl
>>>>             <albert.hirtl-1Exk/Z/VcF+XamxT8X54fw@public.gmane.org
>>>>             <mailto:albert.hirtl-1Exk/Z/VcF+XamxT8X54fw@public.gmane.org>>:
>>>>
>>>>                 If I display the CT using OGLSX it seems to be
>>>>                 bottom up.
>>>>
>>>>
>>>>             You mean OGL*I*X, right ?
>>>>
>>>>                 /gate/patient/placement/setRotationAxis           0 0 1
>>>>                 /gate/patient/placement/setRotationAngle
>>>>                 XXXX  deg
>>>>
>>>>                 it stays the same. In vv it was in the correct
>>>>                 orientation. The box that is plotted around the CT
>>>>                 seems to be rotating, however. Do I make anything
>>>>                 wrong? Or is just the image that I see in OGLSX not
>>>>                 rotating?
>>>>
>>>>
>>>>             can you give the most small macro with the CT showing
>>>>             this behaviour ?
>>>>
>>>>             thanks
>>>>
>>>>             --
>>>>             J?r?me Suhard
>>>
>>>
>>>             --
>>>             Medizinische Universit?t Wien
>>>             Universit?tsklinik f?r Radiologie und Nuklearmedizin
>>>             W?hringer G?rtel 18-20
>>>             1090 Wien
>>>             Austria
>>>
>>>             Tel.:+43 (0) 1 / 40400 55450  <tel:%2B43%20%280%29%201%20%2F%2040400%2055450>
>>>
>>>             Web:
>>>             http://www.meduniwien.ac.at/user/albert.hirtl
>>>             http://www.meduniwien.ac.at/moccamed/
>>>
>>>
>>>
>>>
>>>         --
>>>         J?r?me Suhard
>>
>>
>>         --
>>         Medizinische Universit?t Wien
>>         Universit?tsklinik f?r Radiologie und Nuklearmedizin
>>         W?hringer G?rtel 18-20
>>         1090 Wien
>>         Austria
>>
>>         Tel.:+43 (0) 1 / 40400 55450  <tel:%2B43%20%280%29%201%20%2F%2040400%2055450>
>>
>>         Web:
>>         http://www.meduniwien.ac.at/user/albert.hirtl
>>         http://www.meduniwien.ac.at/moccamed/
>>
>>
>>         _______________________________________________
>>         Gate-users mailing list
>>         Gate-users-ZwoEplunGu0bJ6lf+0Zptg@public.gmane.orgcollaboration.org
>>         <mailto:Gate-users-ZwoEplunGu2uWGBtOU8ma0fXCdDtWGEh8RMB2TjU7RI@public.gmane.orgrg>
>>         http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>
>>
>
>
>     --
>     Medizinische Universit?t Wien
>     Universit?tsklinik f?r Radiologie und Nuklearmedizin
>     W?hringer G?rtel 18-20
>     1090 Wien
>     Austria
>
>     Tel.:+43 (0) 1 / 40400 55450  <tel:%2B43%20%280%29%201%20%2F%2040400%2055450>
>
>     Web:
>     http://www.meduniwien.ac.at/user/albert.hirtl
>     http://www.meduniwien.ac.at/moccamed/
>
>
>     _______________________________________________
>     Gate-users mailing list
>     Gate-users-ZwoEplunGu2uWGBtOU8ma0fXCdDtWGEhSoIsB4E12gc@public.gmane.org
>     <mailto:Gate-users-ZwoEplunGu2uWGBtOU8ma0fXCdDtWGEhSoIsB4E12gc@public.gmane.org>
>     http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>
>
>
>
> --
> J?r?me Suhard


--
Medizinische Universit?t Wien
Universit?tsklinik f?r Radiologie und Nuklearmedizin
W?hringer G?rtel 18-20
1090 Wien
Austria

Tel.: +43 (0) 1 / 40400 55450

Web:
http://www.meduniwien.ac.at/user/albert.hirtl
http://www.meduniwien.ac.at/moccamed/

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End of Gate-users Digest, Vol 98, Issue 18
******************************************

