[Gate-users] Re: Gate-users Digest, Vol 24, Issue 31
Susana Branco Silva
susana.silva at fc.ul.pt
Sun May 25 01:08:48 CEST 2008
Hi Sonal!
I agree with Nicolas!
I had similar problems due to some incompatibilities between GATE versions
and the ROOT framework.
Check your installation versions!!
Cheers,
Susana Branco Silva
untitled
Faculdade de Ciências da Universidade de Lisboa
Campo Grande, 1749-016 Lisboa, Portugal
Phone: (+351) 21 750 01 77 ext.: 20515
Fax: (+351) 21 750 00 30
<mailto:susana.silva at fc.ul.pt> email: susana.silva at fc.ul.pt
url: www.ibeb.fc.ul.pt
-----Original Message-----
From: gate-users-bounces at lists.healthgrid.org
[mailto:gate-users-bounces at lists.healthgrid.org] On Behalf Of Nicolas
Karakatsanis
Sent: sábado, 24 de Maio de 2008 17:41
To: Sonal Ambwani; gate-users at lists.healthgrid.org
Subject: Re: [Gate-users] Re: Gate-users Digest, Vol 24, Issue 31
Hi Sonal,
for the current version of GATE (3.1.2), the recommended version of ROOT
is 5.14. You can find this ROOT distribution at the following link
http://root.cern.ch/root/Version514.html
The error message generated by GATE suggests that the problem is caused
by an incompatibility between the GATE and the ROOT versions that are
installed on your system.
Therefore it is most likely that the problem will be solved when you
install this particular ROOT distribution.
GATE had been tested with this version and no error messages of this
nature were reported.
Please let us know about the outcome of your GATE simulations after
installing ROOT 5.14
Best regards
Nicolas
_____________________________________________________
Nicolas Karakatsanis
PhD Candidate
Biomedical Simulations and Imaging Technologies Laboratory
School of Electrical and Computer Engineer
National Technical University of Athens, Greece
Sonal Ambwani wrote:
> Thanks Jose,
> The thought of reinstalling root occured to me too. Could you tell me
> which version of root you are using? I have 5.18 right now and it is
> causing issues with the digitizer module it seems.
>
> Quoting José Ramos <joserm84 at gmail.com>:
>
>> Hi Sonal
>> I had a similar problem, I solved it, "reinstalling root" and recompile
>> Gate
>> I hope this help
>> Best regards
>> 2008/5/24 <gate-users-request at lists.healthgrid.org>:
>>
>>> Send Gate-users mailing list submissions to
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>>> When replying, please edit your Subject line so it is more specific
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>>>
>>>
>>> Today's Topics:
>>>
>>> 1. Gate digitizer error (Sonal Ambwani)
>>> 2. Re: Gate digitizer error (Sonal Ambwani)
>>> 3. Re: Gate digitizer error---update (Sonal Ambwani)
>>> 4. Re: Transmission tomography (Javier Serrano)
>>>
>>>
>>> ----------------------------------------------------------------------
>>>
>>> Message: 1
>>> Date: Fri, 23 May 2008 12:04:26 -0400
>>> From: Sonal Ambwani <ambwani at bu.edu>
>>> Subject: [Gate-users] Gate digitizer error
>>> To: gate-users at lists.healthgrid.org
>>> Message-ID: <20080523120426.q8daye1hws4k4ckw at www.bu.edu>
>>> Content-Type: text/plain; charset=ISO-8859-1; format="flowed"
>>>
>>> Dear Gate-users,
>>>
>>> I am suddenly getting the following error while running
>>> benchmarkSPECT :
>>>
>>> /gate/physics/setXRayCut 200. keV
>>> /gate/physics/setElectronCut 1. km
>>> /gate/physics/setDeltaRayCut 1. GeV
>>> /run/initialize
>>> WARNING !
>>> SetCutValueForOthers became obsolete.
>>> It is harmless to remove this invokation without any side effects.
>>> This dummy method implementation will be removed soon.
>>> /gate/digitizer/Singles/insert adder
>>> ***** COMMAND NOT FOUND </gate/digitizer/Singles/insert adder> *****
>>>
>>> ***** Batch is interupted!! *****
>>> Idle>
>>>
>>> Can someone please point out what might be wrong. This was working till
>>> a few days ago.
