[gate-users] RE: gate-users Digest, Vol 16, Issue 13
Susana Silva
susana.silva at fc.ul.pt
Mon Jul 18 18:17:26 CEST 2005
Hi, Vandana!
This is my configuration:
- CLHEP 1.8.1.0
- geant4.7.0
on Red Hat Enterprise Linux 3 (gcc 3.2.3).
Cheers,
Susana Silva
-----Mensagem original-----
De: gate-users-bounces at lphe1pet1.epfl.ch em nome de gate-users-request at lphe1pet1.epfl.ch
Enviada: sex 15-07-2005 22:31
Para: gate-users at lphe1pet1.epfl.ch
Cc:
Assunto: gate-users Digest, Vol 16, Issue 13
Send gate-users mailing list submissions to
gate-users at lphe1pet1.epfl.ch
To subscribe or unsubscribe via the World Wide Web, visit
http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
Please use the GATE's site webmaster e-mail to reach the person
managing the list.
Today's Topics:
1. RE: gate-users Digest, Vol 16, Issue 12 (Susana Silva)
2. Re: gcc-4.0 (Mutanga Theodore)
3. Voxelised Phantom (Leighton Barnden)
4. Re: Voxelised Phantom (Mutanga Theodore)
5. Re: RE: gate-users Digest, Vol 16, Issue 12 (Vandana Kohli)
----------------------------------------------------------------------
Message: 1
Date: Fri, 15 Jul 2005 14:16:39 +0100
From: "Susana Silva" <susana.silva at fc.ul.pt>
Subject: [gate-users] RE: gate-users Digest, Vol 16, Issue 12
To: <gate-users at lphe1pet1.epfl.ch>
Message-ID: <DB92A097E63F06499D49DF3501689662520699 at exchange01.ul.pt>
Content-Type: text/plain; charset="windows-1252"
Hi, Vandana!
When i installed GATE i had the same problem.
I really don't know who i did solve my problem, but i think you must try to run the Geant4 example N02 (example/novice/N02). In there I think you will have the same problem, it is not a compilation problem but a linking problem.
Try use clhep 1.8.1.0 and run the examples, maybe you find the problem...
I hope this help you.
Cheers,
Susana Silva
-----Original Message-----
From: gate-users-bounces at lphe1pet1.epfl.ch on behalf of gate-users-request at lphe1pet1.epfl.ch
Sent: Fri 15-07-2005 11:00
To: gate-users at lphe1pet1.epfl.ch
Cc:
Subject: gate-users Digest, Vol 16, Issue 12
Send gate-users mailing list submissions to
gate-users at lphe1pet1.epfl.ch
To subscribe or unsubscribe via the World Wide Web, visit
http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
Please use the GATE's site webmaster e-mail to reach the person
managing the list.
Today's Topics:
1. Positron annihilation distance (message text) (Rutao Yao)
2. Re: gate-users Digest, Vol 16, Issue 10 (Jianfeng He)
3. gcc-4.0 (Vandana Kohli)
----------------------------------------------------------------------
Message: 1
Date: Thu, 14 Jul 2005 16:45:42 -0400
From: "Rutao Yao" <rutaoyao at buffalo.edu>
Subject: [gate-users] Positron annihilation distance (message text)
To: <gate-users at lphe1pet1.epfl.ch>
Message-ID: <200507142045.j6EKjfdT002326 at lphe1pet1.epfl.ch>
Content-Type: text/plain; charset="us-ascii"
Hi,
Maybe someone here can give me some advices. I have trouble to understand
the positron-range results generated with GATE.
For F18, the positron range distribution (see attached gif figure) shows an
unexpected peak between 1 and 2 mm, which is not present in published
literature (Levin and Hoffman, Craig S Levin and Edward J Hoffman 1999 Phys.
Med. Biol. *44* 781-799; Laforest R, Rowland DJ, Welch MJ. 2002. MicroPET
imaging with nonconventional isotopes. IEEE Trans Nucl Sci 49, 2119-2126).
The figure can be easily reproduced by running benchmarkPET scripts, just
remove the Oxygen15 parts in the sources.mac. We saw similar results with
Oxygen15.
The GATE version we are using is v1.0. I don't see this issue mentioned in
the later version's releaseNotes.
Thanks in advance!
Rutao Yao, Ph.D.
