[Gate-users] Gate-users Digest, Vol 168, Issue 42

Thu May 28 14:31:39 CEST 2020

Dear Hui Zhang
Sorry, I didn't notice the last line of your message.

This link may be useful for you:

https://www.creatis.insa-lyon.fr/rio/vv-clitk#clitkDicom2Image

Best

Somayeh Asadi (PhD)
Postdoctoral Researcher
Department of Mechanical Engineering
Politecnico di Milano, Italy

Via Giuseppe La Masa,1
20156 - Milano - Italy
phone: +39 0223998572

somayeh.asadi at polimi.it

________________________________
From: 张晖 <zhanghui at impcas.ac.cn>
Sent: Thursday, May 28, 2020 2:19 PM
To: Somayeh Asadi <somayeh.asadi at polimi.it>
Cc: gate-users at lists.opengatecollaboration.org <gate-users at lists.opengatecollaboration.org>
Subject: Re: Re: [Gate-users] Gate-users Digest, Vol 168, Issue 42

Dear Somayeh Asadi,

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?

Best regards,

Hui Zhang

-----原始邮件-----
发件人:"Somayeh Asadi" <somayeh.asadi at polimi.it>
发送时间:2020-05-28 18:27:12 (星期四)
收件人: "gate-users at lists.opengatecollaboration.org" <gate-users at lists.opengatecollaboration.org>
抄送:
主题: Re: [Gate-users] Gate-users Digest, Vol 168, Issue 42

Dear Hui Zhang
What do you mean from executing when you said you run it. If I understood correct :
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.

Best
Somayeh Asadi (PhD)
Postdoctoral Researcher
Department of Mechanical Engineering
Politecnico di Milano, Italy

Via Giuseppe La Masa,1
20156 - Milano - Italy
phone: +39 0223998572

somayeh.asadi at polimi.it

________________________________
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Sent: Thursday, May 28, 2020 12:00 PM
To: gate-users at lists.opengatecollaboration.org <gate-users at lists.opengatecollaboration.org>
Subject: Gate-users Digest, Vol 168, Issue 42

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Today's Topics:

   1. Replacing gps with phase-space file of gps emissions      not
      working... (Steven Marsh)
   2. VV software (张晖)

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

Message: 1
Date: Thu, 28 May 2020 05:37:18 +0000
From: Steven Marsh <steven.marsh at canterbury.ac.nz>
To: "gate-users at lists.opengatecollaboration.org"
        <gate-users at lists.opengatecollaboration.org>
Subject: [Gate-users] Replacing gps with phase-space file of gps
        emissions       not working...
Message-ID:
        <81C2FA1FAFEA9E45B25965A260B811D6011B55C0A4 at UCEXMBX01-D.canterbury.ac.nz>

Content-Type: text/plain; charset="utf-8"

Hi All

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...

So, I can use the following source definition and successfully collect photon counts (an image of a circle)  in my simulated SPECT system

/gate/source/addSource source gps
/gate/source/source/gps/particle gamma
/gate/source/source/gps/type Volume
/gate/source/source/gps/shape Sphere
/gate/source/source/gps/radius 25 mm
/gate/source/source/gps/angtype iso
/gate/source/source/gps/energytype UserSpectrum
/gate/source/source/gps/setSpectrumFile data/energy_spectrum_Tc99m.txt
/gate/source/source/setForcedHalfLife 242343.36 s
/gate/source/source/setActivity {ACTIVITY} MBq
/gate/source/source/gps/centre 0 0 0 mm

I can also encapsulate this source within a sphere and produce a PSF of photons exiting the sphere

/gate/actor/addActor                         PhaseSpaceActor PhS_g
/gate/actor/PhS_g/attachTo                   phsSphere
/gate/actor/PhS_g/save                                     output/PhS-Gamma-{ACTIVITY}MBq.root
/gate/actor/PhS_g/useVolumeFrame             true  #Not using world coordinates
/gate/actor/PhS_g/storeOutgoingParticles     true
/gate/actor/PhS_g/enableParticleName         false
/gate/actor/PhS_g/enableProductionVolume     false
/gate/actor/PhS_g/enableProductionProcess    false
/gate/actor/PhS_g/addFilter                  particleFilter
/gate/actor/PhS_g/particleFilter/addParticle gamma
/gate/actor/PhS_g/enableZPosition            true
#/gate/actor/PhS_g/saveEveryNSeconds          20

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)

/gate/source/addSource                            src_Heart phaseSpace
/gate/source/src_Heart/addPhaseSpaceFile          data/PhSData/PhS-Gamma-{ACTIVITY}MBq.root
/gate/source/src_Heart/setParticleType            gamma
/gate/source/src_Heart/attachTo                   boundingVolume
/gate/source/src_Heart/useRandomSymmetry          true

/gate/source/src_Heart/setForcedHalfLife  21624.12 s  #6.0 hrs
/gate/source/src_Heart/setForcedUnstableFlag true
/gate/source/src_Heart/setForcedHalfLife 21624.12 s
/gate/source/src_Heart/setActivity {ACTIVITY} MBq

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.

As always any assistance to show me the error of my ways is greatly appreciated :)

Best wishes
Steve

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Message: 2
Date: Thu, 28 May 2020 14:53:08 +0800 (GMT+08:00)
From: 张晖 <zhanghui at impcas.ac.cn>
To: gate-users at lists.opengatecollaboration.org
Subject: [Gate-users] VV software
Message-ID: <302a9943.f8eb.1725a0e5780.Coremail.zhanghui at impcas.ac.cn>
Content-Type: text/plain; charset="utf-8"

Dear Gate user,

I have installed VV software on ubantu and win10 platforms,and can run VV successfully, but I don't know how to execute

other tools like "clitk*" from VV software.Can anyone help me?

Best regards,
Hui Zhang

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End of Gate-users Digest, Vol 168, Issue 42
*******************************************

________________________________
Zhang Hui
University of Chinese Academy of Sciences
Institute of Modern Physics

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