>>>
>>> Sonal Ambwani
>>>
>>> Dept. of Electrical and Computer Engineering
>>> Boston University
>>>
>>>
>>>
>>> ------------------------------
>>>
>>> Message: 2
>>> Date: Fri, 23 May 2008 12:34:14 -0400
>>> From: Sonal Ambwani <ambwani at bu.edu>
>>> Subject: Re: [Gate-users] Gate digitizer error
>>> To: gate-users at lists.healthgrid.org
>>> Message-ID: <20080523123414.rtnx27xw0c04sog0 at www.bu.edu>
>>> Content-Type: text/plain; charset=ISO-8859-1; format="flowed"
>>>
>>> Hi again,
>>>
>>> I am getting the same error for benchmarkPET. I guess it might help to
>>> mention the macro here:
>>>
>>> ###GATE : benchmarkPET.mac
>>> /gate/world/geometry/setXLength 150. cm
>>> /gate/world/geometry/setYLength 150. cm
>>> /gate/world/geometry/setZLength 150. cm
>>>
>>> /control/execute camera.mac
>>>
>>> /control/execute phantom.mac
>>>
>>> /control/execute physics.mac
>>>
>>> # I N I T I A L I Z E
>>> /gate/systems/cylindricalPET/verbose 0
>>> /gate/geometry/enableAutoUpdate
>>> /run/initialize
>>>
>>>
>>> /gate/digitizer/Singles/insert adder
>>> /gate/digitizer/Singles/insert readout
>>> /gate/digitizer/Singles/readout/setDepth 1
>>> /gate/digitizer/Singles/insert blurring
>>> /gate/digitizer/Singles/blurring/setResolution 0.26
>>> /gate/digitizer/Singles/blurring/setEnergyOfReference 511. keV
>>> /gate/digitizer/Singles/insert thresholder
>>> /gate/digitizer/Singles/thresholder/setThreshold 350. keV
>>> /gate/digitizer/Singles/insert upholder
>>> /gate/digitizer/Singles/upholder/setUphold 650. keV
>>>
>>>
>>>
>>> # C O I N C I S O R T E R
>>> /gate/digitizer/Coincidences/setWindow 120. ns
>>> /gate/digitizer/Coincidences/MultiplesPolicy takeWinnerOfGoods
>>>
>>> /gate/digitizer/name delay
>>> /gate/digitizer/insert coincidenceSorter
>>> /gate/digitizer/delay/setWindow 120. ns
>>> /gate/digitizer/delay/setOffset 500. ns
>>> /gate/digitizer/delay/MultiplesPolicy takeWinnerOfGoods
>>>
>>> /control/verbose 0
>>> /grdm/verbose 0
>>> /run/verbose 0
>>> /event/verbose 0
>>> /tracking/verbose 0
>>> /gate/application/verbose 0
>>> /gate/generator/verbose 0
>>> /gate/stacking/verbose 0
>>> /gate/event/verbose 0
>>> /gate/source/verbose 0
>>>
>>> /control/execute sources.mac
>>>
>>> # O U T P U T
>>>
>>> /gate/output/verbose 0
>>>
>>>
>>> /gate/output/ascii/setOutFileHitsFlag 1
>>> /gate/output/ascii/setOutFileSinglesFlag 1
>>> /gate/output/ascii/setOutFileCoincidencesFlag 1
>>> /gate/output/ascii/setOutFiledelayFlag 1
>>>
>>> /gate/output/root/setFileName benchmarkPET
>>> /gate/output/root/setRootHitFlag 0
>>> /gate/output/root/setRootSinglesFlag 0
>>> /gate/output/root/setRootCoincidencesFlag 1
>>> /gate/output/root/setRootdelayFlag 1
>>> /gate/output/root/setRootNtupleFlag 0
>>> /gate/output/root/setSaveRndmFlag 0
>>>
>>>
>>> # S T A R T
>>> /gate/application/setTimeSlice 120. s
>>> /gate/application/setTimeStart 0. s
>>> /gate/application/setTimeStop 240. s
>>> /gate/application/startDAQ
>>>
>>>
>>>
>>> Quoting Sonal Ambwani <ambwani at bu.edu>:
>>>
>>> > Dear Gate-users,
>>> >
>>> > I am suddenly getting the following error while running
>>> benchmarkSPECT :
>>> >
>>> > /gate/physics/setXRayCut 200. keV
>>> > /gate/physics/setElectronCut 1. km
>>> > /gate/physics/setDeltaRayCut 1. GeV
>>> > /run/initialize
>>> > WARNING !
>>> > SetCutValueForOthers became obsolete.
>>> > It is harmless to remove this invokation without any side effects.
>>> > This dummy method implementation will be removed soon.
>>> > /gate/digitizer/Singles/insert adder
>>> > ***** COMMAND NOT FOUND </gate/digitizer/Singles/insert adder> *****
>>> >
>>> > ***** Batch is interupted!! *****
>>> > Idle>
>>> >
>>> > Can someone please point out what might be wrong. This was working
>>> till
>>> > a few days ago.