<div>
<p>&gt; Dear Gate users!<br>&gt;<br>&gt; Can anybody share information or experience for vGate installation on clusters.<br>&gt; I have installed VGate successfully on My main cluster. My question is , do I need to install vGate&nbsp;&nbsp; On each clusters respectively?&nbsp; After that install NFS , and MPI for sharing folder ?<br>
&gt; I shall appreciate for response or suggestion<br>&gt; Best Regards<br>&gt; Jehangir<br><br></p>
<div class="gmail_quote">On Thu, Jul 10, 2014 at 2:49 PM, <span dir="ltr">&lt;<a href="mailto:gate-users-request@..." target="_blank">gate-users-request@...</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@...engatecollaboration.org">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@...ecollaboration.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@...tecollaboration.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: Orientation of mhd file (Albert Hirtl)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Thu, 10 Jul 2014 15:37:26 +0200<br>
From: Albert Hirtl &lt;<a href="mailto:albert.hirtl@...">albert.hirtl@...</a>&gt;<br>To: J?r?me Suhard &lt;<a href="mailto:jerome@...">jerome@...</a>&gt;<br>Cc: gate-users &lt;<a href="mailto:gate-users@...">gate-users@...ngatecollaboration.org</a>&gt;<br>
Subject: Re: [Gate-users] Orientation of mhd file<br>Message-ID: &lt;<a href="mailto:53BE9716.7080306@...">53BE9716.7080306 <at> meduniwien.ac.at</a>&gt;<br>Content-Type: text/plain; charset="utf-8"; Format="flowed"<br><br>Hi,<br><br>Ok thanks for your help and the clarification.<br><br>By the way, is there a method to visualize voxelized sources which are<br>read in from an interfile? At least I wasn't able to visualize it in<br>order to check whether it is located where it should be.<br><br>My workaround would be to read it in as phantom an check the position.<br>However, in the manual it says, that I have to shift the source by half<br>in -x and -y direction. Is there a better way to check the position?<br><br>Cheers,<br>Albert<br><br>On 10/07/14 15:28, J?r?me Suhard wrote:<br>&gt; Hi,<br>&gt;<br>&gt; I can reproduce it.<br>&gt; Technically, my OpenGL custom commands are called one first time even<br>&gt; in Stored mode. At this moment, it seems that the rotation was not yet<br>
&gt; applied.<br>&gt; But with X11 in Stored mode, there is no "refresh" of the graphical<br>&gt; scene thus leading to this artifact, you can remove it by forcing it with:<br>&gt; /vis/viewer/refresh<br>&gt;<br>
&gt; Best regards,<br>&gt;<br>&gt;<br>&gt; 2014-07-10 9:25 GMT+02:00 Albert Hirtl &lt;<a href="mailto:albert.hirtl@...">albert.hirtl <at> meduniwien.ac.at</a><br>&gt; &lt;mailto:<a href="mailto:albert.hirtl <at> meduniwien.ac.at">albert.hirtl@...</a>&gt;&gt;:<br>
&gt;<br>&gt; &nbsp; &nbsp; Dear Simon,<br>&gt;<br>&gt; &nbsp; &nbsp; Thanks for the header. I thought it's best if I simply sent you<br>&gt; &nbsp; &nbsp; some screen shots from my system (attached). I hope the names make<br>&gt; &nbsp; &nbsp; clear what's in the image. Summarized one can say, that OGLIX does<br>
&gt; &nbsp; &nbsp; what it should, OGLSX, however, at least on my system, does not<br>&gt; &nbsp; &nbsp; what I expect it to do.<br>&gt;<br>&gt; &nbsp; &nbsp; The command<br>&gt;<br>&gt; &nbsp; &nbsp; glxinfo | grep "OpenGL version"<br>&gt;<br>&gt; &nbsp; &nbsp; gives<br>
&gt;<br>&gt; &nbsp; &nbsp; OpenGL version string: 2.1 Mesa 9.0-devel<br>&gt;<br>&gt; &nbsp; &nbsp; I am running Scientific Linux 6.0.<br>&gt;<br>&gt; &nbsp; &nbsp; Maybe everything is as it is expected to be? And simply I<br>&gt; &nbsp; &nbsp; misunderstand the properties of OGLSX?<br>
&gt;<br>&gt; &nbsp; &nbsp; Cheers,<br>&gt; &nbsp; &nbsp; Albert<br>&gt;<br>&gt;<br>&gt; &nbsp; &nbsp; On 09/07/14 16:59, Simon Rit wrote:<br>&gt;&gt; &nbsp; &nbsp; Thanks for sharing the data with us. I tested on my computer and<br>&gt;&gt; &nbsp; &nbsp; I have the expected behavior, i.e.,<br>
&gt;&gt; &nbsp; &nbsp; - the image is upside down because Y goes from bottom to the top<br>&gt;&gt; &nbsp; &nbsp; on Gate and it's the opposite in VV,<br>&gt;&gt; &nbsp; &nbsp; - if I set<br>&gt;&gt; &nbsp; &nbsp; /gate/patient/placement/setRotationAngle 180 deg<br>
&gt;&gt; &nbsp; &nbsp; then it is back to its normal position<br>&gt;&gt; &nbsp; &nbsp; - same thing if I use the enclosed mhd but it is now upside down<br>&gt;&gt; &nbsp; &nbsp; in VV<br>&gt;&gt; &nbsp; &nbsp; - if I do the last two points together, it's back to the original<br>
&gt;&gt; &nbsp; &nbsp; position.<br>&gt;&gt; &nbsp; &nbsp; Is this not what you observe?<br>&gt;&gt; &nbsp; &nbsp; Simon<br>&gt;&gt;<br>&gt;&gt;<br>&gt;&gt; &nbsp; &nbsp; On Wed, Jul 9, 2014 at 3:55 PM, Albert Hirtl<br>&gt;&gt; &nbsp; &nbsp; &lt;<a href="mailto:albert.hirtl@...">albert.hirtl@...</a><br>
&gt;&gt; &nbsp; &nbsp; &lt;mailto:<a href="mailto:albert.hirtl <at> meduniwien.ac.at">albert.hirtl@...</a>&gt;&gt; wrote:<br>&gt;&gt;<br>&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; Hi,<br>&gt;&gt;<br>&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; Please find attached my very basic macros and the header of<br>
&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; my image file that I used to play around with the .mhd<br>&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; feature (as tar archive). I can not send the raw data, since<br>&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; even if I gzip them they are larger than 11 MB and my mail is<br>
