[Rtk-users] Unable to Forward Project CT Volume With Correct Orientation

[Brani Rusanov]

Hi all,

I am attempting to forward project a CT volume (previously registered to a CBCT volume) using the geometry of a CBCT volume to generate raw projections. I also have access to the raw CBCT projections. I have used rktprojections to stack the raw CBCT projections and generate .mhd/raw files.

Next, I used rtkvariabprobeamgeometry on the scan.xml file that came with the raw CBCT projections to generate a RTK compatible geometry.xml file.

Next, I have stacked the registered CT dicoms into a .mhd/raw format. The trouble I'm having is creating the projections using rtkforwardprojections. Specifically, I cannot find the correct transformmatrix in the CT header to tell rtkforwardprojetions the conversion from DICOM to IEC geometry. The output projections do not look like the raw projections I have from the CBCT. This may be a stupid question, but I cannot figure it out. From my own estimation, the transformation should be 1 0 0 0 0 -1 0 1 0 based on this diagram (https://www.semanticscholar.org/paper/nuclear-science-and-technology-Radiation-Quantities-Brink-McNitt-Gray/1ec27be3617dfc4e03bba86dcd92db8f3323de21/figure/3
[https://ai2-s2-public.s3.amazonaws.com/figures/2017-08-08/1ec27be3617dfc4e03bba86dcd92db8f3323de21/14-Figure1.4-1.png]<https://www.semanticscholar.org/paper/nuclear-science-and-technology-Radiation-Quantities-Brink-McNitt-Gray/1ec27be3617dfc4e03bba86dcd92db8f3323de21/figure/3>
Figure 1.4 from nuclear science and technology Radiation Quantities and Units , Dose to the Patients , and Image Quality in Computed Tomography ( CT ) ( RAD UNITS ) Author : | Semantic Scholar<https://www.semanticscholar.org/paper/nuclear-science-and-technology-Radiation-Quantities-Brink-McNitt-Gray/1ec27be3617dfc4e03bba86dcd92db8f3323de21/figure/3>
Figure 1.4 (left) The IEC patient coordinate system (the patient is lying in supine position); (right) transformation of coordinates between the IEC and DICOM coordinate systems [IEC, 2000] (cited in ICRU Report 71, 2004, page 35) - "nuclear science and technology Radiation Quantities and Units , Dose to the Patients , and Image Quality in Computed Tomography ( CT ) ( RAD UNITS ) Author :"
www.semanticscholar.org
)

My questions are: Is this the correct transformmatrix to apply?
Do I need to also change the offset values in order to get the correct projections?
Could this have something to do with the fact that I am using variant data?

The .mhd for the registered CT is:
ObjectType = Image
NDims = 3
BinaryData = True
BinaryDataByteOrderMSB = False
CompressedData = False
TransformMatrix = 1 0 0 0 0 -1 0 1 0
Offset = -131.03451538085938 -131.03451538085938 -91.809638977050781
CenterOfRotation = 0 0 0
AnatomicalOrientation = RAI
ElementSpacing = 0.51285523409720002 0.51285523409720002 1.9958648681640625
DimSize = 512 512 93
ElementType = MET_DOUBLE
ElementDataFile = CIRS_6A.raw

Similarly, the .mhd for the raw CBCT projections is:
ObjectType = Image
NDims = 3
BinaryData = True
BinaryDataByteOrderMSB = False
CompressedData = False
TransformMatrix = 1 0 0 0 1 0 0 0 1
Offset = -198.46200000000002 -148.798 0
CenterOfRotation = 0 0 0
AnatomicalOrientation = RAI
ElementSpacing = 0.38800000000000001 0.38800000000000001 1
DimSize = 1024 768 501
ElementType = MET_FLOAT
ElementDataFile = CIRS_6A_SCGH_P.raw

Thank you kindly for your response,
Brani

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