>>> >
>>> > Sonal Ambwani
>>> >
>>> > Dept. of Electrical and Computer Engineering
>>> > Boston University
>>> >
>>> > _______________________________________________
>>> > Gate-users mailing list
>>> > Gate-users at lists.healthgrid.org
>>> > http://lists.healthgrid.org/mailman/listinfo/gate-users
>>> >
>>>
>>>
>>>
>>> Sonal Ambwani
>>>
>>> Dept. of Electrical and Computer Engineering
>>> Boston University
>>>
>>>
>>>
>>> ------------------------------
>>>
>>> Message: 3
>>> Date: Fri, 23 May 2008 13:53:17 -0400
>>> From: Sonal Ambwani <ambwani at bu.edu>
>>> Subject: Re: [Gate-users] Gate digitizer error---update
>>> To: gate-users at lists.healthgrid.org
>>> Message-ID: <20080523135317.uly9soqzc4c8s840 at www.bu.edu>
>>> Content-Type: text/plain; charset=ISO-8859-1; format="flowed"
>>>
>>> benchmarkPET.mac works after disabling the root output completely.
>>> Please help!
>>>
>>>
>>> Quoting Sonal Ambwani <ambwani at bu.edu>:
>>>
>>> > Hi again,
>>> >
>>> > I am getting the same error for benchmarkPET. I guess it might
>>> help to
>>> > mention the macro here:
>>> >
>>> > ###GATE : benchmarkPET.mac
>>> > /gate/world/geometry/setXLength 150. cm
>>> > /gate/world/geometry/setYLength 150. cm
>>> > /gate/world/geometry/setZLength 150. cm
>>> >
>>> > /control/execute camera.mac
>>> >
>>> > /control/execute phantom.mac
>>> >
>>> > /control/execute physics.mac
>>> >
>>> > # I N I T I A L I Z E
>>> > /gate/systems/cylindricalPET/verbose 0
>>> > /gate/geometry/enableAutoUpdate
>>> > /run/initialize
>>> >
>>> >
>>> > /gate/digitizer/Singles/insert adder
>>> > /gate/digitizer/Singles/insert readout
>>> > /gate/digitizer/Singles/readout/setDepth 1
>>> > /gate/digitizer/Singles/insert blurring
>>> > /gate/digitizer/Singles/blurring/setResolution 0.26
>>> > /gate/digitizer/Singles/blurring/setEnergyOfReference 511. keV
>>> > /gate/digitizer/Singles/insert thresholder
>>> > /gate/digitizer/Singles/thresholder/setThreshold 350. keV
>>> > /gate/digitizer/Singles/insert upholder
>>> > /gate/digitizer/Singles/upholder/setUphold 650. keV
>>> >
>>> >
>>> >
>>> > # C O I N C I S O R T E R
>>> > /gate/digitizer/Coincidences/setWindow 120. ns
>>> > /gate/digitizer/Coincidences/MultiplesPolicy takeWinnerOfGoods
>>> >
>>> > /gate/digitizer/name delay
>>> > /gate/digitizer/insert coincidenceSorter
>>> > /gate/digitizer/delay/setWindow 120. ns
>>> > /gate/digitizer/delay/setOffset 500. ns
>>> > /gate/digitizer/delay/MultiplesPolicy takeWinnerOfGoods
>>> >
>>> > /control/verbose 0
>>> > /grdm/verbose 0
>>> > /run/verbose 0
>>> > /event/verbose 0
>>> > /tracking/verbose 0
>>> > /gate/application/verbose 0
>>> > /gate/generator/verbose 0
>>> > /gate/stacking/verbose 0
>>> > /gate/event/verbose 0
>>> > /gate/source/verbose 0
>>> >
>>> > /control/execute sources.mac
>>> >
>>> > # O U T P U T
>>> >
>>> > /gate/output/verbose 0
>>> >
>>> >
>>> > /gate/output/ascii/setOutFileHitsFlag 1
>>> > /gate/output/ascii/setOutFileSinglesFlag 1
>>> > /gate/output/ascii/setOutFileCoincidencesFlag 1
>>> > /gate/output/ascii/setOutFiledelayFlag 1
>>> >
>>> > /gate/output/root/setFileName benchmarkPET
>>> > /gate/output/root/setRootHitFlag 0
>>> > /gate/output/root/setRootSinglesFlag 0
>>> > /gate/output/root/setRootCoincidencesFlag 1
>>> > /gate/output/root/setRootdelayFlag 1
>>> > /gate/output/root/setRootNtupleFlag 0
>>> > /gate/output/root/setSaveRndmFlag 0
>>> >
>>> >
>>> > # S T A R T
>>> > /gate/application/setTimeSlice 120. s
>>> > /gate/application/setTimeStart 0. s
>>> > /gate/application/setTimeStop 240. s
>>> > /gate/application/startDAQ
>>> >
>>> >
>>> >
>>> > Quoting Sonal Ambwani <ambwani at bu.edu>:
>>> >
>>> >> Dear Gate-users,
>>> >>
>>> >> I am suddenly getting the following error while running
>>> benchmarkSPECT :
>>> >>
>>> >> /gate/physics/setXRayCut 200. keV
>>> >> /gate/physics/setElectronCut 1. km
>>> >> /gate/physics/setDeltaRayCut 1. GeV
>>> >> /run/initialize
>>> >> WARNING !
