<p>
Dear Somayeh Asadi,
</p>
<p>
Thanks for your attention! I know how to use VV software, I just want to know how to use those clitk* application programs, such as clitkDicomRTPlan2Gate,clitkSum,and so on. Do you have some advice for that?
</p>
<p>
<br>
</p>
<p>
Best regards,
</p>
<p>
Hui Zhang<br>
</p>
<blockquote class="ReferenceQuote" style="padding-left:5px;margin-left:5px;border-left:#b6b6b6 2px solid;margin-right:0;" name="replyContent">
-----原始邮件-----<br>
<b>发件人:</b><span id="rc_from">"Somayeh Asadi" <somayeh.asadi@polimi.it></span><br>
<b>发送时间:</b><span id="rc_senttime">2020-05-28 18:27:12 (星期四)</span><br>
<b>收件人:</b> "gate-users@lists.opengatecollaboration.org" <gate-users@lists.opengatecollaboration.org><br>
<b>抄送:</b> <br>
<b>主题:</b> Re: [Gate-users] Gate-users Digest, Vol 168, Issue 42<br>
<br>
<style style="display:none;" type="text/css"> P {margin-top:0;margin-bottom:0;} </style>
<div style="font-family:Calibri, Arial, Helvetica, sans-serif;font-size:12pt;color:#000000;">
<span style="color:#201F1E;font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:14.6667px;background-color:#FFFFFF;display:inline !important;">Dear
Hui Zhang</span><br>
</div>
<div style="font-family:Calibri, Arial, Helvetica, sans-serif;font-size:12pt;color:#000000;">
<span style="color:#201F1E;font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:14.6667px;background-color:#FFFFFF;display:inline !important;">What
do you mean from executing when you said you run it. If I understood correct :</span>
</div>
<div style="font-family:Calibri, Arial, Helvetica, sans-serif;font-size:12pt;color:#000000;">
<span style="color:#201F1E;font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:14.6667px;background-color:#FFFFFF;display:inline !important;">Open
the terminal in the folder where your image is placed in, then type vv in the terminal, and click enter. Your image will be open in the VV software. It has tools that you can get help from but if you had any questions about working with it feel free to ask. </span>
</div>
<div style="font-family:Calibri, Arial, Helvetica, sans-serif;font-size:12pt;color:#000000;">
<span style="color:#201F1E;font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:14.6667px;background-color:#FFFFFF;display:inline !important;"><br>
</span>
</div>
<div style="font-family:Calibri, Arial, Helvetica, sans-serif;font-size:12pt;color:#000000;">
<span style="color:#201F1E;font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;font-size:14.6667px;background-color:#FFFFFF;display:inline !important;">Best </span>
</div>
<div>
<div id="Signature">
<div>
</div>
<div id="divtagdefaultwrapper" style="font-size:12pt;color:#000000;font-family:Calibri,Helvetica,sans-serif;" dir="ltr">
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:#000000;">
<div style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;text-align:left;background-color:#FFFFFF;" dir="ltr">
<span style="margin:0px;font-size:11pt;color:#757B80;font-family:"Times New Roman",Times,serif;"><i>Somayeh Asadi (PhD)</i></span>
</div>
<div style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;text-align:left;background-color:#FFFFFF;" dir="ltr">
<span style="margin:0px;font-size:11pt;color:#757B80;font-family:"Times New Roman",Times,serif;"><i>Postdoctoral Researcher </i></span>
</div>
<div style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;text-align:left;background-color:#FFFFFF;" dir="ltr">
<i style="color:#757B80;font-family:"Times New Roman",Times,serif;font-size:11pt;font-variant-ligatures:inherit;font-variant-caps:inherit;font-weight:inherit;">Department of Mechanical Engineering</i>
</div>
<div style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;text-align:left;background-color:#FFFFFF;" dir="ltr">
<i style="color:#757B80;font-family:"Times New Roman",Times,serif;font-size:11pt;font-variant-ligatures:inherit;font-variant-caps:inherit;font-weight:inherit;">Politecnico di Milano, Italy</i>
</div>
<div style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;text-align:start;background-color:#FFFFFF;">
<span style="color:#757B80;font-family:"Times New Roman",Times,serif;font-size:9pt;"><br>
</span>
</div>
<div style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;text-align:start;background-color:#FFFFFF;">
<span style="color:#757B80;font-family:"Times New Roman",Times,serif;font-size:9pt;">Via Giuseppe La Masa,1</span><br>
</div>
</div>
<div>
<span style="color:#757B80;font-size:9pt;font-family:"Times New Roman",Times,serif;">20156 - Milano - Italy</span><br>
<span style="color:#757B80;font-size:9pt;font-family:"Times New Roman",Times,serif;">phone: +39 0223998572</span><br>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:#000000;">
<div style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;text-align:start;background-color:#FFFFFF;">
<span style="margin:0px;font-size:10pt;"></span><span style="margin:0px;font-size:11pt;"></span><span style="margin:0px;color:#757B80;"></span>
