[gate-users] Image Reconstruction of Gate output
Nehmeh, Sadek/Medical Physics
nehmehs at mskcc.org
Thu Dec 23 15:53:53 CET 2004
Theo, the easiest way to use my singrma binner is to build your geometry
with yhe different parts (rsector, block, ...) of the scanner matching
my definitions. I think if you go with cylindricalPET it will be easier.
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: Tuesday, December 21, 2004 7:24 AM
To: GATE feedback and helpline for Users
Subject: RE: [gate-users] Image Reconstruction of Gate output
hi Again Sadek,
I am refering back to the question I asked before, your code is based on
the cylindrical PET system of GATE , but for the ECAT system, the root
output do not contain the moduleID instead they have equivalently
blockID , it seems to use your code as it is, I have to use the
CylindricalPET system to model the DST.
I am saying this because suppose I instead chose to modify the code, the
trees in the rootfile donot match, for instance what is the equivalent
of rsector in the Ecatsystem?
I can see that the Ecat system has crystals grouped as blocks, a
simplified version of the cylindricalPET.
Do you realy think I should remodel the DST using cylindricalPET instead
?
Cheers
theo
Theo,
> My connection dropped while I was sending to you my response to your
> previous message. So sorry if you get it twice.
>
> 1- I don't think itmatters. In my code though, I define theta as
> (ring1-ring2)/2, where ring1 and ring2 depend on the crystalID and
> moduleID. Crystal1 and crystal2 are also defined as function of
> resectorID, moduleID, and crystalID. For the Advance, the crystals
> (crystal in our GE Advance geom) are grouped into blocks (module in
> our geom), and the blocks are grouped into modules (rsector in our
> geom). So if you change those definitions yur DST geometry, you will
> need to modify the corresponding variable in the code accordingly.
>
> 2- My code will look for the coincidences. It does not care
about
> whether other trees are there or not.
>
> 3- I can't see why not!!
>
> 4- You error messsage speaks out the reason; your path does not
> exist:
> "<TFile::TFile>: file /scratch/muathe02/Gate_Reconstruction/run1.root
> does not exist"
>
>
> 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: Monday, December 20, 2004 1:28 PM
> To: GATE feedback and helpline for Users
> Subject: RE: [gate-users] Image Reconstruction of Gate output
>
> 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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