[Gate-users] Re : voxelized phantom

Sun Dec 20 13:11:41 CET 2009

Hi Nouria,
i bhad the problem like you, please send me your phantom and it's header
file (*.h33 and *.i33) to simulate in my OS.

regards.

On Sat, Dec 19, 2009 at 11:01 PM, nouria bendjaballah <nbendj at yahoo.fr>wrote:

> Hi Catarina,
> Thank you very much for your help, the data file can be read  but now I get
> another message:
>  Header read from       'm000-SE2_2.h33'
>  Data file name         'm000-SE2_2.i33'
>  Nb of planes:           55
>  Nb of pixels per plane: 512 512
>  Pixel size:             3.906e-01 3.906e-01
>  Slice thickness:        3.200e+00
>  Matrix size:            2.000e+02 2.000e+02
>  Data type:              UNSIGNED INTEGER
>
> nx ny nz: 512 512 55
> dx dy dz: 3.906e-01 3.906e-01 3.200e+00
> G4PhysicalVolumeModel::Validate() called.
>  Volume of the same name and copy number ("world_P", copy 0) still exists
> and is being used.
>  WARNING: This does not necessarily guarantee it's the same
>  volume you originally specified in /vis/scene/add/.
>
>  *** Break *** segmentation violation
> Attaching to program: /proc/8135/exe, process 8135
> [Thread debugging using libthread_db enabled]
> [New Thread 0xb3cdd6c0 (LWP 8135)]
> 0xb7fae410 in __kernel_vsyscall ()
> error detected on stdin
> The program is running.  Quit anyway (and detach it)? (y or n) [answered Y;
> input not from terminal]
> Detaching from program: /proc/8135/exe, process 8135
> *** glibc detected *** Gate: free(): invalid pointer: 0x08407308 ***
> ======= Backtrace: =========
> /lib/tls/i686/cmov/libc.so.6[0xb3db7a85]
> /lib/tls/i686/cmov/libc.so.6(cfree+0x90)[0xb3dbb4f0]
> /usr/lib/libstdc++.so.6(_ZdlPv+0x21)[0xb3f5db11]
>
> /home/physique/geant4/geant4.9.1.p02/lib/Linux-g++/libG4processes.so(_ZN13G4eIonisationD0Ev+0x35)[0xb4af2fb5]
>
> /home/physique/geant4/geant4.9.1.p02/lib/Linux-g++/libG4processes.so(_ZN18G4LossTableManagerD1Ev+0x38)[0xb4b18098]
>
> /home/physique/geant4/geant4.9.1.p02/lib/Linux-g++/libG4processes.so[0xb4b18340]
> /lib/tls/i686/cmov/libc.so.6(__cxa_finalize+0xb1)[0xb3d7a3b1]
>
> /home/physique/geant4/geant4.9.1.p02/lib/Linux-g++/libG4processes.so[0xb4a56d53]
>
> /home/physique/geant4/geant4.9.1.p02/lib/Linux-g++/libG4processes.so[0xb53587ec]
> /lib/ld-linux.so.2[0xb7fbd00f]
> /lib/tls/i686/cmov/libc.so.6(exit+0xd4)[0xb3d7a084]
>
> /home/physique/root/lib/libCore.so(_ZN11TUnixSystem4ExitEib+0x9f)[0xb75669ff]
>
> /home/physique/root/lib/libCore.so(_ZN11TUnixSystem15DispatchSignalsE8ESignals+0x12d)[0xb75697af]
> /home/physique/root/lib/libCore.so[0xb7569899]
> /home/physique/root/lib/libCore.so[0xb7562d5d]
> [0xb7fae420]
> /usr/lib/dri/fglrx_dri.so[0xb2f49c31]
>
> /home/physique/geant4/geant4.9.1.p02/lib/Linux-g++/libG4OpenGL.so(_ZN26G4OpenGLStoredSceneHandler20AddPrimitivePreambleERK9G4Visible+0x28c)[0xb5e8ae6c]
>
> /home/physique/geant4/geant4.9.1.p02/lib/Linux-g++/libG4OpenGL.so(_ZN26G4OpenGLStoredSceneHandler12AddPrimitiveERK12G4Polyhedron+0x2f)[0xb5e8b2ef]
>
> /home/physique/geant4/geant4.9.1.p02/lib/Linux-g++/libG4vis_management.so(_ZN15G4VSceneHandler17RequestPrimitivesERK8G4VSolid+0x80)[0xb5de8450]
>
> /home/physique/geant4/geant4.9.1.p02/lib/Linux-g++/libG4OpenGL.so(_ZN26G4OpenGLStoredSceneHandler17RequestPrimitivesERK8G4VSolid+0x370)[0xb5e8a8d0]
>
