[Gate-users] How do you perform Image Reconstruction for a SPECT based Imaging procedure?

[tmerlin]

Dear Kurt, and all,


Regarding CASToR, as Panagiotis and Konstantinos mentioned, the software 
contains several tools to convert a GATE output root file to a datafile 
format, which can then be used by CASToR for reconstruction. They are 
described in the section 8.2 of the documentation 
(http://www.castor-project.org/sites/default/files/2017-10/CASToR_general_documentation.pdf)


For SPECT reconstruction, the conversion tool requires to divide the 
crystal surface in "virtual" pixels (assuming a pixel matrix was not 
already defined in the macros), by selecting a number of 
transaxial/axial pixels which the singles will be assigned to, depending 
on their detected position. It is done through the command-line options 
of the conversion tool.


Several information about the geometry of the gamma cameras will be read 
from the macros files of the simulation (i.e number of heads, crystal 
dimensions, number of projections, etc..). These tools have some 
limitations, such as they will not recover information about the 
collimator from the macro files (parallel collimator will be set by 
default). CASToR uses different models to mimic the effect of different 
collimators (parallel, cone-beam, fan-beam, mono or multi convergent, 
etc..). These models are described in the section 5.2 of the 
documentation. The model and their parameters must be set manually.


I can share with you some sample shell scripts to use these tools if you 
wish.


Best regards,

Thibaut





On 01/11/2017 14:11, Panagiotis Papadimitroulas wrote:
>
>
>
> Dear Kurt,
>
>
> As Konstantinos mentioned, there are several tools to apply 
> reconstruction on the SPECT simulated data.
>
> A first step is to extract the projections of your SPECT imaging 
> acquisition. There is one possibility to save them directly in 
> projection format through GATE, or to extract them from your root file.
>
> In our group we are extracting the projections from the root files in 
> order to do the reconstruction, using the QSPECT tool. If you want we 
> can share with you these .c scripts to create your own projections 
> from root.
>
> Also using the Castor software, I think you can apply directly the 
> reconstruction using as input the root file.
>
> Thus I would recommend you to run your simulations, saving your 
> output  in .root format.
>
>
> Kind regards,
> Panagiotis
>
>
>
> -- 
> Panagiotis Papadimitroulas
> Project Director, PhD
> BET Solutions
> 116 Alexandras Av.
> 11472 Athens
> Greece
>
> Tel: +30 2130290586
> Fax: +30 2130290587
> Web: www.betsolutions.gr
> e-mail: panpap at betsolutions.gr
>
> ------------------------------------------------------------------------
> *From:* Gate-users 
> <gate-users-bounces at lists.opengatecollaboration.org> on behalf of 
> Konstantinos P. Chatzipapas, MSc <konhat88 at yahoo.gr>
> *Sent:* Wednesday, November 1, 2017 2:40 PM
> *To:* Kurt V; gate-users at lists.opengatecollaboration.org
> *Subject:* [Gate-users] How do you perform Image Reconstruction for a 
> SPECT based Imaging procedure?
> Hello,
>
> For image reconstruction, as free softwares, I know a few. You can try 
> QSPECT 
> (http://www.bme.teiath.gr/ni/EnglishVersion/Downloads_files/Downloads.html), 
> CASToR (http://www.castor-project.org/) or STIR 
> (http://stir.sourceforge.net/)
>
> Regards,
> Konstantinos
> -----------------------------------------------------
>  Konstantinos Chatzipapas
>     Medical Physicist, MSc
> University of Patras
>
>  web page:Physics Magazine <http://www.physicsmag.com/>
>
>
> Στις 9:14 μ.μ. Δευτέρα, 30 Οκτωβρίου 2017, ο/η Kurt V 
> <kurtv1 at hotmail.com> έγραψε:
>
>
> I am new to image reconstruction using GATE, I was wondering if anyone 
> could provide me with details on how to best perform image 
> reconstruction using a SPECT based imaging procedure?
>
>   * What is the best way?
>   * Can this somehow be done with an ECAT7 workflow?
>   * Is it better to go from ASCII to another software?
>   * Interfile to another software?
>   * Is there another software efficient workflow that anyone knows of?
>
> If anyone has any words of wisdom for me, all advice would be greatly 
> appreciated.
> Thank you very much,
> Sincerely,
> Kurt W. Van Delinder
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-- 
Thibaut MERLIN -- PhD

Docteur en Imagerie Médicale au Laboratoire de Traitement de l'Information Medicale (LaTIM - INSERM UMR 1101)
Bâtiment 1
CHRU Morvan - 2, Av. Foch
29609 Brest CEDEX - FRANCE
Tel: 06.75.12.24.90

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