[Castor-users] Slow simulation

[tmerlin]

Hi,

By default, for list-mode data, the sensitivity image is generated by 
projecting all available lines of response. This process is indeed 
dependent on the number of detectors. The PET list-mode benchmark uses a 
system with ~20k detectors and a normalization datafile to generate the 
sensitivity image. In this case, the processing time depends on the 
number of data channels in the normalization datafile, which also 
depends on the number of detectors, so it still takes some time to process.

Several remarks:

- Make sure that all parallel computing were enabled when you compiled 
the code:  CASTOR_OMP and CASTOR_MPI (if you use a cluster of machine 
compatible with MPI) variables must be set to 1 .
   When using castor-recon, set -th 0 to enable multithreading.

- If you know the minimum transaxial angle between two detectors 
required to form a line a response, you could reduce the computing time 
by setting the following variable in the geometry file of your scanner 
(*.geom file in //config/scanner/):
min angle difference        : x
(x being the angle in degree).

This should moderately reduce the computing time as by default, the code 
blindly projects all lines of response without first checking if they 
will cross the FOV or not. With this option, the lines of response drawn 
by detectors whose transaxial angle is below this value will be ignored.

- It should be possible (though not necessarily trivial) to analytically 
compute a sensitivity image for most systems. You could bypass the 
sensitivity image computation by providing the /castor-recon/ executable 
with such image in interfile format with the option /-sens 
path/to/analytic/sens/image.hdr/
Note that this image should take account of attenuation in the object as 
well as calibration factor.

Hope this helps!
Thibaut


On 26/08/2019 21:20, Sveta wrote:
> Hi,
> We are currently using castor to reconstruct images from GATE Simulation, the process of running castor-GATEMacToGeom and castor-GATERootToCastor is going quite well. However when running castor-recon the generation of the sensitivity image is extremely slow. A simplified version of our problem (~28672 elements) takes 16 minutes to process through this step. We would like to full simulations with nearly 10 times as many elements.
>
> Our question is, is the sensitivity image generation time purely driven by the number of elements? Is there any way to decrease the setup time, available benchmarks were done with it nearly instantaneous.
>
> Any suggestions for us?
> Thank you,
>
>
> Sveta and Peter
> _______________________________________________
> Castor-users mailing list
> Castor-users at lists.castor-project.org
> http://lists.castor-project.org/listinfo/castor-users

-- 
Thibaut MERLIN -- PhD

Docteur en Imagerie Médicale au Laboratoire de Traitement de l'Information Medicale (LaTIM - INSERM UMR 1101)
Institut Brestois de recherche en Bio-Santé (IBRBS)
12 Avenue Foch, 29200 Brest, FRANCE
Tel: 06.75.12.24.90

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