</div>
<div style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;text-align:start;background-color:#FFFFFF;">
<span style="margin:0px;font-size:11pt;"></span>
</div>
<p style="margin-top:0px;margin-bottom:0px;font-family:Calibri,Helvetica,sans-serif,Helvetica,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;text-align:start;background-color:#FFFFFF;">
<span style="margin:0px;font-size:11pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;"></span><span style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;"></span><span style="margin:0px;font-size:11pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;"></span><span style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;"></span><span style="margin:0px;font-size:11pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;"></span><span style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;"></span><span style="margin:0px;font-size:11pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;"></span><span style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;color:#757B80;"></span><span style="margin:0px;font-size:11pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;"></span><span style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;"></span><span style="margin:0px;font-size:11pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;"></span><span style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;"></span><span style="margin:0px;font-size:10pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;"></span><span style="margin:0px;font-size:11pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;"></span><span style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;color:#757B80;"></span><span style="margin:0px;font-size:11pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;"></span><span style="margin:0px;font-size:10pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;"></span><span style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;"></span><span style="margin:0px;font-size:10pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;"></span><span style="margin:0px;font-size:11pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;"></span><span style="margin:0px;font-size:10pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;"></span><span style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;"></span>
</p>
<div style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;text-align:start;background-color:#FFFFFF;">
<span style="margin:0px;font-size:10pt;color:#757B80;font-family:"Times New Roman",Times,serif;">somayeh.asadi@polimi.</span><span style="margin:0px;font-size:10pt;color:#757B80;">it</span>
</div>
<br>
</div>
</div>
</div>
</div>
</div>
<div id="appendonsend">
</div>
<hr tabindex="-1" style="display:inline-block;width:98%;">
<div id="divRplyFwdMsg" dir="ltr">
<span style="font-size:11pt;font-family:'Calibri, sans-serif';color:#000000;"><b>From:</b> Gate-users <gate-users-bounces@lists.opengatecollaboration.org> on behalf of gate-users-request@lists.opengatecollaboration.org <gate-users-request@lists.opengatecollaboration.org><br>
<b>Sent:</b> Thursday, May 28, 2020 12:00 PM<br>
<b>To:</b> gate-users@lists.opengatecollaboration.org <gate-users@lists.opengatecollaboration.org><br>
<b>Subject:</b> Gate-users Digest, Vol 168, Issue 42</span>
<div>
</div>
</div>
<div class="BodyFragment">
<span style="font-size:x-small;"><span style="font-size:11pt;">
<div class="PlainText">
Send Gate-users mailing list submissions to<br>
gate-users@lists.opengatecollaboration.org<br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
<a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users"> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a><br>
or, via email, send a message with subject or body 'help' to<br>
gate-users-request@lists.opengatecollaboration.org<br>
<br>
You can reach the person managing the list at<br>
gate-users-owner@lists.opengatecollaboration.org<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>
1. Replacing gps with phase-space file of gps emissions not<br>
working... (Steven Marsh)<br>
2. VV software (张晖)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 28 May 2020 05:37:18 +0000<br>
From: Steven Marsh <steven.marsh@canterbury.ac.nz><br>
To: "gate-users@lists.opengatecollaboration.org"<br>
<gate-users@lists.opengatecollaboration.org><br>
Subject: [Gate-users] Replacing gps with phase-space file of gps<br>
emissions not working...<br>
Message-ID:<br>
<81C2FA1FAFEA9E45B25965A260B811D6011B55C0A4@UCEXMBX01-D.canterbury.ac.nz><br>
<br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
<br>
Hi All<br>
<br>
A quick query about the use of phase-space files (PSF). A summary of the following is that I can collect projection data for my SPECT simulation if I use, for example a spherical source of Tc-99m, but as soon as I collect a PSF from the spherical gps source
