[gate-users] Image Reconstruction of Gate output
Nehmeh, Sadek/Medical Physics
nehmehs at mskcc.org
Thu Dec 23 16:24:48 CET 2004
When you do fwdtest, you should choose the DST as your scanner. As Kris
mentioned before, the DST is their in his STIR1.3.
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: Thursday, December 23, 2004 9:58 AM
To: GATE feedback and helpline for Users
Subject: RE: [gate-users] Image Reconstruction of Gate output
Hi Sadek,
Thanks for the reply, I have done that but then the interfile header
file projections.hs is for the DLS I can't find information about
generating one for the DST, notably the matrix size and the number of
segments and views.
Can you help on that ?
Theo
Merry Xmas !
> 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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