[gate-users] Image Reconstruction of Gate output
Nehmeh, Sadek/Medical Physics
nehmehs at mskcc.org
Mon Dec 20 22:01:45 CET 2004
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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