&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; rejected. Do you have a mailbox which accepts more than 11 MB?<br>&gt;&gt;<br>&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; Thanks again and cheers,<br>&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; Albert<br>&gt;&gt;<br>&gt;&gt;<br>&gt;&gt;<br>&gt;&gt;<br>&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; On 09/07/14 15:32, J?r?me Suhard wrote:<br>
&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; X stands for X11 (old static window)<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; Qt stands for ... Qt ( GUI with mouse support)<br>&gt;&gt;&gt;<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; S(tored) mode: you just see a box<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; I(mmediate) mode: you see your image with Gate7<br>
&gt;&gt;&gt;<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; so OGLS or OGLI should not change orientation and/or rotation...<br>&gt;&gt;&gt;<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; If you have time to send me your CT/macro, I'm still<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; interested by them<br>
&gt;&gt;&gt;<br>&gt;&gt;&gt;<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; 2014-07-09 15:24 GMT+02:00 Albert Hirtl<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &lt;<a href="mailto:albert.hirtl@...">albert.hirtl <at> meduniwien.ac.at</a><br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &lt;mailto:<a href="mailto:albert.hirtl@...">albert.hirtl@...at</a>&gt;&gt;:<br>
&gt;&gt;&gt;<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Hi,<br>&gt;&gt;&gt;<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Thanks for the prompt answer, it was already enough to<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; solve the problem:<br>&gt;&gt;&gt;<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; I initially copied the following line from the<br>
&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; example_PHANTOM_SOURCE/Voxelized_Phantom_Source/mainMacro.mac<br>&gt;&gt;&gt;<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; /vis/open OGLSX<br>&gt;&gt;&gt;<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Motivated by your answer I tried OGL*I*X and everything<br>
&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; is fine... Now all orientations are correct and<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; rotations work properly.<br>&gt;&gt;&gt;<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; So, could OGLSX be a typo in the example?<br>&gt;&gt;&gt;<br>
&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Thanks a lot for you help!<br>&gt;&gt;&gt;<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Cheers,<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Albert (a bit embarrassed :-[ )<br>&gt;&gt;&gt;<br>&gt;&gt;&gt;<br>&gt;&gt;&gt;<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; On 09/07/14 15:09, J?r?me Suhard wrote:<br>
&gt;&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Hi,<br>&gt;&gt;&gt;&gt;<br>&gt;&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 2014-07-09 15:01 GMT+02:00 Albert Hirtl<br>&gt;&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &lt;<a href="mailto:albert.hirtl@...">albert.hirtl@...</a><br>
&gt;&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &lt;mailto:<a href="mailto:albert.hirtl@...">albert.hirtl@...</a>&gt;&gt;:<br>&gt;&gt;&gt;&gt;<br>&gt;&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; If I display the CT using OGLSX it seems to be<br>
&gt;&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; bottom up.<br>&gt;&gt;&gt;&gt;<br>&gt;&gt;&gt;&gt;<br>&gt;&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; You mean OGL*I*X, right ?<br>&gt;&gt;&gt;&gt;<br>&gt;&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; /gate/patient/placement/setRotationAxis &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 0 0 1<br>
&gt;&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; /gate/patient/placement/setRotationAngle<br>&gt;&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; XXXX &nbsp;deg<br>&gt;&gt;&gt;&gt;<br>&gt;&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; it stays the same. In vv it was in the correct<br>
&gt;&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; orientation. The box that is plotted around the CT<br>&gt;&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; seems to be rotating, however. Do I make anything<br>&gt;&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; wrong? Or is just the image that I see in OGLSX not<br>
&gt;&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; rotating?<br>&gt;&gt;&gt;&gt;<br>&gt;&gt;&gt;&gt;<br>&gt;&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; can you give the most small macro with the CT showing<br>&gt;&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; this behaviour ?<br>
&gt;&gt;&gt;&gt;<br>&gt;&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; thanks<br>&gt;&gt;&gt;&gt;<br>&gt;&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; --<br>&gt;&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; J?r?me Suhard<br>&gt;&gt;&gt;<br>&gt;&gt;&gt;<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; --<br>
