[Gate-users] Gate-users Digest, Vol 168, Issue 42
David Sarrut
David.Sarrut at creatis.insa-lyon.fr
Wed Jun 3 08:35:09 CEST 2020
Hello,
note that part of the clitk* tools (not all) are now in python in the
GateTools package : https://github.com/OpenGATE/GateTools
best,
David
On Thu, May 28, 2020 at 4:02 PM 张晖 <zhanghui at impcas.ac.cn> wrote:
> Dear Somayeh Asadi,
>
> Thank you very much! It really helps me!
>
>
> 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 20:31:39 (星期四)
> *收件人:* "张晖" <zhanghui at impcas.ac.cn>
> *抄送:* "gate-users at lists.opengatecollaboration.org" <
> gate-users at lists.opengatecollaboration.org>
> *主题:* Re: Re: [Gate-users] Gate-users Digest, Vol 168, Issue 42
>
> 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
>
> ------------------------------
> *From:* Gate-users <gate-users-bounces at lists.opengatecollaboration.org>
> on behalf of gate-users-request at lists.opengatecollaboration.org <
> gate-users-request at lists.opengatecollaboration.org>
> *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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> Subject: Digest Footer
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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
>
>
>
>
> ------------------------------
> Zhang Hui
> University of Chinese Academy of Sciences
> Institute of Modern Physics
>
> _______________________________________________
> Gate-users mailing list
> Gate-users at lists.opengatecollaboration.org
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--
David Sarrut, Phd
Directeur de recherche CNRS
CREATIS, UMR CNRS 5220, Inserm U1206
Centre de lutte contre le cancer Léon Bérard
28 rue Laënnec, 69373 Lyon cedex 08
Tel : 04 78 78 51 51 / 06 74 72 05 42
http://www.creatis.insa-lyon.fr/~dsarrut
_________________________________
"2 + 2 = 5, for extremely large values of 2"
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