> /home/physique/geant4/geant4.9.1.p02/lib/Linux-g++/libG4vis_management.so(_ZN15G4VSceneHandler8AddSolidERK5G4Box+0x1b)[0xb5de6ceb]
> .............
> ======= Memory map: ========
> 00048000-00648000 rw-p 00048000 00:00 0
> 00648000-06348000 rw-p 00648000 00:00 0
> 06348000-08048000 rw-p 06348000 00:00 0
> 08048000-08050000 r-xp 00000000 08:01 5701634
>  /home/physique/gate_v4.0.0/bin/Linux-g++/Gate
> 08050000-08051000 rw-p 00007000 08:01 5701634
>  /home/physique/gate_v4.Aborted
>
> Could anyone have any suggestions?
> Best regards,
> Nouria
>
>
>
>
>
> ________________________________
> De : Isabel Catarina Duarte <catarinaduarte86 at hotmail.com>
> À : nbendj at yahoo.fr; Gate_users <gate-users at lists.healthgrid.org>
> Envoyé le : Ven 18 Décembre 2009, 10 h 03 min 59 s
> Objet : RE: [Gate-users] voxelized phantom
>
>
> Hi Nouria,
>
> I had the same problem with my phantom. It became solved when (I think!) I
> used the example of hof3: I copied all the text in the example and i
> replaced the values in the example by my values.
> Try this!
>
> Catarina Duarte
>
>
>
>
> > Date: Thu, 17 Dec 2009 23:31:21 +0000
> > From: nbendj at yahoo.fr
> > To: gate-users at lists.healthgrid.org
> > Subject: [Gate-users] voxelized phantom
> >
> > Dear users' gate,
> > I have some difficulties to run my macro with a voxelized phantom.
> However, I've checked that the pixel is 16 bits unsingned integer (2 bytes
> per pixel) in my header file and I've also verified my data file : its size
> is 127926272 Bytes which corresponds to (512x512x244x2) and its min and max
> values are respectively 0 and 65535 (I read the data easily with Matlab).
> > But when I run my macro I get the following message:
> > 'nrecognised type name 'unsigned integer
> > Header read from 'se2_1.h33'
> > 'Data file name 'se2_1.i33
> > Nb of planes: 244
> > Nb of pixels per plane: 512 512
> > Pixel size: 3.906e-01 3.906e-01
> > Slice thickness: 3.200e+00
> > Matrix size: 2.000e+02 2.000e+02
> > Data type:
> > '!ror: Could not open header file 'se2_1.i33
> > ERROR - G4Box()::G4Box(): randohead_S
> > Dimensions too small ! - 0, 0, 0
> >
> > *** G4Exception : InvalidSetup
> > issued by : G4Box::G4Box()
> > Invalid dimensions. Too small.
> > *** Fatal Exception *** core dump ***
> >
> > *** G4Exception: Aborting execution ***
> > Aborted
> >
> > To construct my interfile, I've grouped my 244 files ( because each slice
> is in one DICOM file and the pixel is encoded with 16 bits signed) in one
> file which its extension becomes .raw and the pixel is now 16 bit unsigned.
> Then I convert the file .raw to interfile by xmedcon.
> > I couldn't see why it couldn't open the data file ? and why it wrote
> > first " 'nrecognised type name 'unsigned integer" while my macro runs
> > very well with the interfile gived in the example gate_v5.0.0 (hof3.h33
> > and hof3.i33).
> > Could anyone help me to resolve this problem?
> > Thanks a lot
> > Nouria
> >
> >
> >
> > _______________________________________________
> > Gate-users mailing list
> > Gate-users at lists.healthgrid.org
> > http://lists.healthgrid.org/mailman/listinfo/gate-users
>
>
> ________________________________
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>
>
>
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>

-- 
Ali Asghar Parach,Ph.D. student in Medical Physics,Tarbiat Modares
University,Tehran,Iran