[gate-users] Image Reconstruction of Gate output

Nehmeh, Sadek/Medical Physics nehmehs at mskcc.org
Thu Dec 23 17:05:24 CET 2004 

Theo, you forward an image to get an emission like (if I may call it
like this) set of sinogram (or projection planes). The inut to the
fwdtest should be your image.hv and not the MichelogramF.ima. The other
parameters in fwdtest define your forward projection. The STIR manual
describes those parameters. 
To get a template header, why don't you check the samples directory in
STIR; there might be a template for the DST there. 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: Thursday, December 23, 2004 10:30 AM
To: GATE feedback and helpline for Users
Subject: RE: [gate-users] Image Reconstruction of Gate output

Thats right, but the fwdtest expects projection data as input, or else
it asks for those paramters(mashing, span etc ). I tried to give the
MichelogramF.ima as input but it can't read that, trying to choose those
values myself may cause me problems in the future cos I don't really
know how to choose them....where can I get information about these , do
you have any idea ?

Regards

Theo

> 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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