&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Medizinische Universit?t Wien<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Universit?tsklinik f?r Radiologie und Nuklearmedizin<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; W?hringer G?rtel 18-20<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 1090 Wien<br>
&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Austria<br>&gt;&gt;&gt;<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Tel.:<a href="tel:%2B43%20%280%29%201%20%2F%2040400%2055450" value="+4314040055450">+43 (0) 1 / 40400 55450</a> &nbsp;&lt;tel:%2B43%20%280%29%201%20%2F%2040400%2055450&gt;<br>
&gt;&gt;&gt;<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Web:<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; <a href="http://www.meduniwien.ac.at/user/albert.hirtl" target="_blank">http://www.meduniwien.ac.at/user/albert.hirtl</a><br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; <a href="http://www.meduniwien.ac.at/moccamed/" target="_blank">http://www.meduniwien.ac.at/moccamed/</a><br>
&gt;&gt;&gt;<br>&gt;&gt;&gt;<br>&gt;&gt;&gt;<br>&gt;&gt;&gt;<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; --<br>&gt;&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; J?r?me Suhard<br>&gt;&gt;<br>&gt;&gt;<br>&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; --<br>&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; Medizinische Universit?t Wien<br>
&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; Universit?tsklinik f?r Radiologie und Nuklearmedizin<br>&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; W?hringer G?rtel 18-20<br>&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; 1090 Wien<br>&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; Austria<br>&gt;&gt;<br>&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; Tel.:<a href="tel:%2B43%20%280%29%201%20%2F%2040400%2055450" value="+4314040055450">+43 (0) 1 / 40400 55450</a> &nbsp;&lt;tel:%2B43%20%280%29%201%20%2F%2040400%2055450&gt;<br>
&gt;&gt;<br>&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; Web:<br>&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; <a href="http://www.meduniwien.ac.at/user/albert.hirtl" target="_blank">http://www.meduniwien.ac.at/user/albert.hirtl</a><br>&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; <a href="http://www.meduniwien.ac.at/moccamed/" target="_blank">http://www.meduniwien.ac.at/moccamed/</a><br>
&gt;&gt;<br>&gt;&gt;<br>&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; _______________________________________________<br>&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; Gate-users mailing list<br>&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; <a href="mailto:Gate-users@...">Gate-users@...collaboration.org</a><br>
&gt;&gt; &nbsp; &nbsp; &nbsp; &nbsp; &lt;mailto:<a href="mailto:Gate-users <at> lists.opengatecollaboration.org">Gate-users@...rg</a>&gt;<br>&gt;&gt; &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>
&gt;&gt;<br>&gt;&gt;<br>&gt;<br>&gt;<br>&gt; &nbsp; &nbsp; --<br>&gt; &nbsp; &nbsp; Medizinische Universit?t Wien<br>&gt; &nbsp; &nbsp; Universit?tsklinik f?r Radiologie und Nuklearmedizin<br>&gt; &nbsp; &nbsp; W?hringer G?rtel 18-20<br>&gt; &nbsp; &nbsp; 1090 Wien<br>&gt; &nbsp; &nbsp; Austria<br>
&gt;<br>&gt; &nbsp; &nbsp; Tel.:<a href="tel:%2B43%20%280%29%201%20%2F%2040400%2055450" value="+4314040055450">+43 (0) 1 / 40400 55450</a> &nbsp;&lt;tel:%2B43%20%280%29%201%20%2F%2040400%2055450&gt;<br>&gt;<br>&gt; &nbsp; &nbsp; Web:<br>&gt; &nbsp; &nbsp; <a href="http://www.meduniwien.ac.at/user/albert.hirtl" target="_blank">http://www.meduniwien.ac.at/user/albert.hirtl</a><br>
&gt; &nbsp; &nbsp; <a href="http://www.meduniwien.ac.at/moccamed/" target="_blank">http://www.meduniwien.ac.at/moccamed/</a><br>&gt;<br>&gt;<br>&gt; &nbsp; &nbsp; _______________________________________________<br>&gt; &nbsp; &nbsp; Gate-users mailing list<br>
&gt; &nbsp; &nbsp; <a href="mailto:Gate-users@....org">Gate-users@...</a><br>&gt; &nbsp; &nbsp; &lt;mailto:<a href="mailto:Gate-users@...">Gate-users@...</a>&gt;<br>
&gt; &nbsp; &nbsp; <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a><br>&gt;<br>&gt;<br>&gt;<br>&gt;<br>&gt; --<br>&gt; J?r?me Suhard<br><br><br>--<br>Medizinische Universit?t Wien<br>Universit?tsklinik f?r Radiologie und Nuklearmedizin<br>W?hringer G?rtel 18-20<br>1090 Wien<br>Austria<br><br>Tel.: <a href="tel:%2B43%20%280%29%201%20%2F%2040400%2055450" value="+4314040055450">+43 (0) 1 / 40400 55450</a><br><br>Web:<br><a href="http://www.meduniwien.ac.at/user/albert.hirtl" target="_blank">http://www.meduniwien.ac.at/user/albert.hirtl</a><br><a href="http://www.meduniwien.ac.at/moccamed/" target="_blank">http://www.meduniwien.ac.at/moccamed/</a><br><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: &lt;<a href="http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140710/b9bc7416/attachment.html" target="_blank">http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140710/b9bc7416/attachment.html</a>&gt;<br>
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</blockquote>
</div>
<br>
</div>
heythem bouziri | 10 Jul 12:12 2014
Picon

