Comments (3)
I'm confused by this. I didn't think STIR was able to read GATE interfile headers, but you seem to imply it does. Nevertheless, its interpretation of the location is very wrong.
I don't know what GATE does for the output (does it centre it or do you specify where the output has to be in GATE coordinates)? Is it guaranteed to be aligned with the GATE_Atten_input
? (only then would the work-around work, but I wouldn't recommend it anyway, as really stir_math
should have complained very loudly about adding images with different location, please create a STIR issue on that...).
By the way, can't we ask GATE to write something else then Interfile, even if it's only as an option or for checking?
from stir-gate-connection.
I'm confused by this. I didn't think STIR was able to read GATE interfile headers, but you seem to imply it does. Nevertheless, its interpretation of the location is very wrong.
STIR can read the GATE interfile headers with ITK installed, hence that whole palaver (UCL/STIR#654 and UCL/STIR#531).
I don't know what GATE does for the output (does it centre it or do you specify where the output has to be in GATE coordinates)?
The outputs are the sourcemaps and the mu-maps. The mu-maps are the attenuation map used by GATE in the simulation. There is no additional specification the the output position in GATE coordinates than
This is unrelated to
STIR-GATE-Connection/VoxelisedSimulation/RunGATE.sh
Lines 39 to 58 in f3c5f8f
I forced these values to be 0 and the resulting output is the same. Outputing these images as
.mhd
(the interfile alternative) gives the same non-zero origin that is expected with list_image_info
. Assume ITK and STIR are reading these files correctly to get the origin, meaning it is a GATE issue?
Is it guaranteed to be aligned with the GATE_Atten_input? (only then would the work-around work, but I wouldn't recommend it anyway, as really stir_math should have complained very loudly about adding images with different location, please create a STIR issue on that...).
There is an issue, I forgot to link it in the original post UCL/STIR#494 . The work around does allign the GATE output with GATE_Atten_input
but I guess that is by exploting a bug. Probably shouldn't incorporate bugs into features 😄.
from stir-gate-connection.
I'm too confused about this and have no time anyway (sorry), but I doubt ITK reads interfile. https://itk.org/Wiki/ITK/File_Formats If it does, it certainly won't return correct origin etc as Interfile doesn't define this.
would be worth posting the mhd header that it outputs. if it doesn't depend on the position etc (while the image remains the same), it would certainly be a GATE bug
from stir-gate-connection.
Related Issues (20)
- EstimateSTIRGATENorm mistakenly adds 1s to the normalisation sinogram
- RandomsEstimate problems
- ComputePoissonDataCorrections script requires flip in z of attenuation map from GATE HOT 2
- Computation of the multiplicative factors
- Proposal for a general corrections script to compute all corrections for reconstruction HOT 2
- ComputePoissonDataCorrections will fail if not called from `VoxelisedSimulation` directory HOT 1
- Scripts are depenant on running from SGC VoxelisedSimulation directory HOT 5
- source this_SGC.sh from a different directory issue
- Example/Debugging unlisting scripts for demonstrating the exclusion of different types of events
- Limit unlisting to a particular number of events.
- Combining many ROOT files using `hadd` can exeed the (default) 100GB limit HOT 1
- Something wrong with the script ExampleSTIR-GATE.sh HOT 12
- Example GATE geometries may not be compatable with STIR 5.0.1 due to rotation/offset changes
- about norm factors of mMR HOT 2
- Example mMR geometry may be out of date?
- STIR ray tracing parameters restrict to cylindrical fov HOT 1
- Add a Citation.cff file
- the unit of reconstructed image HOT 3
- Mistakes in `ComputePoissonDataCorrections.sh` documentation HOT 1
- D690 Geometry Inconsistency HOT 1
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