>>> >> SetCutValueForOthers became obsolete.
>>> >> It is harmless to remove this invokation without any side effects.
>>> >> This dummy method implementation will be removed soon.
>>> >> /gate/digitizer/Singles/insert adder
>>> >> ***** COMMAND NOT FOUND </gate/digitizer/Singles/insert adder> *****
>>> >>
>>> >> ***** Batch is interupted!! *****
>>> >> Idle>
>>> >>
>>> >> Can someone please point out what might be wrong. This was
>>> working till
>>> >> a few days ago.
>>> >>
>>> >> Sonal Ambwani
>>> >>
>>> >> Dept. of Electrical and Computer Engineering
>>> >> Boston University
>>> >>
>>> >> _______________________________________________
>>> >> Gate-users mailing list
>>> >> Gate-users at lists.healthgrid.org
>>> >> http://lists.healthgrid.org/mailman/listinfo/gate-users
>>> >>
>>> >
>>> >
>>> >
>>> > Sonal Ambwani
>>> >
>>> > Dept. of Electrical and Computer Engineering
>>> > Boston University
>>> >
>>> > _______________________________________________
>>> > Gate-users mailing list
>>> > Gate-users at lists.healthgrid.org
>>> > http://lists.healthgrid.org/mailman/listinfo/gate-users
>>> >
>>>
>>>
>>>
>>> Sonal Ambwani
>>>
>>> Dept. of Electrical and Computer Engineering
>>> Boston University
>>>
>>>
>>>
>>> ------------------------------
>>>
>>> Message: 4
>>> Date: Fri, 23 May 2008 19:51:50 +0200
>>> From: "Javier Serrano" <fjaviersr at usal.es>
>>> Subject: Re: [Gate-users] Transmission tomography
>>> To: gate-users at lists.healthgrid.org
>>> Message-ID:
>>> <89978e4d0805231051m2239f53ci102cb532b02309c3 at mail.gmail.com>
>>> Content-Type: text/plain; charset=ISO-8859-1
>>>
>>> > Richard Taschereau wrote:
>>> > While it is technically possible to simulate an x-ray CT, the
>>> amount of
>>> photons you would need is prohibitive.
>>>
>>> Yes, I think so too. I did try to simulate this with Geant4 some time
>>> ago and I found this problem.
>>>
>>> > Franca Cassol-Brunner wrote:
>>> > this will be available in the next Gate release, where a CT system
>>> will
>>> be
>>> > added.
>>>
>>> This is very interesting for me, especially if the next release is
>>> coming soon. I would like to simulate a CT system with Gate even with
>>> a limited number of photons or projections. I will keep waiting for
>>> the next release.
>>>
>>> Thank you all.
>>> Greetings, Javi.
>>>
>>>
>>>
>>>
>>>
>>> 2008/5/22 Franca Cassol-Brunner <cassol at cppm.in2p3.fr>:
>>> > Javier Serrano wrote:
>>> >
>>> >> Is it possible to use Gate to simulate an x-ray scanner with an
>>> >> external cone-beam source?
>>> >
>>> > Hello Javier,
>>> >
>>> > this will be available in the next Gate release, where a CT system
>>> will
>>> be
>>> > added. With the present release you can simulate the cone beam
>>> source but
>>> > there is no adapted output for the CT images.
>>> >
>>> > Don't hesitate to contact me directly to get more details.
>>> >
>>> > Cheers
>>> >
>>> > Franca
>>> >
>>> >
>>> > ****************************************************
>>> > Dr. F. Cassol Brunner
>>> > CPPM/IN2P3 (CNRS) Office: 305
>>> > 163, Avenue de Luminy Phone : (+33) 491827248
>>> > 13288, Marseille Fax : (+33) 491827299
>>> > France
>>> > ****************************************************
>>> >
>>>
>>>
>>> ------------------------------
>>>
>>> _______________________________________________
>>> Gate-users mailing list
>>> Gate-users at lists.healthgrid.org
>>> http://lists.healthgrid.org/mailman/listinfo/gate-users
>>>
>>>
>>> End of Gate-users Digest, Vol 24, Issue 31
>>> ******************************************
>>>
>>
>>
>>
>> --
>> e- + e+ -> ~~>
>>
>
>
>
> Sonal Ambwani
>
> Dept. of Electrical and Computer Engineering
> Boston University
>
> _______________________________________________
> Gate-users mailing list
> Gate-users at lists.healthgrid.org
> http://lists.healthgrid.org/mailman/listinfo/gate-users
>
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