How to irradiate juste one Crystal

H i,
 
I am a new user of Gate, I want study the effect of Inter-Crystal scattering, So I want know how it is possible to irradiate just one Crystal to see the effects in the cristals around.
 
Thanks
<div><div dir="ltr">H i, <br>&nbsp;<br>I am a new user of Gate, I want study the effect of Inter-Crystal scattering, So I want know how it is possible to irradiate just one Crystal to see the effects in the cristals around. <br>&nbsp;<br>Thanks<br>
</div></div>
Psoroulas Serena | 10 Jul 11:39 2014
Picon

Folder sharing with vGate v. 3

Dear all,

 

I have just downloaded the new version of vGate (v. 3), and I am having weird problems I did not have with the previous version. For example, I am not able to use a shared folder; once I set a shared folder for access from the virtual machine (using the mount command as explained in the VirtualBox manual), I am not able to enter it, and even running a simple “ls” command on the folder causes the command to use 50% of CPU or more and freeze the terminal. In the old version, folder sharing worked as a charm. Has anyone experience something similar? Is there a difference with the new virtual machine wrt vGate v. 2.1, that I should take into account when I configure or run the virtual machine? (the settings of the two virtual machines are the same)

 

Thank you very much

Yours faithfully

Serena Psoroulas

__________________________________________
PSI - Paul Scherrer Institut

Mrs. Dr. Serena Psoroulas

Scientific officer – Beam technologies development

Centre for Proton Therapy

WMSA/C13
5232 Villigen PSI

Switzerland

Phone +41 56 310 56 79

serena.psoroulas-QlBsmsa8rgI@public.gmane.org

p-therapie.web.psi.ch

 

