[Rtk-users] Reconstruction geometry

Tue Jun 4 14:15:27 CEST 2024

Hi,
The way I calculate the --neworigin depends on the spacing as it passes the
coordinates of the center of the first pixel which would change if you bin
the data. Maybe you can use the first parameter I gave you originally. Note
that you can keep the full resolution and bin the data with --binning 6,6
if you'd like, the origin is then automatically adjusted.
For iterative reconstruction, I use rtkconjugategradient by default with a
quadratic regularization of the gradient (parameter --gamma). But be aware
that such truncated data are difficult to reconstruct. BTW, you might want
to try the option --pad 1 to manage truncation in rtkfdk.
Good luck!
Simon

On Tue, Jun 4, 2024 at 12:41 PM Christian Riesch <christian.riesch at live.com>
wrote:

> Hello Simon,
>
> First of all, thank you for your efforts. The command line below indeed
> produces the best result I have seen using RTK so far.
> When going back to the full resolution images, is it correct to just set
> --newspacing=0.09, or do I need to modify something else too? It seems that
> this results in a much noisier reconstruction compared to the downscaled
> images.
>
> I also remember you mentioning iterative reconstruction. Do you have any
> pointers for that, besides using rtksart instead of rtkfdk?
>
> Best regards,
> Christian
>
> ------------------------------
> *Von:* Simon Rit <simon.rit at creatis.insa-lyon.fr>
> *Gesendet:* Montag, 3. Juni 2024 16:14
> *An:* Christian Riesch <christian.riesch at live.com>
> *Cc:* rtk-users at openrtk.org <rtk-users at openrtk.org>
> *Betreff:* Re: [Rtk-users] Reconstruction geometry
>
> Hi,
> FDK's formula is an integral over 360°. If there is an angular gap above
> --short (20° by default), rtkfdk will try to apply Parker short scan. If
> you disable Parker's weighting (with --short 360), then you'll get huge
> artifact because the two projections adjacents to the angular gap will get
> ~135° weights whereas the other projections get ~1° weight. I don't know
> what Astra does, it might simply apply a constant angular weights but
> rtkfdk is able to calculate non constant weights (which is required for,
> e.g. Elekta CBCT acquisitions).
> If you want to circumvent that, you can add 0-filled projections at the
> beginning and at the end of the acquisition. But rtk also guesses the flat
> field constant of your projections so you need to account for that too....
> So I got some results by adding a 7000 filled 000.tif and 092.tif
> projections and running
> rtksimulatedgeometry -o"geo.xml" -n93 -f-46 --sdd=482.53 --sid=75.46 --arc
> 92
> rtkfdk -p . -r '.*.tif' -o fdk.mha  --newspacing=0.594
> --neworigin=-151.767,-151.47,0  -g geo.xml --spacing 0.09 --dimension 512
> --hardware cuda --short 360 --i0 7000
> I can't say if the result is good, I don't know what I'm looking at and
> 90° is a really short scan. But you can maybe try if it's close to ASTRA's
> result.
> Cheers,
> Simon
>
> On Mon, Jun 3, 2024 at 11:16 AM Christian Riesch <
> christian.riesch at live.com> wrote:
>
> Hello Simon,
>
> I realize that a 90° scan only allows for a partial reconstruction of the
> volume. This approach seems to be quite common in industrial applications
> due to space and time constraints, but I have not found much information
> about it in the literature.
> The Astra toolbox's FDK implementation seems to cope with this quite well,
> at least in the center of the volume.
>
> The rescaled pixel size should be 6 * 0.099 mm = 0.594 mm.
>
> Best regards,
> Christian
> ------------------------------
> *Von:* Simon Rit <simon.rit at creatis.insa-lyon.fr>
> *Gesendet:* Sonntag, 2. Juni 2024 08:00
> *An:* Christian Riesch <christian.riesch at live.com>
> *Cc:* rtk-users at openrtk.org <rtk-users at openrtk.org>
> *Betreff:* Re: [Rtk-users] Reconstruction geometry
>
> Hi Christian,
