[Gate-users] Make an image from GATE

Tue Jun 21 16:27:37 CEST 2016

Hi Andrea,

When using create_projdata_template, if your output name (.hv) is equal to
the name of the sinogram (.s) the .s file gets empty.
For example, I'm using Bin_GATE to create 'sinogram.s' and
create_projdata_template to create 'sinogram.hs'. After this last step
'sinogram.s' gets empty. I suggest using a different name as output for
create_projdata_template.

Kind regards,

Gonçalo Cosme

2016-06-16 16:17 GMT+01:00 Pietrzyk, Uwe <u.pietrzyk at fz-juelich.de>:

>
> Hi Andrea,
>
> for reasonable reconstruction you need much more data, i.e. many more
> coincidences. The root-files may become quite large and need space.
>
> Kind regards,
>
> Uwe Pietrzyk
>
> /----------------------------------------------------------------------
> Prof. Dr. Uwe Pietrzyk
> Diplom-Physiker
> Institut für Neurowissenschaften und Medizin / INM-4
> Forschungszentrum Jülich GmbH
> 52425 Jülich
> Tel: +49-2461-61 4763
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> http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html
> &
> Bergische Universität Wuppertal
> Fakultät für Mathematik und Naturwissenschaften
> Büro:  D.08.01
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> 42097 Wuppertal
> Tel: +49-(0)202-439-3523
> Fax: +49-(0)202-439-2811
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> <Uwe.Pietrzyk at physik.uni-wuppertal.de>
> http://www.medizinphysik.uni-wuppertal.de
> ----------------------------------------------------------------------/
>
> On 16 Jun 2016, at 14:51, Andrea Colantuono S221003 <
> andrea.colantuono at studenti.polito.it> wrote:
>
> okey, I will try this AMIDE tool. Now I used the line list_image_info for
> retrieving information about my image, but, as I supposed, image min, image
> max and image sum are zero. Now I have to understand if the problem is in
> GATE or in STIR. Can you check if my steps in STIR are all right? So, after
> I had the root file from GATE, I used the code Bill_Gate_v1.0.C to take the
> sinogram. Then, I reconstructed the image in format .v with FBP2D, using
> the line ">FBP2D FBP2D.par" changing the file name inside the .par file.
> Maybe are the coincidences too few? they are 1447.
>
> Il 2016-06-15 17:43 Pietrzyk, Uwe ha scritto:
>
> Hi Andrea,
>
> as long as you keep the structure of your system the same
> and have introduced the appropriate parameters into the
> conversion / sorting tool, the structure of the file remains the
> same as does the file size.
> I am not sure, but I remember that you should be able to
> visualise the "sinograms” with a tool like “amide”. Since the
> concersion is for producing input to STIR you may check
> the respective users guide.
> Maybe this is helpful for you.
> Kind regards,
> U. Pietrzyk
> /----------------------------------------------------------------------
> Prof. Dr. Uwe Pietrzyk
> Diplom-Physiker
> Institut für Neurowissenschaften und Medizin / INM-4
> Forschungszentrum Jülich GmbH
> 52425 Jülich
> Tel: +49-2461-61 4763
> Fax: +49-2461-61 2820
> Mobil: +49-162-103-4871
> eMail: U.Pietrzyk at fz-juelich.de
> http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html
> &
> Bergische Universität Wuppertal
> Fakultät für Mathematik und Naturwissenschaften
> Büro:  D.08.01
> Gaußstr. 20
> 42097 Wuppertal
> Tel: +49-(0)202-439-3523
> Fax: +49-(0)202-439-2811
> eMail: Uwe.Pietrzyk at uni-wuppertal.de
> http://www.medizinphysik.uni-wuppertal.de [1]
>
> ----------------------------------------------------------------------/
> On 15 Jun 2016, at 16:38, Andrea Colantuono S221003
> <andrea.colantuono at studenti.polito.it> wrote:
>
> thank you for the answer!
> I tried with that code but I don't understand if the output is
> right. Indeed, the dimension of the file in output (107.3 MB) is the
> same for evrey input. So, for me this is wierd and I am afraid the
> output is always empty. Moreover, threee warnings occur, but I don't
> know if this is for them.
> The warning are:
> "Input file name is outputDerenzo*.root
> Michelogram file name is = Mich_sinog.s
> Projection file name is = Proj_sinog.s
> Warning in <TClass::TClass>: no dictionary for class TH1 is
> available
> Warning in <TClass::TClass>: no dictionary for class TAxis is
> available
> Warning in <TClass::TClass>: no dictionary for class TH1D is
> available
> Total Number of Coincidence Events:= 1447 "
> regards,
> Andrea
> Il 2016-06-14 18:27 Pietrzyk, Uwe ha scritto:
> Hi Andrea,
> on the GATE-WebPage
> http://www.opengatecollaboration.org/STIR
> you can find a link to source code for reading
> ROOT file and convert it for STIR.
> Kind regards and best wishes,
> Uwe Pietrzyk
>
> /----------------------------------------------------------------------
>
> Prof. Dr. Uwe Pietrzyk
> Diplom-Physiker
> Institut für Neurowissenschaften und Medizin / INM-4
> Forschungszentrum Jülich GmbH
> 52425 Jülich
> Tel: +49-2461-61 4763
> Fax: +49-2461-61 2820
> Mobil: +49-162-103-4871
> eMail: U.Pietrzyk at fz-juelich.de
> http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html
> &
> Bergische Universität Wuppertal
> Fakultät für Mathematik und Naturwissenschaften
> Büro:  D.08.01
> Gaußstr. 20
> 42097 Wuppertal
> Tel: +49-(0)202-439-3523
> Fax: +49-(0)202-439-2811
> eMail: Uwe.Pietrzyk at uni-wuppertal.de
> http://www.medizinphysik.uni-wuppertal.de [1]
>
> ----------------------------------------------------------------------/
>
> On 13 Jun 2016, at 10:19, Andrea Colantuono S221003
> <andrea.colantuono at studenti.polito.it> wrote:
> Hi everybody!
> I am working on a cylindrical PET and I have to evaluate the impact
> of the positron range on the quality of the images. I have some
> issues about retrieve an image from the coincidences of my system. I
> installed STIR, because I know GATE can not make an image, but how
> can I use my root or ASCII coincidences file on STIR?
> I installed also the packege GATE_PET_2_STIR but the root file is
> not recognized. Do you have alternatives?
> thank you,
> regards,
> Andrea
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