What do you more precisely mean by "The output projections do not look like the raw projections I have from the CBCT" Are they flipped, are they all black, are they much brighter or darker, or do they not align?
If alignment: Consider if you need to sort the projections by gantry angle before visual comparison, the Xim reader just reads sequentially by the given regex, so a ProBeam CB (with two imagers) may interleave projections from different angles. This is unlikely to be a problem for a gantry with only one imager. If flipped or all black: Your transformation matrix looks correct to me, so I think the problem may be elsewhere. It's always a mess to figure out. Be careful, that when you flip axes manually like that that you also remember to flip offsets (origin), spacing, etc. accordingly. In particular orientation (directions), I can see it says RAI for "AnatomicalOrientation", but I think you'll need the "Orientation" tag with direction cosines if you want to specify the directions manually. https://itk.org/Wiki/ITK/MetaIO/Documentation#MetaObject_Tags All this being said, I would suggest to instead use ITK's readers and the built-in filters for image transformation if that's even necessary, to avoid the hell of trying to keep track of all these values manually. If intensity is darker or brighter: Check if you have preprocessed the CB projections correctly for bow-tie filter and the like. I hope this gives a hint to where the problem might be. /Andreas __________________________________ Andreas Gravgaard Andersen Danish Center for Particle Therapy, Aarhus University Hospital Palle Juul-Jensens Blvd. 99, 8200, Aarhus Mail: [email protected] Cell: +45 3165 8140 On Tue, 26 May 2020 at 05:08, Brani Rusanov <[email protected]> wrote: > 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://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 > > _______________________________________________ > Rtk-users mailing list > [email protected] > https://public.kitware.com/mailman/listinfo/rtk-users >
_______________________________________________ Rtk-users mailing list [email protected] https://public.kitware.com/mailman/listinfo/rtk-users
