[gate-users] Image Reconstruction of Gate output
Mutanga Theodore
muathe02 at student.umu.se
Sun Dec 26 15:57:41 CET 2004
Hello there,
I was wondering if you could help me a bit more with
converting your code for the DST,
At this level, I modified the GEAdvance3D_Sinogram_Bin.c with the DST
parameters and all was ok, I got the output michelogramF.ima
Now, I dont know if I have to modify GateToStir.c also, ? if so what are
the places to modify ?
You also mentioned running fwdtest , I did that and generated a .hs
header file which I later renamed to projections.hs . and I also changed
its input projection data to projections.stir.
I tried to run sensitivity and I got a segmentation fault.
I really don't know all the parts of your codes that need to be changed,
can you help me, if not I'd rather simulate another scanner, I was
thinking your code could do everything and give me an image for the DST
geometry.
******** example or projections.hs ******************
!INTERFILE :=
name of data file := projections.stir
originating system := GE Discovery ST
!GENERAL DATA :=
!GENERAL IMAGE DATA :=
!type of data := PET
imagedata byte order := LITTLEENDIAN
!PET STUDY (General) :=
!PET data type := Emission
applied corrections := {arc correction}
!number format := float
!number of bytes per pixel := 4
number of dimensions := 4
matrix axis label [4] := segment
!matrix size [4] := 15
matrix axis label [3] := view
!matrix size [3] := 210
matrix axis label [2] := axial coordinate
!matrix size [2] := { 7,13,19,25,31,37,43,47,43,37,31,25,19,13,7}
matrix axis label [1] := tangential coordinate
!matrix size [1] := 249
minimum ring difference per segment := {
-22,-19,-16,-13,-10,-7,-4,-1,2,5,8,11,14,17,20}
maximum ring difference per segment := {
-20,-17,-14,-11,-8,-5,-2,1,4,7,10,13,16,19,22}
number of rings := 24
number of detectors per ring := 420
ring diameter (cm) := 90.3
distance between rings (cm) := 0.652916
bin size (cm) := 0.31695
number of blocks_per_bucket in axial direction := 4
number of blocks_per_bucket in transaxial direction := 2
number of crystals_per_block in axial direction := 6
number of crystals_per_block in transaxial direction := 6
number of detector layers := 1
image scaling factor[1] := 1
data offset in bytes[1] := 0
number of time frames := 1
!END OF INTERFILE :=
*************************************************
I am really stuck now with the DST geometry, I wanted to get some images
so I could at least measure the spatial resolution from my simulation
results.
thanks
Theo
> 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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