[gate-users] Image Reconstruction of Gate output
Mutanga Theodore
muathe02 at student.umu.se
Thu Dec 23 16:16:35 CET 2004
Hello , I have the attenuation image
image_lung_8_1_30mm.ahv
image_lung_8_1_30mm.hv
image_lung_8_1_30mm.v
As in your example, can I use these ? or should I generate an image of my
own phantom ?
What about the mash factors, span and ring difference ?
Do I set those at my convenience ?
Theo
> You can generate an attenuation image using generate_image from STIR,
> then fwdtest (also from STIR). In fwdtest do a full forward projection.
> You get fwdtest_out.hs as output, that you may copy to projections.hs.
> Make sure you modify the input file in the copied file from
> fwdtest_out.s to projections.s.
>
> 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 6:33 PM
> To: GATE feedback and helpline for Users
> Subject: RE: [gate-users] Image Reconstruction of Gate output
>
> Hello Sadek,
>
> The files projections.hs is specific to GE Advance and clue as to how to
> generate that for the DST ?
>
> Im close to getting the images now ....
> Ill send you some screenshots
>
> Regards
>
> Theo
>
>
>> I'm not sure if ithe code crashes if the root file is not properly
>> closed. You shouldtry it with a non-corrupted file. You should enter 0
>
>> for the number of runs.
>>
>> 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: Monday, December 20, 2004 4:44 PM
>> To: GATE feedback and helpline for Users
>> Subject: RE: [gate-users] Image Reconstruction of Gate output
>>
>> Hello there,
>>
>> Thanks for the mail and the help , its no problem I didn't get the
>> mail twice after all.
>>
>> For now I have used the ecat system for the DST, 24 rings, 6*6
>> crystals per block, 4 block rings,420 detectors per ring. I haven't
>> renamed anything , except the numbers (ring, blocks , crystals)
>>
>> For the error message, I had just one root file in the directory, and
>> I selected 1 as number of runs, i would have expected it to stop
>> there, or does the number of runs start from 0 ?
>>
>> 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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