[Gate-users] Voxellized phantom problem?

[Sonal Ambwani]

Hi Susana,

It does show up in my system now. As you pointed out, I needed to 
enable the color attributes.

Thanks a ton!
Sonal
Quoting Susana Branco Silva <susana.silva at fc.ul.pt>:

> Hi Sonal!
>
>
>
> The answer is yes!!
>
> You can see an example in attachment (the MOBY phantom inside the FOCUS
> system).
>
>
>
>
>
>
>
>  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: gate-users-bounces at lists.healthgrid.org
> [mailto:gate-users-bounces at lists.healthgrid.org] On Behalf Of Sonal Ambwani
> Sent: segunda-feira, 19 de Maio de 2008 21:05
> To: gate-users at lists.healthgrid.org
> Subject: RE: [Gate-users] Voxellized phantom problem?
>
>
>
> Hello Wei and Susana,
>
>
>
> I have a question about voxelized phantoms. With visualization turned
>
> on, do you see the voxellized hoffman phantom during the simulation
>
> like one sees the cylindrical phantom? I dont, and I was just wondering.
>
>
>
>
>
> Thanks,
>
> Sonal
>
> Quoting Susana Branco Silva <susana.silva at fc.ul.pt>:
>
>
>
>> 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
>
>>
>
>>  <mailto:susana.silva at fc.ul.pt> 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
>
>>
>
>>
>
>
>
>
>
>
>
> Sonal Ambwani
>
>
>
> Dept. of Electrical and Computer Engineering
>
> Boston University
>
>
>
> _______________________________________________
>
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>
> Gate-users at lists.healthgrid.org
>
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>
>



Sonal Ambwani

Dept. of Electrical and Computer Engineering
Boston University