<div><div class="WordSection1">
<p class="MsoNormal">Dear all,<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal"><span lang="EN-US">I have just downloaded the new version of vGate (v. 3), and I am having weird problems I did not have with the previous version. For example, I am not able to use a shared folder; once I set a shared folder for access from the virtual machine (using the mount command as explained in the VirtualBox manual), I am not able to enter it, and even running a simple &ldquo;ls&rdquo; command on the folder causes the command to use 50% of CPU or more and freeze the terminal. In the old version, folder sharing worked as a charm. Has anyone experience something similar? Is there a difference with the new virtual machine wrt vGate v. 2.1, that I should take into account when I configure or run the virtual machine? (the settings of the two virtual machines are the same)<p></p></span></p>
<p class="MsoNormal"><span lang="EN-US"><p>&nbsp;</p></span></p>
<p class="MsoNormal"><span lang="EN-US">Thank you very much<p></p></span></p>
<p class="MsoNormal"><span lang="EN-US">Yours faithfully<p></p></span></p>
<p class="MsoNormal"><span lang="EN-US">Serena Psoroulas<p></p></span></p>
<p class="MsoNormal"><span lang="EN-US"> <p></p></span></p>
<p class="MsoNormal"><span lang="EN-US">__________________________________________<br>PSI - Paul Scherrer Institut <p></p></span></p>
<p class="MsoNormal"><span lang="EN-US">Mrs. Dr. Serena Psoroulas<p></p></span></p>
<p class="MsoNormal"><span lang="EN-US">Scientific officer &ndash; Beam technologies development<br><br><p></p></span></p>
<p class="MsoNormal"><span lang="EN-US">Centre for Proton Therapy<p></p></span></p>
<p class="MsoNormal"><span lang="EN-US">WMSA/C13<br>5232 Villigen PSI<p></p></span></p>
<p class="MsoNormal"><span>Switzerland<br><br>Phone +41 56 310 56 79 <p></p></span></p>
<p class="MsoNormal"><span>serena.psoroulas@...</span><span><p></p></span></p>
<p class="MsoNormal"><span><a href="http://p-therapie.web.psi.ch/">p-therapie.web.psi.ch</a><p></p></span></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
</div></div>
Paul RETIF | 10 Jul 11:14 2014
Picon

setAugerElectron problem

Dear GATE users,

I try to assess the impact of Auger electrons on a dose image with the radiation therapy module of GATE V7.0 (geant4.9.6.p03) on a system.

In my physics list I set the following parameters :
...
/gate/physics/addProcess PhotoElectric
/gate/physics/processes/PhotoElectric/setModel PenelopeModel
/gate/physics/processes/PhotoElectric/setAugerElectron boolean
...

With setAugerElectrons boolean being true or false.

Unfortunately I see absolutely no differences between the Auger true or false in the resulting dose image which is not likely reflect the reality...

Did I miss something ?

Thanks,
Paul
<div><div dir="ltr">
<div>
<div>
<div>
<div>
<div>Dear GATE users,<br><br>I try to assess the impact of Auger electrons on a dose image with the radiation therapy module of GATE V7.0 (geant4.9.6.p03) on a system.<br><br>
</div>In my physics list I set the following parameters :<br>...<br>/gate/physics/addProcess PhotoElectric<br>/gate/physics/processes/PhotoElectric/setModel PenelopeModel<br>/gate/physics/processes/PhotoElectric/setAugerElectron boolean<br>...<br><br>
</div>With setAugerElectrons boolean being true or false.<br><br>
</div>Unfortunately I see absolutely no differences between the Auger true or false in the resulting dose image which is not likely reflect the reality...<br><br>
</div>Did I miss something ?<br><br>
</div>Thanks,<br>Paul<br>
</div></div>
Jehangir | 10 Jul 02:04 2014
Picon

VGate installation

Dear Gate users!

Can anybody share information or experience for vGate installation on clusters. 
I have installed VGate successfully on My main cluster. My question is , do I need to install vGate   On each
clusters respectively?  After that install NFS , and MPI for sharing folder ? 
I shall appreciate for response or suggestion 
Best Regards 
Jehangir 

LARS.EWELL | 10 Jul 00:13 2014

Transfering Files to Shared Folder

To Whom it May Concern,

 

  I have been transferring files from our linux cluster to my local desktop, on which I’m running a copy of vGATE.

 

  Per the instructions in the Oracle Virtual Box manual, I  mount the Windows folder onto a directory in the virtual machine running Ubutnu linux, and I can transfer the files.

 

  The problem arises when I look over the files in Ubutnu.  Sometimes the files, which are GATE ‘.mac’ text files, appear in red text when looking at them in Ubutnu linux.  The system does not recognize them and if I do an ‘ls –l’, I get a series of question marks where the read-write information would normally be.  I thought it was due to the file extension (mac), but that turned out not to be the case.

 

  It seems random and I have a hard time getting Ubutnu linux to recognize the .mac files I have been transferring from my Windows machine to the virtual machine running Ubutnu via a sharred folder.

 

  Any suggestions?  I have played with ascii and binary transfer with my copy of WinSCP I’m using to transfer the files from our linux cluster to my Windows machine.

 

  Thanks in advance.

