GATE output images shifted, does not allow for forward projection

[robbietuk]

Example: I am trying to estimate scatter. I am using an attenuation map output by a GATE (.hdr) but I am running into the following error.

ERROR: ProjMatrixByBinUsingRayTracing sadly doesn't support shifted x/y origin yet
terminate called after throwing an instance of 'std::string'

The image has the following properties:

AttenuationImage=Phantom1-MuMap.hdr

list_image_info $AttenuationImage

WARNING: Unable to determine patient position. Internally this will generally be handled by assuming HFS

Origin in mm {z,y,x}    :{-150.42, 210, 210}
Voxel-size in mm {z,y,x}:{3.27, 3, 3}
Min_indices {z,y,x}     :{0, -70, -70}
Max_indices {z,y,x}     :{46, 70, 70}
Number of voxels {z,y,x}:{47, 141, 141}
Physical coordinate of first index in mm {z,y,x} :{-150.42, 0, 0}
Physical coordinate of last index in mm {z,y,x}  :{0, 420, 420}
Physical coordinate of first edge in mm {z,y,x} :{-152.055, -1.5, -1.5}
Physical coordinate of last edge in mm {z,y,x}  :{1.63499, 421.5, 421.5}
Image min: 0.00011125
Image max: 0.130242
Image sum: 29608.8

---

I have a temporary work around to fix this translation

## Create zeros image with same origin as GATE input
stir_math --times-scalar 0.0 --including-first zeros.hv $GATE_Atten_input
## Add the GATE output mu-map to the template
stir_math --add STIR_AttenuationImage zeros.hv $AttenuationImage

It is correct to use the GATE output as the mu-map as $GATE_Atten_input in the simulation setup, see VoxelisedSimulation/GATESubMacros/AttenuationConv.dat and #44 issue.

[KrisThielemans]

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?

[robbietuk]

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

STIR-GATE-Connection/VoxelisedSimulation/GATESubMacros/PhantomActivity.mac

Line 20 in f3c5f8f

/gate/source/SourcePhantom/setPosition {SourcePositionX} {SourcePositionY} {SourcePositionZ} mm

and

STIR-GATE-Connection/VoxelisedSimulation/GATESubMacros/PhantomAttenuation.mac

Line 26 in f3c5f8f

/gate/VoxPhantom/placement/setTranslation {AttenuationTranslationX} {AttenuationTranslationY} {AttenuationTranslationZ} mm

This is unrelated to

STIR-GATE-Connection/VoxelisedSimulation/RunGATE.sh

Lines 39 to 58 in f3c5f8f

	## Get the activity source position in x,y,z
	SourcePositions=$( SubScripts/GetSourcePosition.sh $ActivityFilename 2>/dev/null )
	SourcePositionX=`echo ${SourcePositions} |awk '{print $1}'`
	SourcePositionY=`echo ${SourcePositions} |awk '{print $2}'`
	SourcePositionZ=`echo ${SourcePositions} |awk '{print $3}'`
	if [ $? -ne 0 ]; then
	echo "Error in SubScripts/GetSourcePosition.sh"
	exit 1
	fi
	## Get the attenuation map translation in x,y,z
	AttenuationTranslations=$( SubScripts/GetAttenuationTranslation.sh $AttenuationFilename 2>/dev/null )
	AttenuationTranslationX=`echo ${AttenuationTranslations} |awk '{print $1}'`
	AttenuationTranslationY=`echo ${AttenuationTranslations} |awk '{print $2}'`
	AttenuationTranslationZ=`echo ${AttenuationTranslations} |awk '{print $3}'`
	if [ $? -ne 0 ]; then
	echo "Error in SubScripts/GetAttenuationTranslation.sh"
	exit 1
	fi

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 😄.

[KrisThielemans]

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