University at Buffalo
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------------------------------
Message: 2
Date: 15 Jul 2005 10:00:53 +1000
From: Jianfeng He <jfenghe at petnm.unimelb.edu.au>
Subject: [gate-users] Re: gate-users Digest, Vol 16, Issue 10
To: gate-users at lphe1pet1.epfl.ch
Cc: schmidtr at mskcc.org
Message-ID: <1121385653.14367.8.camel at smeagol>
Content-Type: text/plain; charset=UTF-8
Hi Ross,
I am intrested in the root Cint program. Can I get the program? Thanks
in advance.
Best regards,
Jianfeng
On Thu, 2005-07-14 at 20:00, gate-users-request at lphe1pet1.epfl.ch wrote:
> Send gate-users mailing list submissions to
> gate-users at lphe1pet1.epfl.ch
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
>
> Please use the GATE's site webmaster e-mail to reach the person
> managing the list.
>
>
> Today's Topics:
>
> 1. Sinogram output with cylindrical PET system (Ana Iriarte)
> 2. RE: Sinogram output with cylindrical PET system
> (Schmidtlein, Ross/Sloan-Kettering Institute)
> 3. pb with BGO material (Bastien Gu?rin)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 13 Jul 2005 15:04:39 +0200
> From: Ana Iriarte <ana at cnb.uam.es>
> Subject: [gate-users] Sinogram output with cylindrical PET system
> To: gate-users at lphe1pet1.epfl.ch
> Message-ID: <42D51167.9080301 at cnb.uam.es>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
> Hi everybody
>
> Is it possible to have sinogram output when using cylindrical PET as
> system or it is exclusively for using with ecat system?
>
> Thank you in advance.
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 13 Jul 2005 10:32:22 -0400
> From: "Schmidtlein, Ross/Sloan-Kettering Institute"
> <schmidtr at mskcc.org>
> Subject: RE: [gate-users] Sinogram output with cylindrical PET system
> To: "GATE feedback and helpline for Users"
> <gate-users at lphe1pet1.epfl.ch>
> Message-ID:
> <C7E28BA5A8C2B84AAD401F815B1ABA5C01482823 at smskpexmbx4.mskcc.root.mskcc.org>
>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Ana,
>
> The sinogram output is for the ECAT system only. Our group has written
> a root Cint program that will bin coincidences into sinograms for
> cylindricalPET system. Let me know if you are interested.
>
> ross
>
> -----Original Message-----
> From: gate-users-bounces at lphe1pet1.epfl.ch
> [mailto:gate-users-bounces at lphe1pet1.epfl.ch] On Behalf Of Ana Iriarte
> Sent: Wednesday, July 13, 2005 9:05 AM
> To: gate-users at lphe1pet1.epfl.ch
> Subject: [gate-users] Sinogram output with cylindrical PET system
>
>
> Hi everybody
>
> Is it possible to have sinogram output when using cylindrical PET as
> system or it is exclusively for using with ecat system?
>
> Thank you in advance.
>
> _______________________________________________
> gate-users mailing list
> gate-users at lphe1pet1.epfl.ch
> http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: 14 Jul 2005 14:57:21 -0400
> From: "Bastien Gu?rin" <guerin at bwh.harvard.edu>
> Subject: [gate-users] pb with BGO material
> To: gate-users at lphe1pet1.epfl.ch
> Message-ID: <BEFC2DD1.56C%guerin at bwh.harvard.edu>
> Content-Type: text/plain; charset="ISO-8859-1"
>
> Dear All,
>
> I have a problem when using the BGO material as it is defined in GATE. I
> simulate a 511 kev photons beam on a BGO single block detector. The overall
> spectra seem correct (photopeak @ 511 keV, Compton plateau with compton edge
> @ 340 keV) but I have a peak (comparable to the compton edge) between the
> compton edge and the photopeak. This clearly doesn't correspond to any
> physical effect and something is wrong in this simulation. I check pretty
> much everything but the mistake doesn't seem trivial to find.
>
> Does one of you already encountered this problem?
>
> Thanks a lot for your support!
>
> BG
>
> ----
>
> Bastien Guérin
> PhD candidate, University of Paris
> Visiting Fellow, Harvard University
> work: 617-525-6629
> urgent: 617-817-2762
>
>
>
>
> ------------------------------
>
> _______________________________________________
> gate-users mailing list
> gate-users at lphe1pet1.epfl.ch
> http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
>
> End of gate-users Digest, Vol 16, Issue 10
> ******************************************
>
------------------------------
Message: 3
Date: Thu, 14 Jul 2005 20:01:08 -1000
From: Vandana Kohli <kohli.vandana at gmail.com>
Subject: [gate-users] gcc-4.0
To: gate-users at lphe1pet1.epfl.ch
Message-ID: <298e9e170507142301726cc6ba at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Dear Gate members,
I am able to compile geant4.7.1 and clhep1.9.2 on Fedora core3 with gcc 4.0.
