[Rtk-users] Half Fan dataset

Thu Jan 23 15:50:37 EST 2020

Thanks for the report, I'll try to fix this issue (I have noted it on
github here <https://github.com/SimonRit/RTK/issues/290>). And thanks in
advance for the code!
Simon

On Wed, Jan 22, 2020 at 4:11 PM <gabriele.belotti.bergamo at gmail.com> wrote:

> Thanks Simon!
> My best guess is that the artefact is strongly related to the “theta”
> dependant weighting in DDF weighting.
> An interesting fact is that displacing the isocenter projection on the
> detector less and less, the artefact tends to disappear (see the attached
> figures as reference).
> On a smaller note, there is some inconsistency in the inferior/superior
> image corner calculation between positive and negative isocenter projection
> displacements of the same entity (say + or - 140), which in turn affect
> “theta” calculation.
>
> Thanks a lot for the literature reference, I’ll gladly study it.
>
> Regarding the code, I’ll transfer the changes to a clone of the current
> release and share it as soon as possible and we’ll look into optimizing it.
>
> Best wishes,
> Gabriele
>
>
>
> *Da:* Simon Rit <simon.rit at creatis.insa-lyon.fr>
> *Inviato:* mercoledì 22 gennaio 2020 11.46
> *A:* gabriele.belotti.bergamo at gmail.com
> *Cc:* rtk-users <rtk-users at public.kitware.com>
> *Oggetto:* Re: [Rtk-users] Half Fan dataset
>
>
>
> Congratulations! Glad to here it worked out. From your attachment, I have
> the feeling that something is wrong since there is an artefact at the
> center. Do you know what that could be?
>
> Maybe you can read the Knaup's paper in the 13th fully 3D meeting
> proceedings (available here
> <http://www.fully3d.org/uploadfile/2017/0112/20170112020253842.pdf>): A
> General Projection Weight for Feldkamp–Type Cone–Beam Image Reconstruction
> from Arbitrary CT Scan Trajectories.
>
> Defining optimal weights is difficult because you have two competing
> criteria: best use of the dose to minimize dose and a smooth weighting (as
> described by Parker).
>
> It might be worth being included but the best would be to do it with
> minimal code copy. You can share the current code if you want us to have a
> look.
>
> Cheers,
>
> Simon
>
>
>
> On Tue, Jan 21, 2020 at 5:11 PM <gabriele.belotti.bergamo at gmail.com>
> wrote:
>
> Dear Simon and Rtk users,
>
> I picked this topic up again after some time.
> I was able to properly weight my projections stack in order to accommodate
> for two different detector displacement in a dual-rotation configuration (
> I
> modified both CPU and GPU implementations of DisplacedDetectorImageFilter )
> under the same geometry.xml file.
> Following, it was possible to directly use ParkerShortScanFilter to
> compensate for the short scan conditions of two successive incomplete
> rotations.
>
> The resulting reconstruction can be superimposed on a single-rotation
> Half-Fan reconstruction with no difference except for a cylindrical
> artefact
> which is centred and extends along the Y axis of the reconstructed volume
> (figure attached).
> I suspect the weighting I’m using (which is a transposition of the one
> currently implemented) is not ideal for dual-rotation reconstruction
> whenever the detector is not fully displaced.
> However I struggle to find literature on this topic! If you have any
> suggestion I would be interested in investigating further on this topic, as
> limited Range of Motion is a key factor in my project.
>
>
> Of course if you feel this feature could be merged into Rtk tree I would be
> glad to open a pull request on git and dive more into details.
>
> Best regards,
> Gabriele
>
>
>
> Da: Simon Rit <simon.rit at creatis.insa-lyon.fr>
> Inviato: giovedì 31 ottobre 2019 00.22
> A: gabriele.belotti.bergamo at gmail.com
> Cc: rtk-users <rtk-users at public.kitware.com>
> Oggetto: Re: [Rtk-users] Half Fan dataset
>
>
>
> Hi,
>
> with --proj_iso_x, you only move the detector, not the source. If you also
> want to move the source, --source_x needs to be used. Hopefully the drawing
> on the  <http://www.openrtk.org/Doxygen/DocGeo3D.html> doc page helps to
> understand this. So since you don't have any source offset in your geometry
> file, you are in the first line and last line situation of your drawing
> image.
>
> Now, on the last line, what you're actually doing is imaging with the same
> source arc but actually shifting the detector. This is equivalent to a 180°
> source rotation with a larger rotation. You only need a weighting function
> to account for the redundancy but this is not going to be the same one as
> the one implemented because it needs to be on different side of the
> detector/projections (as on the first line of your projections). In any
> case, 180° is not enough, you need at least 180+fan angle and to combine
> this with a short scan Parker weighting.
>
> Simon
>
>
>
> On Wed, Oct 30, 2019 at 6:00 PM <
> <mailto:gabriele.belotti.bergamo at gmail.com>
> gabriele.belotti.bergamo at gmail.com> wrote:
>
> Hi Simon,
>
> Sorry for the late reply.
> I drew a sketch in two part to explain my doubts.
> First I drew 3 configurations for the geometry, representing my doubt
> towards what exactly is achieved by Isocenter Projection translation in the
> RTK geometry; i.e. does it result in a source translation or in a cone beam
