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

Tue May 26 04:51:49 EDT 2020

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:     agravgaard at protonmail.com

Cell:      +45 3165 8140

On Tue, 26 May 2020 at 05:08, Brani Rusanov <Brani_Rusanov at hotmail.com>
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
>
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