[Rtk-users] FirstReconstruction example

Tue Oct 16 04:55:04 EDT 2012

Hi,

thanks!! Yep, I would be very interested in the script since I would like to try first whether my geometry is generally a no go for the FDK-based approaches in RTK (which I cannot exclude at the moment), before shaping the code and implementing C++-based converters.

Lars

-------- Original-Nachricht --------
> Datum: Tue, 16 Oct 2012 10:23:17 +0200
> Von: Simon Rit <simon.rit at creatis.insa-lyon.fr>
> An: Lars Friedrich Lars <lars-friedrich at gmx.net>
> CC: rtk-users at openrtk.org
> Betreff: Re: [Rtk-users] FirstReconstruction example

> I agree, geometry is irritating! I'm sorry my comments were part of
> this irritation... It seemed obvious to me that the origin and the
> direction in itk::Image has to be accounted for but I'll add a comment
> in the header to make it clearer. Bear in mind that this on-going work
> so feel free to suggest improvements and clarifications.
> 
> Regarding geometry conversion, we had done a work with my colleagues
> from the Université Catholique de Louvain to convert their geometry
> parameterization to RTK parameterization using Maxima. That allowed us
> to spare some hours spent on deriving the correct formulas... Would
> you be interested in the script file?
> 
> Simon
> 
> On Tue, Oct 16, 2012 at 10:03 AM, Lars Friedrich Lars
> <lars-friedrich at gmx.net> wrote:
> > Hi Simon,
> >
> > thanks for your reply!
> >
> > I read the geometry-doc and played around with
> rtk::ThreeDCircularProjectionGeometry before I was writing the question in the last mail.
> > Basically, the first sentence in section 6 of the doc
> > "This class is meant to define a set of 2D projection images, acquired
> with a at panel along a circular trajectory, around a 3D tomography."
> > along with another sentence in this section
> > "9 parameters are used per projection to define the position of the
> source and the detector relatively to the fixed coordinate system."
> > irritated me a bit. I thought that the 3DCircGeom's task is, in addition
> to defining the source position, to define the position and orientation of
> the 2D projection images, and the 3DCircGeom is defined in the IEC WCS
> (relates to it). I did not expect essential projection image metrics except
> dimension (pixel size) and spacing (because image size in physical units is
> not part of 3DCircGeom) having any influence on the position and orientation
> of it, since this is already defined with the 3DCircGeom object.
> >
> > My issue at the moment is simply that I have source position, detector
> position and detector row/column vectors defined in IEC WCS for each
> projection, and have to convert it somehow into your projection geometry format +
> (and that's news for me) adjust the image origin of the projection stack.
> Unfortunately, my geometry is not really a standard circular one (as in case
> of XVI, OBI etc.). Will try to derive an adaptor for conversion ...
> >
> > Thanks so far!
> >
> > LF
> >
> > -------- Original-Nachricht --------
> >> Datum: Mon, 15 Oct 2012 22:17:59 +0200
> >> Von: Simon Rit <simon.rit at creatis.insa-lyon.fr>
> >> An: Lars Friedrich Lars <lars-friedrich at gmx.net>
> >> CC: rtk-users at openrtk.org
> >> Betreff: Re: [Rtk-users] FirstReconstruction example
> >
> >> Hi Lars,
> >> The geometry is described in the document geometry.tex, I have added
> >> links at the end of the user's wiki page
> >> http://wiki.openrtk.org/index.php/RTK/Users. Briefly, the point with
> >> coordinates 0,0,0 of your volume is the isocenter, the point with
> >> coordinate 0,0 in projection images is the intersection of your flat
> >> panel with the line going through the x-ray source and the isocenter.
> >> The image origin is defined by ITK as the center of the pixel with
> >> index 0 in memory (first pixel in memory).
> >> I hope this helps,
> >> Simon
> >>
> >> On Mon, Oct 15, 2012 at 7:53 PM, Lars Friedrich Lars
> >> <lars-friedrich at gmx.net> wrote:
> >> > Hello,
> >> >
> >> > I have questions concerning the FirstReconstruction example:
> >> > Using the rtk::RayEllipsoidIntersectionImageFilter and
> >> rtk::ConstantImageSource artificial projections of an ellipsoid are
> generated which are
> >> packed in the form of an image stack. The geometry of the projections
> is
> >> described by an rtk::ThreeDCircularProjectionGeometry object. Moreover,
> the
> >> images' metrics are described by the image stack itself (spacing, size
> and
> >> ORIGIN).
> >> >
> >> > How should I interpret the origin? As far as I could find out by
> minor
> >> modifications of the example, the origin of the projeciton image stack
> plays
> >> a role (if I change it to 0,0,0, and retain constantImageSource2's
> origin
> >> at -127,-127,-127, just half of the ellipsoid is reconstructed). Why
> does
> >> the origin of the image stack matter? Isn't the origin of a single
> >> projection fully defined by the corresponding entry in the
> >> rtk::ThreeDCircularProjectionGeometry object (I thought the
> projOffsetX,projOffsetY args define the
> >> offset from the detector central axis crossing point)? Am I right that
> the
> >> effective origin of a single projection image emerges basically from
> the
> >> detector (x/y of origin of image stack) and from consecutive
> application of
> >> the projOffsetX,projOffsetY args? Otherwise, deviating detector
> positions,
> >> e.g. caused by gravity, wouldn't be simulatable.
> >> >
> >> > Morever, which point exactly does the image origin (x/y components)
> of
> >> the projection stack describe? Is it the outer corner of the projection
> or
> >> the center of the first voxel (as in DICOM). The size of a projection
> in the
> >> example is 256.0x256.0 units. However, the stack's origin is at
> >> -127.0,-127.0. If the origin should refer to the center of the first
> projection
> >> pixel, it should be essentially -127.5,-127.5, right?
> >> >
> >> > Sorry for the detailed questions, I just would like to understand how
> >> RTK is working.
> >> >
> >> > Thanks a lot!
> >> >
> >> > LF
> >> > _______________________________________________
> >> > Rtk-users mailing list
> >> > Rtk-users at openrtk.org
> >> > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users