[Gate-users] cylindrical volume crash: 2nd try
Eugene Gualtieri PhD
gualtier at mail.med.upenn.edu
Wed Sep 1 15:59:52 CEST 2010
All:
I'm trying this question again...
I believe there is a problem with defining cylindrical crystal volumes in GATE.
When defining a scanner as in the CPET example in section 4.4.4 of GATE manual v. 5.0.0, the simulation gives a segmentation fault after the crystal is attached (see below).
I have seen this problem in GATE v. 5.0.0 and 6.0.0.
I would greatly appreciate it if someone could try coding the CPET example to see if they can reproduce this seg fault.
Thanks very much.
-gene gualtieri
-----
/gate/systems/CPET/crystal/attach crystal
*** Break *** segmentation violation
Attaching to program: /proc/28902/exe, process 28902
[Thread debugging using libthread_db enabled]
0x00007f4edd7dbb0e in waitpid () from /lib/libc.so.6
error detected on stdin
A debugging session is active.
Inferior 1 [process 28902] will be detached.
Quit anyway? (y or n) [answered Y; input not from terminal]
Detaching from program: /proc/28902/exe, process 28902
*** glibc detected *** Gate: free(): invalid pointer: 0x00000000020fb268 ***
IAll:
>>
>> I am encountering a segmentation fault when specifying cylindrical crystal volumes, as in the CPET scanner example.
>> The seg fault occurs right after the "/gate/systems/CPET/crystal/attach crystal" line (see below). ?Commenting it out eliminates the crash.
>>
>> I am running ?GATE version name: gate_v5.0.0 ?(1-May-2009)
>>
>> Thanks.
>>
>> Gene
On Aug 25, 2010, at 5:49 AM, gate-users-request at lists.opengatecollaboration.org wrote:
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> Today's Topics:
>
> 1. Re: Corrigendum: My mistake in pprevious messaga: Problem
> running GATE and ROOT with regularMatrix argument (Javier Ors An?a)
> 2. Re: Corrigendum: My mistake in pprevious messaga: Problem
> running GATE and ROOT with regularMatrix argument (Simon Stute)
> 3. Total number of decays by the source (Eunsin Lee)
> 4. Re: Total number of decays by the source (Park MinJae)
> 5. sinogram output (???)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 24 Aug 2010 12:21:23 +0200
> From: Javier Ors An?a <Javier.Ors at ific.uv.es>
> Subject: Re: [Gate-users] Corrigendum: My mistake in pprevious
> messaga: Problem running GATE and ROOT with regularMatrix argument
> To: gate-users at lists.opengatecollaboration.org
> Message-ID: <1282645283.28452.10.camel at evalu145.uv.es>
> Content-Type: text/plain; charset="UTF-8"
>
> I can't tell you a precise answer for your displacement problems, but I
> can tell you to be very careful with rotations and translations
> involving regularMatrix volumes.
>
> I see in you code that you apply a rotation to you volume, and I can
> tell you that there is a bug in the code that prevents rotations and
> translations being applied at all to regularMatrix volumes. Now I'm not
> sure about whether this bug also affects compressedMatrix volumes, but I
> think that this is not the case. So this is probably the origin of the
> differences you see between using one or another type of volume. Make a
> try with a big translation in one axis and you'll see what I say.
>
> I reported this problem about one month ago and also sent a patch that
> I'm using right now for it, but nobody answered, this is the link to my
> message in the list archives:
>
> http://lists.opengatecollaboration.org/mailman/private/gate-users/2010-June/004328.html
>
> El dom, 22-08-2010 a las 23:51 -0700, shahrokh nasseri escribi?:
>> Thank you for your help very much. I have another question.
>>
>> There is a perception (with me at least) that the "compressedMatrix" option
>> is led to displace voxels in the geometric structure of voxellized phantom.
>> Perhaps this does not happen to use "regularMatrix" option. However, I think
>> that "compressedMatrix" has performed more quickly from "regularMatrix".
>>
>> As I mentioned in the previous message, in using "compressedMatrix" option,
>> it ?mismatches between voxellized source and voxellized phantom in the
>> spatial coordinates.
>>
>> Is it true that "regularMatrix" option is initialized the geometric
>> structure of voxellized phantom better or more precise than "compressedMatrix"
>> option?
>>
>> Your sincerely
>> Shahrokh
>>
>>
>> On Sun, Aug 22, 2010 at 1:37 PM, Simon Stute <gate.stute at gmail.com> wrote:
>>
>>> Then if you need visualization, no matter whether you use compressed or
>>> regular.
>>> When you'll finish debugging your simulation, just disable the visu and
>>> switch to regular.
