[gate-users] Image Reconstruction of Gate output

Mutanga Theodore muathe02 at student.umu.se
Mon Dec 20 19:27:57 CET 2004 

Hello Sadek,
I have three questions about using your software for the DST,

1) What system does one use for the scanner geometry design? ECAT or
   CYLINDRICALPET ? I am asking this because the root outputs will be
   different ( ie different trees and leaves )
2*) What should the root output contain ? only concidences ? or can it have
    singles, Hits and Ntuples ?
3) Does it work with all root versions ?

Here is a sample out I just did from my tets, the rootfile wasnt closed
tho, i was just testing.

*********************************************************
root [0] .x GE_DST_3D_Sinogram_Bin.c
Please enter the number of runs: 1
Warning in <TFile::Init>: file
/scratch/muathe02/Gate_Reconstruction/run0.root probably not closed,
trying to recover
Info in <TFile::Recover>: /scratch/muathe02/Gate_Reconstruction/run0.root,
recovered key TNtuple:Gate at address 900100505
Info in <TFile::Recover>: /scratch/muathe02/Gate_Reconstruction/run0.root,
recovered key TTree:Coincidences at address 934750544
Info in <TFile::Recover>: /scratch/muathe02/Gate_Reconstruction/run0.root,
recovered key TTree:Hits at address 947005851
Warning in <TFile::Init>: successfully recovered 3 keys
Error in <TFile::TFile>: file
/scratch/muathe02/Gate_Reconstruction/run1.root does not exist

Total Number of Coincidence Events:= 1234567890
... 0

 *** Break *** segmentation violation
 Generating stack trace...


> Theo,
>
> the DST parameters are listed in my code under "Define the scanner
> geometry parameters" section. Those are the parameters suggested by GE.
>
>     Sadek
>
>
>
> -----Original Message-----
> From:	gate-users-bounces at lphe1pet1.epfl.ch on behalf of Mutanga Theodore
> Sent:	Mon 12/20/2004 12:43 PM
> To:	GATE feedback and helpline for Users
> Cc:
> Subject:	RE: [gate-users] Image Reconstruction of Gate output
> Hello there
>
> I am trying to modify Sadeks code for the GE Discovery ST,
> Does anyone know where/how I can get the
>                                         parameters,
>
> Max Theta (??)
> Number of projection planes (225)
> Sinogram width (249)
>
> for the Discovery ST ?
>
> The values in brackets are the ones I have found out. Could someone verify
> if they are correct ?
>
>
> Cheers
> theodore
>
>
>
>
>  Theodore, for the STIR reconstruction you should have everything you
>> need in that attachment I sent earlier today. In the beginning of the
>> code I define the parameters of the DLS, and I have all the DST
>> parameters mentioned their as well. Change the DLS parameters to DST,
>> and then just follow the instrcutions in the README.txt file I have in
>> my attachment. If you get any problems/questions please let me know. OH,
>> you should run version 1.3 of STIR which has the DST geometry as Kris
>> mentioned. Good luck.
>>
>> 	Sadek
>>
>> -----Original Message-----
>> From: gate-users-bounces at lphe1pet1.epfl.ch
>> [mailto:gate-users-bounces at lphe1pet1.epfl.ch] On Behalf Of Mutanga
>> Theodore
>> Sent: Wednesday, December 15, 2004 3:21 PM
>> To: GATE feedback and helpline for Users
>> Subject: RE: [gate-users] Image Reconstruction of Gate output
>>
>> Hello Sadek,
>> Well as you say it  will be easier for everyone  if I use STIR. It's ok
>> by me, I was hoping to import the data and use the GE stuff. But if you
>> send me the other tools I need to use STIR for the DST geometry it will
>> be fine.
>> Or I can ask our guys at Uppsala IMANET to work out a permission from GE
>> for you to release the information.
>>
>> Thanks
>> Theo
>>>
>>> If you can manage to reconstruct your Gate data with STIR it will be
>>> easier for everybody. Otherwise we will have to work out another
>>> permission from GE, because reconstructing on the GE console requires
>>> giving information about the GE data format, which I don't have
>>> permission to release.
>>>
>>> 	Sadek
>>>
>>> -----Original Message-----
>>> From: gate-users-bounces at lphe1pet1.epfl.ch
>>> [mailto:gate-users-bounces at lphe1pet1.epfl.ch] On Behalf Of Mutanga
>>> Theodore
>>> Sent: Wednesday, December 15, 2004 12:13 PM
>>> To: GATE feedback and helpline for Users
>>> Subject: Re: [gate-users] Image Reconstruction of Gate output
>>>
>>> Hello Sadek,
>>> I just got the codes, thanks, as I told you my interest in with the
>>> DST geometry so if you don't mind I wold like to have the other tools.
>>> I plan to export the data ona DST station, since STIR doesn't yet
>>> recognise DST geometry. I could work with Kris on that one but I don't
>>
>>> know how much of programming it will require.
>>>
>>> Regards
>>> Theodore
>>>
>>>
>>>>
>>>> 	Dear Gaters, in particular GE PET users,
>>>>
>>>> 	Please find attached an image reconstruction tool for Gate root
>>>> output. First untar
>>>>       Gate_Reconstrcution.tar (tar -xvf Gate_Reconstrcution.tar); you
>>
>>>> should find the following files in
>>>>       the Gate_Reconstrcution:
>>>>
>>>> 	1- GEAdvance3D_Sinogram_Bin.c
>>>> 	2- Gate_To_Stir.c
>>>> 	3- few .par files for STIR based reconstructions
>>>> 	4- README.txt
>>>>
>>>>
>>>> "GEAdvance3D_Sinogram_Bin.c" is mainly to read multiple .root files
>>>> and bin the data according to the GE Advance/DLS PET scanner. If to
>>>> be
>>>
>>>> used for the GE DST, some defined variables at the beginning of the
>>>> code need to be modified according to the DST geometry. The DST
>>>> geometry parameters are included in the file. The binning
>>>> formulations
>>>
>>>> have been approved by GE, and released under GE permission.
>>>>
>>>> "Gate_To_Stir.c" reads the GE Michelogram, and writes it in STIR
>>>> format for the GE Advance, so that the final output may be
>>>> reconstructed using STIR.
>>>>
>>>> In README.txt I tried to describe step-by-step how to run these
>>>> tools,
>>>
>>>> and reconstruct the Gate images with STIR. The attached .par files
>>>> are
>>>
>>>> modified copies from the STIR "samples" directory.
>>>>
>>>>
>>>> "GEAdvance3D_Sinogram_Bin.c" also outputs the Gate data in a GE
>>>> format
>>>
>>>> that may be imported to the GE PET scanner console for
>> reconstruction.
>>>> If anybody is interested in doing that please le me know, so that I
>>>> will provide you with the couple additional tools.
>>>>
>>>> Hope this will be helpful.
>>>>
>>>> P.S. Kris, I would appreciate if you may take a look at my REAME.txt
>>>> file to make sure I'm not doing something
>>>>      wrong when using STIR.
>>>>
>>>>
>>>> 	Regards,
>>>>
>>>> 	Sadek
>>>>
>>>>
>>>> ----------------------------------------
>>>>  Sadek A. Nehmeh, Ph.D.
>>>>  Assistant Attending Physicist
>>>>  Medical Physics Department
>>>>  Nuclear Medicine Service
>>>>  Memorial Sloan-Kettering Cancer Center
>>>>  Tel: (212)-639-2175
>>>>  Email: nehmehs at mskcc.org
>>>> ------------------------------------------
>>>>
>>>>
>>>>
>>>>
>>>>
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