[Gate-users] How convert atn.BIN from 32 bit to 16 bit?

[Didier Benoit]

Hi Chang-Lea,

In fact in your act.bin you have to just assign a number, 20 for instance for the heart, 30 for the liver etc… After in GATE you have to create a map activity file, for instance activitymap.dat, in this file you have to indicate the activity in Bq/voxel. The structure of this file is:
"Number of regions"
"min of region" "max of region" "activity"

For instance if you have assign 20 for the heart and 30 for the liver, you activity map will be:

2
20 20 4
30 30 10

(4 Bq/voxel for the heart and 10 Bq/voxel for the liver)

But I have no idea about the initial activity for your mouse. Maybe you could find the activity in some articles.

Kind regards,
Didier


On Nov 17, 2011, at 8:56 AM, changlae lee wrote:

> Dear Didier,
>  
> I really appreciate your comments.
>  
> As I mention that I would like to do X-ray CT dosimetry, appliying MOBY mouse phantom to GATE(ver 6.0).
> I am considering whether I should apply using atn.bin or act. bin when I calculate the dose of each organ using MOBY mouse phantom.
> I have applied act.BIN for SPECT simulation using activity.dat file, so I know for sure how to use act.BIN
> I made MOBY mouse phantom and applied to GATE as you suggested act.BIN. However, I have some problems. To get the MOBY phantom, we assign numbers(activity) for each organ in MOBY_parfile.par.
> From GATE Actordose results, the dosimetry has different results depending on what numbers are assigned to the activity for each organ.
>  
> So, I'd like to ask some questions.
> To estimate x-ray dosimetry for mouse phantom organ using act.bin, what number should I choose for activity each brain organ? The attached file is an example for better explanation.
>  
> I would appreciate your comments and suggestions on this matter.
> I look forward to receiving your reply.
>  
> Thank you,
>  
> Kind regards.
> Chang-Lae Lee
>  
> Doctoral student,
> Dept. of Radiological Science
> Yonsei University College of Health Science
> 
>  
> 2011/11/17 Didier Benoit <benoit at imnc.in2p3.fr>
> Hi Chang-Lae
> 
> All values in your atn.bin are inferior to 0, so if you convert to unsigned short (uint16) all your values will be 0. You have to use the file act.bin in GATE to simulate a voxellized phatom. After you create your own activity map in a file activity.dat for instance. You have an example in the following folder:
> 
> $GATEHOME/examples/example_PHANTOM_SOURCE/Voxelized_Phantom_Source
> 
> Kind regards,
> Didier
> 
> 
> On 11/16/2011 06:26 AM, changlae lee wrote:
> 
> Dear gate-users,
> 
> I am doing study on x-ray CT MOBY modelling for dose calculation with GATE.
> GATE can't read float data (32 bit). So I have converted unsigned integer (16bit) format using MATLAB.
> I converted "act.BIN" from 32 bit to 16 bit, and I could see the imaging well (amide, XMedCon, Image-J).
> 
> And I am trying to do x-ray CT dosimetry using attenuation map(atn.BIN). However, when I converted 'atn.BIN' from 32 bit to 16 bit, I couldn't see the 16 bit image. What I could see was only black box.
> Is there a particular way to convert atn.BIN from 32 bit to 16 bit?
> 
> The codes I used is below (MATLAB)...
> 
> >> uiopen('C:\MOBY\atn_32bit.bin',1);
> >> a=fopen('atn_32bit.bin','rb','ieee-le');
> c=zeros(128,128,4);
> for i=1:4;
> [b,co]=fread(a,[128 128],'float32=>uint16');
> c(:,:,i)=b;
> end
> >> a2=fopen('atn_32bit.bin','wb');
> fwrite(a2,c,'uint16');
> fclose(a);
> fclose(a2);
> 
> The attached files are "atn.BIN" of 32bit and detail explain file.
> Thank you,
> 
> Kind regards.
> Chang-Lae
> 
> Doctoral student,
> Dept. of Radiological Science
> Yonsei University College of Health Science, korea
> 
> 
> 
> -- 
> ----------------------------------------------------------------
> Didier BENOIT, GATE Engineer
> Imagerie et Modélisation en Neurobiologie et Cancérologie (IMNC)
> IMNC – UMR 8165 CNRS – Université Paris 7 – Université Paris 11
> Campus d’Orsay
> Bâtiment 440
> 91406 ORSAY Cedex
> 
> Tél : (33) 1 69 15 68 76
> E-mail : benoit at imnc.in2p3.fr
> http://www.imnc.in2p3.fr
> ----------------------------------------------------------------
> 
> 
> <detail data.pdf>
----------------------------------------------------------------
Didier BENOIT, GATE Engineer
Imagerie et Modélisation en Neurobiologie et Cancérologie (IMNC)
IMNC – UMR 8165 CNRS – Université Paris 7 – Université Paris 11
Campus d’Orsay
Bâtiment 440
91406 ORSAY Cedex

Tél : (33) 1 69 15 68 76
E-mail : benoit at imnc.in2p3.fr
http://www.imnc.in2p3.fr
----------------------------------------------------------------