When I try to install Gate on, I get the following error message
Linking Gate ...
/usr/bin/ld: cannot find -lXt
collect2: ld returned 1 exit status
Any suggestions will be very helpful.
Thanks
Vandana
------------------------------
_______________________________________________
gate-users mailing list
gate-users at lphe1pet1.epfl.ch
http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
End of gate-users Digest, Vol 16, Issue 12
******************************************
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------------------------------
Message: 2
Date: Fri, 15 Jul 2005 17:18:10 +0200 (MET DST)
From: "Mutanga Theodore" <muathe02 at student.umu.se>
Subject: Re: [gate-users] gcc-4.0
To: "Vandana Kohli" <kohli.vandana at gmail.com>, "GATE feedback and
helpline for Users" <gate-users at lphe1pet1.epfl.ch>
Message-ID: <3740.81.172.169.69.1121440690.squirrel at 81.172.169.69>
Content-Type: text/plain;charset=iso-8859-1
What distro are you using? The problem is GATE isn't finding the libXt
library files either you have it somewhere else or its not installed. try
apt-get install libXt if you are on Debian or search around for how to
install libXt.
Cheers
> Dear Gate members,
> I am able to compile geant4.7.1 and clhep1.9.2 on Fedora core3 with gcc
> 4.0.
> When I try to install Gate on, I get the following error message
> Linking Gate ...
> /usr/bin/ld: cannot find -lXt
> collect2: ld returned 1 exit status
>
> Any suggestions will be very helpful.
> Thanks
> Vandana
>
> _______________________________________________
> gate-users mailing list
> gate-users at lphe1pet1.epfl.ch
> http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
>
------------------------------
Message: 3
Date: Fri, 15 Jul 2005 16:59:23 +0100
From: Leighton Barnden <l.barnden at nucmed.ucl.ac.uk>
Subject: [gate-users] Voxelised Phantom
To: GATE-users <gate-users at lphe1pet1.epfl.ch>
Message-ID: <42D7DD5B.6070609 at nucmed.ucl.ac.uk>
Content-Type: text/plain; charset=us-ascii; format=flowed
Hi everyone,
Jan Sebastien's mail of June 29 suggests that the voxelised phantom
option in Gate 1.2.0 does not work. Is this correct?
He also mentioned a new version of Gate that would fix the problems.
What is the status of this?
Thanks in advance
Leighton Barnden
Visiting Scientist
UCL Institute of Nuclear Medicine
London, UK
------------------------------
Message: 4
Date: Fri, 15 Jul 2005 18:46:41 +0200 (MET DST)
From: "Mutanga Theodore" <muathe02 at student.umu.se>
Subject: Re: [gate-users] Voxelised Phantom
To: "GATE feedback and helpline for Users"
<gate-users at lphe1pet1.epfl.ch>
Message-ID: <4842.81.172.169.69.1121446001.squirrel at 81.172.169.69>
Content-Type: text/plain;charset=iso-8859-1
Hi
It is correct and lets all be patient Im pretty sure they are working hard
to get the release out soon ! Im waiting for that myself.
Cheers
Theo
> Hi everyone,
>
> Jan Sebastien's mail of June 29 suggests that the voxelised phantom
> option in Gate 1.2.0 does not work. Is this correct?
> He also mentioned a new version of Gate that would fix the problems.
> What is the status of this?
>
> Thanks in advance
>
> Leighton Barnden
> Visiting Scientist
> UCL Institute of Nuclear Medicine
> London, UK
>
> _______________________________________________
> gate-users mailing list
> gate-users at lphe1pet1.epfl.ch
> http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
>
------------------------------
Message: 5
Date: Fri, 15 Jul 2005 11:29:24 -1000
From: Vandana Kohli <kohli.vandana at gmail.com>
Subject: Re: [gate-users] RE: gate-users Digest, Vol 16, Issue 12
To: GATE feedback and helpline for Users
<gate-users at lphe1pet1.epfl.ch>
Message-ID: <298e9e17050715142977fabb4 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Dear Susana
Did you use clhep 1.8 with geant 4.7 on Fedora core 4 (gcc -4.0).