and then use that PSF as the source, I no longer get counts on my SPECT camera. This is not what I was expecting and assume I have made an error so I have included what I believe to be the essential pieces of code below...<br>
<br>
So, I can use the following source definition and successfully collect photon counts (an image of a circle) in my simulated SPECT system<br>
<br>
/gate/source/addSource source gps<br>
/gate/source/source/gps/particle gamma<br>
/gate/source/source/gps/type Volume<br>
/gate/source/source/gps/shape Sphere<br>
/gate/source/source/gps/radius 25 mm<br>
/gate/source/source/gps/angtype iso<br>
/gate/source/source/gps/energytype UserSpectrum<br>
/gate/source/source/gps/setSpectrumFile data/energy_spectrum_Tc99m.txt<br>
/gate/source/source/setForcedHalfLife 242343.36 s<br>
/gate/source/source/setActivity {ACTIVITY} MBq<br>
/gate/source/source/gps/centre 0 0 0 mm<br>
<br>
<br>
I can also encapsulate this source within a sphere and produce a PSF of photons exiting the sphere<br>
<br>
/gate/actor/addActor PhaseSpaceActor PhS_g<br>
/gate/actor/PhS_g/attachTo phsSphere<br>
/gate/actor/PhS_g/save output/PhS-Gamma-{ACTIVITY}MBq.root<br>
/gate/actor/PhS_g/useVolumeFrame true #Not using world coordinates<br>
/gate/actor/PhS_g/storeOutgoingParticles true<br>
/gate/actor/PhS_g/enableParticleName false<br>
/gate/actor/PhS_g/enableProductionVolume false<br>
/gate/actor/PhS_g/enableProductionProcess false<br>
/gate/actor/PhS_g/addFilter particleFilter<br>
/gate/actor/PhS_g/particleFilter/addParticle gamma<br>
/gate/actor/PhS_g/enableZPosition true<br>
#/gate/actor/PhS_g/saveEveryNSeconds 20<br>
<br>
<br>
Inspection of the PSF produced with root suggests that this works correctly (many 0.14 MV photons exit the sphere and these are visualisable when used as a source in the next bit of code) - but the problem arises when I place the PHS for the sphere into the
identical SPECT simulation and use it to replace the original point source. The issue is I get essentially no counts on the SPECT camera (a few random dots appear only). My code for including the PSF is the following (note, when I include this I remove the
gps definition for the source above)<br>
<br>
/gate/source/addSource src_Heart phaseSpace<br>
/gate/source/src_Heart/addPhaseSpaceFile data/PhSData/PhS-Gamma-{ACTIVITY}MBq.root<br>
/gate/source/src_Heart/setParticleType gamma<br>
/gate/source/src_Heart/attachTo boundingVolume<br>
/gate/source/src_Heart/useRandomSymmetry true<br>
<br>
/gate/source/src_Heart/setForcedHalfLife 21624.12 s #6.0 hrs<br>
/gate/source/src_Heart/setForcedUnstableFlag true<br>
/gate/source/src_Heart/setForcedHalfLife 21624.12 s<br>
/gate/source/src_Heart/setActivity {ACTIVITY} MBq<br>
<br>
<br>
Am I doing things correctly? I have tried to disentangle it all and it appears to me as though the SPECT detector (as defined in the gate-examples and modified and tested successfully for tc-99m) recognizes and counts photons from the gps as per above but
not for the PSF source as I have included it.<br>
<br>
As always any assistance to show me the error of my ways is greatly appreciated :)<br>
<br>
Best wishes<br>
Steve<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200528/8ed288cd/attachment-0001.html">http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200528/8ed288cd/attachment-0001.html</a>><br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Thu, 28 May 2020 14:53:08 +0800 (GMT+08:00)<br>
From: 张晖 <zhanghui@impcas.ac.cn><br>
To: gate-users@lists.opengatecollaboration.org<br>
Subject: [Gate-users] VV software<br>
Message-ID: <302a9943.f8eb.1725a0e5780.Coremail.zhanghui@impcas.ac.cn><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Gate user,<br>
<br>
I have installed VV software on ubantu and win10 platforms,and can run VV successfully, but I don't know how to execute<br>
<br>
other tools like "clitk*" from VV software.Can anyone help me?<br>
<br>
<br>
<br>
Best regards,<br>
Hui Zhang<br>
<br>
<br>
<br>
<br>
<br>
<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200528/8ff5a67b/attachment-0001.html">http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200528/8ff5a67b/attachment-0001.html</a>><br>
<br>
------------------------------<br>
<br>
Subject: Digest Footer<br>
<br>
_______________________________________________<br>
Gate-users mailing list<br>
Gate-users@lists.opengatecollaboration.org<br>
<a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a><br>
<br>
------------------------------<br>
<br>
End of Gate-users Digest, Vol 168, Issue 42<br>
*******************************************<br>
</div>
</span></span>
</div>
</blockquote>
<br>
<br>
<br>
<span class="spnEditorSign">
<hr align="left" class="signature-separator" style="margin:0.5em 0;width:10em;height:1px;background-color:#999;border:none;">
Zhang Hui
<div>
University of Chinese Academy of Sciences
</div>
<div>
Institute of Modern Physics<br>
<div>
<br>
</div>
</div>
</span>