[Rtk-users] Reconstruction geometry

Simon Rit simon.rit at creatis.insa-lyon.fr
Wed Jun 5 13:18:26 CEST 2024 

Hi,
Sorry for the trouble. Cuda 12 is now handled by the master HEAD:
https://github.com/RTKConsortium/RTK/pull/589. I'm working on a release.
I don't fully understand the other errors but RTK 2.5.0 is not compatible
with ITK 5.3 but ITK 5.4rc01
https://github.com/RTKConsortium/RTK/releases/tag/v2.5.0. RTK is only
compatible with the latest tag of the release branch and ITK master, see
INSTALLATION.md
<https://github.com/RTKConsortium/RTK/blob/master/INSTALLATION.md>.
I can let you know if the GPU memory issue is expected if you provide more
details. There's recently been a fix for memory
<https://github.com/RTKConsortium/RTK/pull/598>.
Simon

On Wed, Jun 5, 2024 at 12:17 PM Christian Riesch <christian.riesch at live.com>
wrote:

> Hello Simon,
>
> I finally managed to build RTK-2.5.0 against ITK-5.3.0 with CUDA support
> on Windows with VS2022.
> Since I have met some problems along the way, maybe this will help someone:
>
>    - Current CUDA 12.5 doesn't work, 11.8 does. Maybe the documentation
>    should be updated? See
>    https://discourse.itk.org/t/about-gpu-version-compilation-of-rtk/5905
>    - Before building ITK, I had to add "find_package(CUDAToolkit
>    REQUIRED)" in the CMakeList.txt of the CudaCommon module to fix a CMake
>    error
>    - There still was a linker error in some ITK test project, which I
>    ignored
>    - There is a missing const in
>    ITK-5.3.0\Modules\IO\XML\include\itkDOMNode.h which caused a compiler error
>    when building RTK. This is fixed in ITK/master
>
> It also turns out that I apparently don't have enough GPU memory (8GB) to
> even use CUDA on full-resolution data: Description: ITK ERROR: CUDA ERROR:
> out of memory
>
> Best regards,
> Christian
> ------------------------------
> *Von:* Simon Rit <simon.rit at creatis.insa-lyon.fr>
> *Gesendet:* Dienstag, 4. Juni 2024 14:15
> *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,
> 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
>
>
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