Is that what your configuration is right now.
Thanks for your help.
Vandana
On 7/15/05, Susana Silva <susana.silva at fc.ul.pt> wrote:
>
> Hi, Vandana!
>
> When i installed GATE i had the same problem.
> I really don't know who i did solve my problem, but i think you must try to run the Geant4 example N02 (example/novice/N02). In there I think you will have the same problem, it is not a compilation problem but a linking problem.
> Try use clhep 1.8.1.0 and run the examples, maybe you find the problem...
>
> I hope this help you.
>
> Cheers,
>
> Susana Silva
>
>
> -----Original Message-----
> From: gate-users-bounces at lphe1pet1.epfl.ch on behalf of gate-users-request at lphe1pet1.epfl.ch
> Sent: Fri 15-07-2005 11:00
> To: gate-users at lphe1pet1.epfl.ch
> Cc:
> Subject: gate-users Digest, Vol 16, Issue 12
> Send gate-users mailing list submissions to
> gate-users at lphe1pet1.epfl.ch
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
>
> Please use the GATE's site webmaster e-mail to reach the person
> managing the list.
>
>
> Today's Topics:
>
> 1. Positron annihilation distance (message text) (Rutao Yao)
> 2. Re: gate-users Digest, Vol 16, Issue 10 (Jianfeng He)
> 3. gcc-4.0 (Vandana Kohli)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 14 Jul 2005 16:45:42 -0400
> From: "Rutao Yao" <rutaoyao at buffalo.edu>
> Subject: [gate-users] Positron annihilation distance (message text)
> To: <gate-users at lphe1pet1.epfl.ch>
> Message-ID: <200507142045.j6EKjfdT002326 at lphe1pet1.epfl.ch>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
> Maybe someone here can give me some advices. I have trouble to understand
> the positron-range results generated with GATE.
>
> For F18, the positron range distribution (see attached gif figure) shows an
> unexpected peak between 1 and 2 mm, which is not present in published
> literature (Levin and Hoffman, Craig S Levin and Edward J Hoffman 1999 Phys.
> Med. Biol. *44* 781-799; Laforest R, Rowland DJ, Welch MJ. 2002. MicroPET
> imaging with nonconventional isotopes. IEEE Trans Nucl Sci 49, 2119-2126).
> The figure can be easily reproduced by running benchmarkPET scripts, just
> remove the Oxygen15 parts in the sources.mac. We saw similar results with
> Oxygen15.
>
> The GATE version we are using is v1.0. I don't see this issue mentioned in
> the later version's releaseNotes.
>
> Thanks in advance!
>
>
> Rutao Yao, Ph.D.
>
> University at Buffalo
>
>
>
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://lphe1pet1.epfl.ch/mailman/private/gate-users/attachments/20050714/6dc42f66/attachment-0001.htm
>
> ------------------------------
>
> Message: 2
> Date: 15 Jul 2005 10:00:53 +1000
> From: Jianfeng He <jfenghe at petnm.unimelb.edu.au>
> Subject: [gate-users] Re: gate-users Digest, Vol 16, Issue 10
> To: gate-users at lphe1pet1.epfl.ch
> Cc: schmidtr at mskcc.org
> Message-ID: <1121385653.14367.8.camel at smeagol>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Ross,
>
> I am intrested in the root Cint program. Can I get the program? Thanks
> in advance.
>
> Best regards,
>
> Jianfeng
>
>
>
>
>
>
>
> On Thu, 2005-07-14 at 20:00, gate-users-request at lphe1pet1.epfl.ch wrote:
> > Send gate-users mailing list submissions to
> > gate-users at lphe1pet1.epfl.ch
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
> >
> > Please use the GATE's site webmaster e-mail to reach the person
> > managing the list.
> >
> >
> > Today's Topics:
> >
> > 1. Sinogram output with cylindrical PET system (Ana Iriarte)
> > 2. RE: Sinogram output with cylindrical PET system
> > (Schmidtlein, Ross/Sloan-Kettering Institute)
> > 3. pb with BGO material (Bastien Gu?rin)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Wed, 13 Jul 2005 15:04:39 +0200
> > From: Ana Iriarte <ana at cnb.uam.es>
> > Subject: [gate-users] Sinogram output with cylindrical PET system
> > To: gate-users at lphe1pet1.epfl.ch
> > Message-ID: <42D51167.9080301 at cnb.uam.es>
> > Content-Type: text/plain; charset=us-ascii; format=flowed
> >
> > Hi everybody
> >
> > Is it possible to have sinogram output when using cylindrical PET as
> > system or it is exclusively for using with ecat system?
