UCL / STIR-GATE-Connection

Example files on how to run STIR on GATE data
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Proposal for a general corrections script to compute all corrections for reconstruction #70

Closed robbietuk closed 3 years ago

robbietuk commented 3 years ago

There should be a script to call each of the correction estimations scripts after a GATE simulation and unlisting into STIR sinograms. The following are comments on each of the correction computation scripts that should or should not be included in a general corrections computation script.

Randoms:

INCLUDE in general corrections script https://github.com/UCL/STIR-GATE-Connection/blob/master/VoxelisedSimulation/SubScripts/EstimateRandomsFromDelayed.sh

Attenuation Coefficent Factors

INCLUDE in general corrections script

Normalisation:

DO NOT INCLUDE in general corrections script https://github.com/UCL/STIR-GATE-Connection/blob/master/VoxelisedSimulation/SubScripts/EstimateGATESTIRNorm.sh This is a hard script to include in the propsed idea as it should only be run once per scanner and is really GATE "scan" indepenant. It should be assumed this has been precomputed.

Scatter correction:

INCLUDE in general corrections script https://github.com/UCL/STIR-GATE-Connection/blob/master/VoxelisedSimulation/SubScripts/EstimateScatter.sh

Multiplicative Factors:

INCLUDE in general corrections script

robbietuk commented 3 years ago

I took a harder look at what is involved here. It is easier to repurpose EstimateScatter.sh to be ComputeCorrections.sh because only the Random estimation needs to be included (delayed sinogram as a parameter). Furthermore, seperating the computation of Attenuation Coefficent Factors from the scatter estimation is hard due to the need to export the variables, which may include an attenuation map that may be flipped in z.

I propose that

robbietuk commented 3 years ago

Closed via #71