> Thanks for the share. It was not clear to me that you had a 90° scan
> sorry. FDK is not appropriate for such a 90° scan, it's meant for a full
> 360° scan. rtkfdk tries to apply a short scan but Parker weighting is for
> 180°+fan-angle. So I'm not sure what to expect from FDK with such a scan.
> The projections that you shared are 512x511, can you please clarify the
> pixel size? I would try iterative reconstruction with such a scan.
> Cheers,
> Simon
>
> On Fri, May 31, 2024 at 12:25 PM Christian Riesch <
> christian.riesch at live.com> wrote:
>
> Hello Simon,
>
> Thanks for the quick response.
> So I have tried rtksimulatedgeometry with --arc 273 together with adding
> --neworigin=-153.5985,-153.2025,0 to rtkfdk.
> The result is different than before, but still looks very wrong (two
> ribbons and some vertical lines).
>
> I may be able to share some data later.
>
> Best regards,
> Christian
>
> ------------------------------
> *Von:* Simon Rit <simon.rit at creatis.insa-lyon.fr>
> *Gesendet:* Donnerstag, 30. Mai 2024 08:48
> *An:* Christian Riesch <christian.riesch at live.com>
> *Cc:* rtk-users at openrtk.org <rtk-users at openrtk.org>
> *Betreff:* Re: [Rtk-users] Reconstruction geometry
>
> Hi,
> I can see two problems:
> - you need to indicate the short scan to rtksimulatedgeometry, e.g. --arc
> 273 or, if the angle convention is opposite in your system, --arc -273. You
> may have to tune the --first_angle option to position the volume as you
> wish but that should not prevent accurate reconstruction.
> - you need to center your projections, i.e., add the option
> --neworigin=-153.5985,-153.2025,0 to rtkfdk, computed with
> -0.5*(3104-1)*0.099 and -0.5*(3096-1)*0.099.
> Don't hesitate to share a dataset if that does not help.
> Good luck!
> Simon
>
>
> On Thu, May 30, 2024 at 6:58 AM Christian Riesch <
> christian.riesch at live.com> wrote:
>
> Hello,
>
>
>
> I'm currently trying to use RTK for a reconstruction from a stack of
> images that resulted from a 90° scan, but struggling to get the parameters
> right.
>
> On the other hand, I was able to get what looks like a faithful
> reconstruction using the Astra toolbox and the script from
> https://tomroelandts.com/articles/astra-toolbox-tutorial-reconstruction-from-projection-images-part-1
>
>
>
> I have these parameters from the X-ray device that captured the images
> (size 3104x3096):
>
>             "fod_mm": 75.46, (focus to object distance)
>
>             "odd_mm": 407.07, (object to detector distance)
>
>             "pixel_size_mm": 0.099,
>
>             "start_arc_deg": 45.0,
>
>             "stop_arc_deg": -45.0
>
> (There is also "detector_offset_mm": 9.8, which I have ignored so far with
> both Astra and RTK.)
>
>
>
> So I have tried to create a geometry using
>
> .\rtksimulatedgeometry.exe -o"geo.xml" -n91 -f45 -a90 --sdd=482.53
> --sid=75.46
>
> where sdd = fod_mm + odd_mm and sid = fod_mm,
>
> and a reconstruction with
>
> .\rtkfdk.exe -p"images" -r".*tif" -g"geo.xml" -o"out.tif"
> --dimension=512,512,200 --newspacing=0.099
>
>
>
> However, out.tif contains mostly zeros and a weird ribbon-like shape in
> the center. So I think my geometry is wrong, but I don't know how to fix it.
>
>
>
> For comparison, here are the input parameters for the Astra script:
>
> distance_source_origin = 75.46  # [mm]
>
> distance_origin_detector = 407.07  # [mm]
>
> detector_pixel_size = 0.099 # [mm]
>
> num_projections = 91
>
> start_angle_deg = 45
>
> stop_angle_deg = 135
>
>
>
> Any pointers would be appreciated.
>
>
>
> Best regards,
>
> Christian Riesch
>
>
> _______________________________________________
> Rtk-users mailing list
> rtk-users at openrtk.org
> https://www.creatis.insa-lyon.fr/mailman/listinfo/rtk-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.creatis.insa-lyon.fr/pipermail/rtk-users/attachments/20240604/ee8d09c3/attachment-0001.htm>