 

  Regards,

 

  Lars Ewell

The information contained in this message is intended only for the recipient, and may otherwise be privileged and confidential. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, please be aware that any dissemination or copying of this communication is strictly prohibited. If you have received this communication in error, please immediately notify us by replying to the message and deleting it from your computer. This footnote also confirms that this email has been scanned for all viruses by the Hampton University Center for Information Technology Enterprise Systems service.
<div>
<div class="WordSection1">
<p class="MsoNormal">To Whom it May Concern,<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">&nbsp; I have been transferring files from our linux cluster to my local desktop, on which I&rsquo;m running a copy of vGATE.<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">&nbsp; Per the instructions in the Oracle Virtual Box manual, I&nbsp; mount the Windows folder onto a directory in the virtual machine running Ubutnu linux, and I can transfer the files.<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">&nbsp; The problem arises when I look over the files in Ubutnu.&nbsp; Sometimes the files, which are GATE &lsquo;.mac&rsquo; text files, appear in red text when looking at them in Ubutnu linux.&nbsp; The system does not recognize them and if I do an &lsquo;ls &ndash;l&rsquo;, I get
 a series of question marks where the read-write information would normally be.&nbsp; I thought it was due to the file extension (mac), but that turned out not to be the case.<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">&nbsp; It seems random and I have a hard time getting Ubutnu linux to recognize the .mac files I have been transferring from my Windows machine to the virtual machine running Ubutnu via a sharred folder.<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">&nbsp; Any suggestions?&nbsp; I have played with ascii and binary transfer with my copy of WinSCP I&rsquo;m using to transfer the files from our linux cluster to my Windows machine.<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">&nbsp; Thanks in advance.<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">&nbsp; Regards,<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">&nbsp; Lars Ewell <p></p></p>
</div>

<div>
The information contained in this message is intended only for the recipient, and may otherwise be privileged and confidential. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, please be aware that any dissemination or copying of this communication is strictly prohibited. If you have received this communication in error, please immediately notify us by replying to the message and deleting it from your computer. This footnote also confirms that this email has been scanned for all viruses by the Hampton University Center for Information Technology Enterprise Systems service.<br>
</div>
</div>
Y.Asano | 9 Jul 18:13 2014
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VoxelReader: too high values


Dear Gate-users,

I am currently trying to read-in a reconstruction of mine into Gate. I  
followed the guide and managed to open to file via the  
interfileReader. But unfortunately the values are far too high (around  
some 40000). If I check with vv, the values are correctly around 1.3.  
What could be wrong?

Thanks, Yuki

Albert Hirtl | 9 Jul 15:01 2014
Picon

Orientation of mhd file

Dear Colleagues,

I have a question regarding the orientation of a CT which I stored as 
.mhd file (using vv) and read in into GATE (v7.0). If I display the CT 
using OGLSX it seems to be bottom up. No matter what I do with the commands

/gate/patient/placement/setRotationAxis           0 0 1
/gate/patient/placement/setRotationAngle         XXXX  deg

it stays the same. In vv it was in the correct orientation. The box that 
is plotted around the CT seems to be rotating, however. Do I make 
anything wrong? Or is just the image that I see in OGLSX not rotating?

Any help would be very much appreciated.

Best regards,
Albert

-- 
Medizinische Universität Wien
Universitätsklinik für Radiologie und Nuklearmedizin
Währinger Gürtel 18-20
1090 Wien
Austria

Tel.: +43 (0) 1 / 40400 55450

Web:
http://www.meduniwien.ac.at/user/albert.hirtl
http://www.meduniwien.ac.at/moccamed/

Attachment (albert_hirtl.vcf): text/x-vcard, 409 bytes
Dear Colleagues,

I have a question regarding the orientation of a CT which I stored as 
.mhd file (using vv) and read in into GATE (v7.0). If I display the CT 
using OGLSX it seems to be bottom up. No matter what I do with the commands

/gate/patient/placement/setRotationAxis           0 0 1
/gate/patient/placement/setRotationAngle         XXXX  deg

it stays the same. In vv it was in the correct orientation. The box that 
is plotted around the CT seems to be rotating, however. Do I make 
anything wrong? Or is just the image that I see in OGLSX not rotating?

Any help would be very much appreciated.

Best regards,
Albert

--

-- 
Medizinische Universität Wien
Universitätsklinik für Radiologie und Nuklearmedizin
Währinger Gürtel 18-20
1090 Wien
Austria

Tel.: +43 (0) 1 / 40400 55450

Web:
http://www.meduniwien.ac.at/user/albert.hirtl
http://www.meduniwien.ac.at/moccamed/

Paweł Kowalski | 9 Jul 14:34 2014
Picon

Interpretation of volumeID variable in root file in optical simulation

Hello,

I have a question about volumeID variable.