> >
> > Thank you in advance.
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Wed, 13 Jul 2005 10:32:22 -0400
> > From: "Schmidtlein, Ross/Sloan-Kettering Institute"
> > <schmidtr at mskcc.org>
> > Subject: RE: [gate-users] Sinogram output with cylindrical PET system
> > To: "GATE feedback and helpline for Users"
> > <gate-users at lphe1pet1.epfl.ch>
> > Message-ID:
> > <C7E28BA5A8C2B84AAD401F815B1ABA5C01482823 at smskpexmbx4.mskcc.root.mskcc.org>
> >
> > Content-Type: text/plain; charset=us-ascii
> >
> > Hi Ana,
> >
> > The sinogram output is for the ECAT system only. Our group has written
> > a root Cint program that will bin coincidences into sinograms for
> > cylindricalPET system. Let me know if you are interested.
> >
> > ross
> >
> > -----Original Message-----
> > From: gate-users-bounces at lphe1pet1.epfl.ch
> > [mailto:gate-users-bounces at lphe1pet1.epfl.ch] On Behalf Of Ana Iriarte
> > Sent: Wednesday, July 13, 2005 9:05 AM
> > To: gate-users at lphe1pet1.epfl.ch
> > Subject: [gate-users] Sinogram output with cylindrical PET system
> >
> >
> > Hi everybody
> >
> > Is it possible to have sinogram output when using cylindrical PET as
> > system or it is exclusively for using with ecat system?
> >
> > Thank you in advance.
> >
> > _______________________________________________
> > gate-users mailing list
> > gate-users at lphe1pet1.epfl.ch
> > http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: 14 Jul 2005 14:57:21 -0400
> > From: "Bastien Gu?rin" <guerin at bwh.harvard.edu>
> > Subject: [gate-users] pb with BGO material
> > To: gate-users at lphe1pet1.epfl.ch
> > Message-ID: <BEFC2DD1.56C%guerin at bwh.harvard.edu>
> > Content-Type: text/plain; charset="ISO-8859-1"
> >
> > Dear All,
> >
> > I have a problem when using the BGO material as it is defined in GATE. I
> > simulate a 511 kev photons beam on a BGO single block detector. The overall
> > spectra seem correct (photopeak @ 511 keV, Compton plateau with compton edge
> > @ 340 keV) but I have a peak (comparable to the compton edge) between the
> > compton edge and the photopeak. This clearly doesn't correspond to any
> > physical effect and something is wrong in this simulation. I check pretty
> > much everything but the mistake doesn't seem trivial to find.
> >
> > Does one of you already encountered this problem?
> >
> > Thanks a lot for your support!
> >
> > BG
> >
> > ----
> >
> > Bastien GuÃ(c)rin
> > PhD candidate, University of Paris
> > Visiting Fellow, Harvard University
> > work: 617-525-6629
> > urgent: 617-817-2762
> >
> >
> >
> >
> > ------------------------------
> >
> > _______________________________________________
> > gate-users mailing list
> > gate-users at lphe1pet1.epfl.ch
> > http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
> >
> > End of gate-users Digest, Vol 16, Issue 10
> > ******************************************
> >
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 14 Jul 2005 20:01:08 -1000
> From: Vandana Kohli <kohli.vandana at gmail.com>
> Subject: [gate-users] gcc-4.0
> To: gate-users at lphe1pet1.epfl.ch
> Message-ID: <298e9e170507142301726cc6ba at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Gate members,
> I am able to compile geant4.7.1 and clhep1.9.2 on Fedora core3 with gcc 4.0.
> When I try to install Gate on, I get the following error message
> Linking Gate ...
> /usr/bin/ld: cannot find -lXt
> collect2: ld returned 1 exit status
>
> Any suggestions will be very helpful.
> Thanks
> Vandana
>
>
> ------------------------------
>
> _______________________________________________
> gate-users mailing list
> gate-users at lphe1pet1.epfl.ch
> http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
>
> End of gate-users Digest, Vol 16, Issue 12
> ******************************************
>
>
>
>
> _______________________________________________
> gate-users mailing list
> gate-users at lphe1pet1.epfl.ch
> http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
>
>
>
------------------------------
_______________________________________________
gate-users mailing list
gate-users at lphe1pet1.epfl.ch
http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
End of gate-users Digest, Vol 16, Issue 13
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