> rotation (in XZ plane) to accommodate for the panel displacement? (I’m
> expecting the latter but I couldn’t properly check).
>
> The last two sketches represent the same concept with two of the possible
> geometries(of course I’d prefer the latter):
> The idea is to first rotate with the detector displaced on one side by 180°
> and then displace in the opposite direction and rotate of additional 180°
> (always clockwise rotation).
> Any comment or suggestion would be highly appreciated and eventually I will
> try to impose weights according to improve the reconstruction.
>
> PS: zoom in on the sketch, the resolution should be sufficient to read
> PPS: I’m also attaching a screenshot of a reconstruction achieved with the
> exotic geometry :^] and the xml I generated for it (beware that my detector
> is 298 mm wide and the displacement is of +/-120 mm)
>
> Best regards,
> Gabriele
>
>
>
> Da: Simon Rit < <mailto:simon.rit at creatis.insa-lyon.fr>
> simon.rit at creatis.insa-lyon.fr>
> Inviato: martedì 29 ottobre 2019 18.21
> A:  <mailto:gabriele.belotti.bergamo at gmail.com>
> gabriele.belotti.bergamo at gmail.com
> Cc: rtk-users < <mailto:rtk-users at public.kitware.com>
> rtk-users at public.kitware.com>
> Oggetto: Re: [Rtk-users] Half Fan dataset
>
>
>
> Hi Gabriele,
>
> Great that you moved forward.
>
> It's quite sure that the current implementation does not handle this new
> exotic geometry. So my suggestion would be to implement your own weights
> (e.g., using the python package).
>
> It's not clear to me what you're trying to achieve here but it seems to me
> that only the central part seen by all source positions has enough data
> (point of space which see at least 180° of source positions) to be
> reconstructible. Maybe you should draw your two cones at 90° and -90° to be
> sure of what you're doing? Don't hesitate to share such a drawing on which
> we could comment.
>
> Best regards,
>
> Simon
>
>
>
> On Tue, Oct 29, 2019 at 4:10 PM <
> <mailto:gabriele.belotti.bergamo at gmail.com>
> gabriele.belotti.bergamo at gmail.com> wrote:
>
> Dear Simon and RTK users,
>
> I’ve been experimenting on the generation of Half Fan CBCT images
> successfully from reprojections of CTs starting from Simon’s suggestions.
> So far I was able to reconstruct images by displacing the detector in the X
> direction (+ or -) and completing a single rotation. Results were good and
> the FOV was of course larger than the one obtained from using the same
> virtual detector without displacement.
>
> I’ve taken the simulation a step further and I’m currently creating a
> geometry which is similar to the combination of “rtksimulatedgeometry -n
> 180
> --proj_iso_x <displacement> -o g_1” and “rtksimulatedgeometry -n 180
> --proj_iso_x <(-1)*displacement> -o g_2 -f 180” (I’m rotating first between
> 0° and 180° while displacing by half detector size on +X and then 180° and
> 360° while displacing by half detector size on -X).
> With this single .xml I’m reprojecting a CT into a single .mha using
> rtkforwardprojections and then I’m using the output as input for rtkfdk.
>
> My results however suffer from a centered artifact, of semi-cylindrical
> shape, in my opinion caused by the superimposition of rays from the two
> beams around the isocenter.
> This is further supported by the fact that the more I displace the detector
> the smaller the artefact becomes (of course I can’t displace more than 50%
> of detector size).
> I guess a possible solution would be to have a perfect half-cone x-ray beam
> by shaping it using a collimator, but I’m not sure how to proceed on this
> in
> the simulated environment.
> Have you got any suggestions or observation on how to achieve a
> reconstruction based on this? (two rotations/acquistion given two opposite
> detector displacements)
>
> Thanks in advance,
> Gabriele
>
>
>
>
>
>
>
> Da: Simon Rit < <mailto:simon.rit at creatis.insa-lyon.fr>
> simon.rit at creatis.insa-lyon.fr>
> Inviato: venerdì 11 ottobre 2019 13.10
> A:  <mailto:gabriele.belotti.bergamo at gmail.com>
> gabriele.belotti.bergamo at gmail.com
> Cc: rtk-users < <mailto:rtk-users at public.kitware.com>
> rtk-users at public.kitware.com>
> Oggetto: Re: [Rtk-users] Half Fan dataset
>
>
>
> Hi,
>
> It's easy to generate, you need to offset your detector, either via the RTK
> geometry or by setting the first coordinate of the origin of your
> projection
> to something which makes the projection uncentered. For example, in the
> geometry :
>
> rtksimulatedgeometry -n 180 --proj_iso_x 100 -o g
>
> rtkprojectshepploganphantom -g g -o proj.mha
>
> rtkfdk -p . -g g -r proj.mha -o fdk.mha
>
> You can simulate from a CT image by following
> <http://wiki.openrtk.org/index.php/RTK/Scripts/ForwardProjection> this
> example.
>
> Simon
>
>
>
> On Fri, Oct 11, 2019 at 9:58 AM <
> <mailto:gabriele.belotti.bergamo at gmail.com>
> gabriele.belotti.bergamo at gmail.com> wrote:
>
> Dear RTK users and developers,
>
> I’m currently experimenting with FDK reconstruction and I’m struggling to
> find a Half-Fan projection dataset to fiddle around.. Do you know where I
> can find one? I’ve taken into consideration generating a set of DRRs from
> an
> existing phantom. Any help or advice you can give me would be greatly
> appreciated, thanks!
>
> Gabriele Belotti
>
>
>
>
>
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