[Gate-users] Voxellized phantom problem?
Susana Branco Silva
susana.silva at fc.ul.pt
Tue May 20 18:58:16 CEST 2008
Hi Wei!
The ActivityRange.dat file is where you define the activity distribution inside the phantom (for each voxel or voxels range) = match activity values to the voxels number/range,...., is the definition of the voxelized source in your simulation!
You have the information about the voxels numbers (assigned an each organ or tissue) in the parameters file on the MOBY program. The same information is reproduced in the log file at the moment of the generation of the phantom files by the program.
You can also check this values if you visualize your phantom file, using an image software...
The definition of the range.dat file is where you define each tissue/organ of your MOBY phantom (for each voxel or voxels range) = match attenuation materials to the voxels number/range, ..., is the definition of the voxelized phantom in your simulation!
You can specify the materials of MOBY using the materials database (GateMaterials.db) and update the same with new materials (this file contains all material parameters required by Geant4 to calculate the interaction cross-sections and is easy to modify). In the 2 last GATE releases (if I’m correct) the MOBY organs/tissues are all defined on the materials database… you don’t need to worry about this.
If you don't want to simulate the attenuation information you don’t need to define the phantom! You just need to define the source (shape; type of source; distribution of the emission; placement of the source…).
Hope this help you!
Try to launch the examples in the GATE distribution package... and read the same information in the User's Guide.
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: wqy [mailto:wqy04 at mails.tsinghua.edu.cn]
Sent: terça-feira, 20 de Maio de 2008 15:37
To: Susana Branco Silva; Ravindranath, Bosky; gate-users at lists.healthgrid.org
Subject: RE: [Gate-users] Voxellized phantom problem?
Hello Susana and Bosky,
Thanks for your help!
I've converted the phantom file to unsigned interger and edited the
header file the same format as the hoffman header file.And it seems
correctly now.However, I have no idea of how to write the range.dat and
activityRange.dat.
the range.dat:
"
5
0 600 Air true 0.0 0.0 0.0 0.2
600 6000 Lung true 1.0 0.0 0.0 0.2
6000 160000 Breast true 0.0 1.0 0.0 0.2
160000 36000000 Plastic true 0.0 0.0 1.0 0.2
36000000 1.073742e+09 Air true 0.0 0.0 0.0 0.2
"
I want to know how to define the the range each line . The range.dat
listed is wrote arbitrarily.
the ActivityRange.dat:
10
3 3 9
6 6 12
10 10 24
14 14 43
16 16 49
17 17 52
23 23 70
24 24 74
50 50 154
100 100 24
Do you have an example?
Best regards and thanks!
Wei
在 2008-05-19一的 17:44 +0100，Susana Branco Silva写道：
> Hello wei!
>
>
> I’m using the MOBY phantom too!
>
>
>
> You have to be care with one thing: GATE can’t read float data (32
> bit)! So you'll need to convert your phantom file to unsigned interger
> (16 bit) format (with IDL or MATLAB for instance).
>
>
>
> Just do the data conversion and follow the hoffman brain example
> inside the GATE distribution!!
>
> Careful: check you image conversion before launch your simulation… If
> all scripts are well defined and you got the message above, probably
> is because the conversion wasn't done correctly:
>
>
>
> GateSourceVoxelImageReader::ReadFile : fileName: moby.h33
>
> Header read from 'moby.h33'
>
> Data file name 'moby.i33'
>
> Nb of planes: 122
>
> Nb of pixels per plane: 40 40
>
> Pixel size: 5.000e-01 5.000e-01
>
> Slice thickness: 5.000e-01
>
> Matrix size: 2.000e+01 2.000e+01
>
> Data type: UNSIGNED INTEGER
>
>
>
> Ignoring confine condition
>
> Source ---------------> voxel_mouse
>
> ID : 0
>
> type : backtoback
>
> startTime (s) : 0.000e+00
>
> time (s) : 0.000e+00
>
> forcedUnstable : 1
>
> forcedLifetime (s) : 9.502e+03
>
> verboseLevel : 0
>
> -----------------------
>
>
>
> Voxel reader ----------> number of voxels : 0
>
> total activity (Bq) : 0.000e+00
>
>
>
>
>
> Hope this help you.
>
>
>
> 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
>
> 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 wqy
> Sent: segunda-feira, 19 de Maio de 2008 16:33
> To: gate-users at lists.healthgrid.org
> Subject: [Gate-users] Voxellized phantom problem?
>
>
>
> Hello Gate User,
>
>
>
> I have used Gate to simulate the Moby Phantom and
> encountered
>
> an error.The following is the error which Gate output:
>
> "...
>
> ...
>
> 'nrecognised type name 'short float
>
> 'nrecognised type name 'short float
>
> Header read from 'm007-heart_act_1.h33'
>
> 'Data file name 'm007-heart_act_1.i33
>
> Nb of planes: 0
>
> Nb of pixels per plane: 256 256
>
> Pixel size: 1 1
>
> Slice thickness: 0
>
> Matrix size: 256 256
>
> Data type:
>
>
>
>
>
> Error: one of the matrix dimensions is zero!
>
> ERROR - G4Box()::G4Box(): hof_brain_S
>
> Dimensions too small ! - 0, 0, 0
>
>
>
> *** G4Exception : InvalidSetup
>
> issued by : G4Box::G4Box()
>
> Invalid dimensions. Too small.
>
> *** Fatal Exception *** core dump ***
>
> "
>
>
>
> By the way: 1.the interfile is correct, it can be read by xmedcon
>
> exactly.
>
> 2. the Gate is installed correctly, it can
> be
>
> simulated the example Voxellized phantom (hof3.h33,hof3.i33)
>
>
>
> I have no idea how to dealwith the problem. Could someone help me？
>
> Best regards and thanks!
>
>
>
>
>
> wei
>
> Dept. of Engineering Physics
>
> Tsinghua University
>
>
>
>
>
> _______________________________________________
>
> Gate-users mailing list
>
> Gate-users at lists.healthgrid.org
>
> http://lists.healthgrid.org/mailman/listinfo/gate-users
>
>
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