>>>
>>> On Sun, Aug 22, 2010 at 7:38 PM, shahrokh nasseri <
>>> shahrokh.nasseri at gmail.com> wrote:
>>>
>>>> Hi,
>>>>
>>>> I must correct my mistake. After I used "regularMatrix" argument in my
>>>> macro file as mentioned in the following commands, I get ?the error
>>>> messages mentioned in previous above. But when I used
>>>> "compressedMatrix" ?argument, I do not get any error or warning
>>>> message.?
>>>>
>>>> ?/gate/world/daughters/name jaszcak_phantom?
>>>> ?/gate/world/daughters/insert regularMatrix
>>>> ?#?
>>>> ?/gate/jaszcak_phantom/geometry/insertReader interfile
>>>> ?/gate/jaszcak_phantom/interfileReader/insertTranslator range?
>>>> ?/gate/jaszcak_phantom/interfileReader/rangeTranslator/readTable
>>>> ?range.dat
>>>> ?/gate/jaszcak_phantom/interfileReader/rangeTranslator/describe 1?
>>>> ?/gate/jaszcak_phantom/interfileReader/readFile rods.h33?
>>>> ?#?
>>>> ?# off center Y-axis is +0 cm
>>>> ?/gate/jaszcak_phantom/placement/setTranslation 0 0 0 cm?
>>>> ?/gate/jaszcak_phantom/placement/setRotationAxis 0 1 0?
>>>> ?/gate/jaszcak_phantom/placement/setRotationAngle 180 deg?
>>>> ? ?
>>>> Please guide me,?
>>>> Shahrokh
>>>>
>>>>
>> _______________________________________________
>> Gate-users mailing list
>> Gate-users at lists.opengatecollaboration.org
>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 24 Aug 2010 15:52:53 +0200
> From: Simon Stute <gate.stute at gmail.com>
> Subject: Re: [Gate-users] Corrigendum: My mistake in pprevious
> messaga: Problem running GATE and ROOT with regularMatrix argument
> To: Javier Ors An?a <Javier.Ors at ific.uv.es>
> Cc: gate-users at lists.opengatecollaboration.org
> Message-ID:
> <AANLkTinqgYfF+Ac9jn0N67m64bZkwgFDap=aNjUoZRUS at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Javier,
>
> Thank you very much for all patches that you sent.
> This important bug fix will be included in the next gate version.
> But Shahrokh uses the v4 and (I am not 100% sure) and translations and
> rotations should work in this version.
>
> Thanks again,
> Cheers,
> Simon
>
>
> On Tue, Aug 24, 2010 at 12:21 PM, Javier Ors An?a <Javier.Ors at ific.uv.es>wrote:
>
>> I can't tell you a precise answer for your displacement problems, but I
>> can tell you to be very careful with rotations and translations
>> involving regularMatrix volumes.
>>
>> I see in you code that you apply a rotation to you volume, and I can
>> tell you that there is a bug in the code that prevents rotations and
>> translations being applied at all to regularMatrix volumes. Now I'm not
>> sure about whether this bug also affects compressedMatrix volumes, but I
>> think that this is not the case. So this is probably the origin of the
>> differences you see between using one or another type of volume. Make a
>> try with a big translation in one axis and you'll see what I say.
>>
>> I reported this problem about one month ago and also sent a patch that
>> I'm using right now for it, but nobody answered, this is the link to my
>> message in the list archives:
>>
>>
>> http://lists.opengatecollaboration.org/mailman/private/gate-users/2010-June/004328.html
>>
>> El dom, 22-08-2010 a las 23:51 -0700, shahrokh nasseri escribi?:
>>> Thank you for your help very much. I have another question.
>>>
>>> There is a perception (with me at least) that the "compressedMatrix"
>> option
>>> is led to displace voxels in the geometric structure of voxellized
>> phantom.
>>> Perhaps this does not happen to use "regularMatrix" option. However, I
>> think
>>> that "compressedMatrix" has performed more quickly from "regularMatrix".
>>>
>>> As I mentioned in the previous message, in using "compressedMatrix"
>> option,
>>> it ?mismatches between voxellized source and voxellized phantom in the
>>> spatial coordinates.
>>>
>>> Is it true that "regularMatrix" option is initialized the geometric
>>> structure of voxellized phantom better or more precise than
>> "compressedMatrix"
>>> option?
>>>
>>> Your sincerely
>>> Shahrokh
>>>
>>>
>>> On Sun, Aug 22, 2010 at 1:37 PM, Simon Stute <gate.stute at gmail.com>
>> wrote:
>>>
>>>> Then if you need visualization, no matter whether you use compressed or
>>>> regular.
>>>> When you'll finish debugging your simulation, just disable the visu and
>>>> switch to regular.
