[Gate-users] Re: Gate-users Digest, Vol 24, Issue 31
Sonal Ambwani
ambwani at bu.edu
Tue May 27 18:54:49 CEST 2008
Hi Nicolas and Susana,
Thanks for the reply and the clarification. However, even with root
5.14 installed I am getting the same error on running benchmark.mac as
I had with 5.18
The strangest thing is that Gate works fine with root disabled. I am
going to investigate further.
***** COMMAND NOT FOUND </gate/digitizer/Singles/insert adder> *****
***** Batch is interupted!! *****
Ignoring confine condition
Ignoring confine condition
GateSourceMgr::ListSources: List of the sources in the source managaer
Source --------------> F18LineSource
ID : 0
type :
activity (Bq) : 100000
startTime (s) : 0
time (s) : 0
forcedUnstable : 1
forcedHalfLife (s) : 6586.2
verboseLevel : 0
----------------------
Source --------------> O15LineSource
ID : 1
type :
activity (Bq) : 100000
startTime (s) : 0
time (s) : 0
forcedUnstable : 1
forcedHalfLife (s) : 122.24
verboseLevel : 0
----------------------
***** COMMAND NOT FOUND </gate/output/ascii/setOutFileHitsFlag 1> *****
***** Batch is interupted!! *****
Idle> exit
I'd appreciate any inputs at this point. I'm working on a 64 bit linux
machine.
Thanks again.
Sonal
Quoting Nicolas Karakatsanis <knicolas at mail.ntua.gr>:
> 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
>>>> gate-users at lists.healthgrid.org
>>>>
>>>> To subscribe or unsubscribe via the World Wide Web, visit
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>>>> or, via email, send a message with subject or body 'help' to
>>>> gate-users-request at lists.healthgrid.org
>>>>
>>>> You can reach the person managing the list at
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>>>>
>>>> When replying, please edit your Subject line so it is more specific
>>>> than "Re: Contents of Gate-users digest..."
>>>>
>>>>
>>>> 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
>>
>> __________ NOD32 3128 (20080523) Information __________
>>
>> This message was checked by NOD32 antivirus system.
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>>
>
Sonal Ambwani
Dept. of Electrical and Computer Engineering
Boston University
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