In my simulation I have a system of two plastic scintillating strips. At both ends of each strip, there are photomultipliers.

System looks like that:

PMT1==========PMT2 - strip with two PMTs 

                  S           - point source of back-to-back gamma in the middle of the system 

PMT3==========PMT4

In my case, coincidence is a situation when I have optical photons at each of 4 photomultipliers at both strips.

When I analyze root output, I check if in single event there were hits with different volumeID[1]. Unfortunately for each event volumeID[1] has the same value for all hits so it gives me no coincidences.

But when I analyze positions of hits in each event and numbers of photons at each of four PMTs, I have many coincidences. Results of analysis looks like that:

Nr of photons at PMT1 || PMT2 || PMT3 || PMT4 || Nr of photons with volumeID[1]==0 || volumeID[1]==1
...
412 163 63 49 892 0
339 455 475 295 0 2314
184 82 599 696 2305 0
588 423 293 375 2487 0
553 478 51 56 0 1685
212 266 85 151 0 1045
269 345 79 81 1127 0
491 692 32 39 1876 0
387 602 31 8 1476 0
522 625 34 58 0 1825
587 722 46 57 2097 0
485 452 163 277 2060 0
89 144 619 640 2170 0
9 17 59 51 197 0
52 96 376 91 788 0
...

All photons from all photomultipliers has only one value of volumeID[1] though they are from different volumes.

Is this a problem with my interpretation of volumeID variable or there is an error in GATE software?
It looks like GATE gives value of volumeID[1] of first hit in event for all hits in an event. 

Thank you in advance for your help.

Best regards,
Paweł Kowalski,
National Centre for Nuclear Research,
Świerk Computing Centre
<div><div dir="ltr">Hello,<div><br></div>
<div>I have a question about volumeID variable.</div>
<div><br></div>
<div>In my simulation I have a system of two plastic scintillating strips. At both ends of each strip, there are photomultipliers.</div>

<div><br></div>
<div>System looks like that:</div>
<div><br></div>
<div>PMT1==========PMT2 - strip with two PMTs&nbsp;</div>
<div><br></div>
<div>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; S &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; - point source of back-to-back gamma in the middle of the system&nbsp;</div>

<div><br></div>
<div><div>PMT3==========PMT4</div></div>
<div><br></div>
<div>In my case, coincidence is a situation when I have optical photons at each of 4 photomultipliers at both strips.</div>
<div><br></div>
<div>When I analyze root output, I check if in single event there were hits with different volumeID[1]. Unfortunately for each event volumeID[1] has the same value for all hits so it gives me no coincidences.</div>

<div><br></div>
<div>But when I analyze positions of hits in each event and numbers of photons at each of four PMTs, I have many coincidences. Results of analysis looks like that:</div>
<div><br></div>
<div>Nr of photons at PMT1 || PMT2 || PMT3 || PMT4 || Nr of photons with volumeID[1]==0 || volumeID[1]==1</div>

<div>...</div>
<div>
<div>412 163 63 49 892 0</div>
<div>339 455 475 295 0 2314</div>
<div>184 82 599 696 2305 0</div>
<div>588 423 293 375 2487 0</div>
<div>553 478 51 56 0 1685</div>
<div>212 266 85 151 0 1045</div>
<div>269 345 79 81 1127 0</div>

<div>491 692 32 39 1876 0</div>
<div>387 602 31 8 1476 0</div>
<div>522 625 34 58 0 1825</div>
<div>587 722 46 57 2097 0</div>
<div>485 452 163 277 2060 0</div>
<div>89 144 619 640 2170 0</div>
<div>9 17 59 51 197 0</div>
<div>

52 96 376 91 788 0</div>
</div>
<div>...<br>
</div>
<div><br></div>
<div>All photons from all photomultipliers has only one value of volumeID[1] though they are from different volumes.</div>
<div><br></div>
<div>Is this a problem with my interpretation of volumeID variable or there is an error in GATE software?</div>

<div>It looks like GATE gives value of volumeID[1] of first hit in event for all hits in an event.&nbsp;</div>
<div><br></div>
<div>Thank you in advance for your help.</div>
<div><br></div>
<div>Best regards,</div>
<div>Pawe&#322; Kowalski,<br>
</div>
<div>National Centre for Nuclear Research,</div>
<div>&#346;wierk Computing Centre</div>
</div></div>

Gmane