>>>>
>>>> On Sun, Aug 22, 2010 at 7:38 PM, shahrokh nasseri <
>>>> shahrokh.nasseri at gmail.com> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I must correct my mistake. After I used "regularMatrix" argument in my
>>>>> macro file as mentioned in the following commands, I get ?the error
>>>>> messages mentioned in previous above. But when I used
>>>>> "compressedMatrix" ?argument, I do not get any error or warning
>>>>> message.?
>>>>>
>>>>> ?/gate/world/daughters/name jaszcak_phantom?
>>>>> ?/gate/world/daughters/insert regularMatrix
>>>>> ?#?
>>>>> ?/gate/jaszcak_phantom/geometry/insertReader interfile
>>>>> ?/gate/jaszcak_phantom/interfileReader/insertTranslator range?
>>>>> ?/gate/jaszcak_phantom/interfileReader/rangeTranslator/readTable
>>>>> ?range.dat
>>>>> ?/gate/jaszcak_phantom/interfileReader/rangeTranslator/describe 1?
>>>>> ?/gate/jaszcak_phantom/interfileReader/readFile rods.h33?
>>>>> ?#?
>>>>> ?# off center Y-axis is +0 cm
>>>>> ?/gate/jaszcak_phantom/placement/setTranslation 0 0 0 cm?
>>>>> ?/gate/jaszcak_phantom/placement/setRotationAxis 0 1 0?
>>>>> ?/gate/jaszcak_phantom/placement/setRotationAngle 180 deg?
>>>>> ? ?
>>>>> Please guide me,?
>>>>> Shahrokh
>>>>>
>>>>>
>>> _______________________________________________
>>> Gate-users mailing list
>>> Gate-users at lists.opengatecollaboration.org
>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>
>>
>> _______________________________________________
>> Gate-users mailing list
>> Gate-users at lists.opengatecollaboration.org
>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 24 Aug 2010 11:05:29 -0400
> From: Eunsin Lee <eunsin at mail.med.upenn.edu>
> Subject: [Gate-users] Total number of decays by the source
> To: gate-users at lists.opengatecollaboration.org
> Message-ID: <EE3B739D-60EF-4064-8232-3D2270700370 at mail.med.upenn.edu>
> Content-Type: text/plain; charset=us-ascii
>
> Dear Users,
>
> How do I know the total number of decays by the source before hitting the detector?
> Are there any flags to set for this in root or ascii outputs?
>
> Thanks very much in advance,
> Eunsin
> ******************************************************
> Eunsin Lee
> Postdoctoral Research Associate
> PET Center, Department of Radiology
> University of Pennsylvania School of Medicine
> eunsin at mail.med.upenn.edu
> (215) 349-5751 (office)
> (979) 574-7235 (cell)
> ******************************************************
>
>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 24 Aug 2010 11:37:12 -0400
> From: Park MinJae <MJ at JHMI.edu>
> Subject: Re: [Gate-users] Total number of decays by the source
> To: Eunsin Lee <eunsin at mail.med.upenn.edu>
> Cc: gate-users at lists.opengatecollaboration.org
> Message-ID:
> <AANLkTi=gtEaWFhvu0vr1xyqbcBm5qpsv5-6i_NDCWSc5 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Eunsin,
>
> You may know through eventID.
>
> Cordially yours,
> MJ
>
> //=================================================
> //? Ph.D. Park MinJae
> //
> //? Johns Hopkins University
> //? School of Medicine, Dept of Radiology
> //? Division of Medical Imaging Physics
> //
> //? DialTo:+1-410-955-2684 (Office)
> //? MailTo:MJ at ToTi.us, MJ at JHMI.edu
> //
> //? "You see, But you do not Observe"? - Sherlock Holmes -
> //=================================================
>
>
>
> On Tue, Aug 24, 2010 at 11:05 AM, Eunsin Lee <eunsin at mail.med.upenn.edu> wrote:
>> Dear Users,
>>
>> How do I know the total number of decays by the source before hitting the detector?
>> Are there any flags to set for this in root or ascii outputs?
>>
>> Thanks very much in advance,
>> Eunsin
>> ******************************************************
>> Eunsin Lee
>> Postdoctoral Research Associate
>> PET Center, Department of Radiology
>> University of Pennsylvania School of Medicine
>> eunsin at mail.med.upenn.edu
>> (215) 349-5751 (office)
>> (979) 574-7235 (cell)
>> ******************************************************
>>
>>
>>
>>
>> _______________________________________________
>> Gate-users mailing list
>> Gate-users at lists.opengatecollaboration.org
>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 25 Aug 2010 18:48:49 +0900 (KST)
> From: ??? <great_jh at kaist.ac.kr>
> Subject: [Gate-users] sinogram output
> To: gate-users at lists.opengatecollaboration.org
> Message-ID: <1895811.1282729729786.JavaMail.root at webmail.kaist.ac.kr>
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>
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