[Gate-users] Re : voxelized phantom

Sat Dec 19 20:31:12 CET 2009

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
> 
> 
> 
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> Gate-users at lists.healthgrid.org
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