[Gate-users] reading CylindricalPET ROOT files in STIR

[Hanieh Jozi]

Dear Kris,

It depends on how you want to make a geometry structure. As you know, in  GATE, in the cylindricalPET scanner, the geometrical volumes containing crystal are grouped in matrices, themselves assembled in submodules and modules ( if you want, you can define submodules) and the Rsectors composed of modules are repeated on a cylindrical surface to build up the whole system. So I answer you by an example, I define a biograph6 PET, it is a cylindricalPET system composed of 12 rsectors, 3 modules (repeated along z axis) 4 modules ( repeated along Y axis that it equals to : 3 submodules repeated in Y axis( one submodule has 3 modules in z axis= 3*1) and 13*13 crystals.( 39 crystal in z axis).
So in STIR header file and in stir_master ( template_for_ROOTscanner. hs):
Num- block _per bucket in transaxial(y) = 4 and num- block _per bucket in axis(z) = 3 
Num_crystal _per block in y= 13
Num_crystal _per block in z= 13
Num_crystal _per singles unit in z and  Y = 13
Thus ,bucket= rsector, module =block
Or you can define it like this:
Num- block _per bucket in transaxial(y) = 1, and num- block _per bucket in axis(z) = 1
Num_crystal _per block in y= 39( 41 in a real scanner)
Num_crystal _per block in z= 52( 56 in a real scanner)
Num_crystal _per singles unit in z =39 and in Y = 52, so in this structure, the bucket equals to block = rsector=1.
2 models has a same answering. But when I convert a root file to sinogram by gate_pet_2_stir , it makes this header file:
Num- block _per bucket in transaxial(y) = 1 and num- block _per bucket in axis(z) = 3 
Num_crystal _per block in y= 13
Num_crystal _per block in z= 13
Num_crystal _per singles unit in z and  Y = 13.
And about deadtime, for choosing DTVloume, its corresponding system level.

Cheers,

Hanieh
Envoyé de mon iPhone

> Le 27 juin 2017 à 20:17, MOREL Christian <morel at cppm.in2p3.fr> a écrit :
> 
> Dear Kris,
> 
> Normally, RSector as defined in the LMF library (see below) can also be repeated along the scanner axis.
> 
> Kind regards, Christian Morel
> 
> <LMF_geometry.pdf>
> 
>> Le 27 juin 2017 à 15:52, Thielemans, Kris <k.thielemans at ucl.ac.uk> a écrit :
>> 
>> Hi all
>>  
>> As you know, Nikos put code into our development version of STIR to read ROOT files (it needs an additional text file to specify some scanner info). This should handle CylindricalPET and ECAT output. We’re checking this now and have identified 2 “issues”
>>  
>> https://github.com/UCL/STIR/issues/80
>> https://github.com/UCL/STIR/issues/79
>>  
>> The main problem is that CylindricalPET has 1 extra level of hierarchy:
>> CylindricalPET: RSector, Module, Submodule, Crystal
>> STIR: bucket, block, crystal
>>  
>> We’re debating how to map the CylindricalPET case to STIR. However to make a sensible decision, can someone please clarify what the consequences are of the cylindricalPET hierarchy? I realise you can use this do specify geometry (via the repeaters). Does it also have anything to do with dead-time processing?
>>  
>> Also, can RSector to repetition along the scanner axis as well, or only rotation?
>>  
>> Of course, feel free to add comments to the Issues above. If not, I’ll summarise this email thread and put it on github as well.
>> Please reply to both gate-users at lists.opengatecollaboration.org and stir-devel at lists.sourceforge.net
>>  
>> Many thanks
>>  
>> Kris Thielemans
>> Reader in Medical Imaging Physics at University College London,
>> Institute of Nuclear Medicine, UCL Hospital, Tower 5,
>> 235 Euston Road, London NW1 2BU, UK
>>  
>> _______________________________________________
>> Gate-users mailing list
>> Gate-users at lists.opengatecollaboration.org
>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> 
> __________________
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> 
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