[Rtk-users] Cone Beam Reconstruction using Open RTK

[Simon Rit]

Hi,
You can read both raw projections or line integrals. The ProjectionsReader
does different things depending on its input data. If the files have real
pixel type (float or double), it assumes they are line integrals. If they
are integers, it tries to convert them to line integrals depending on many
things (image file type, pixel type, etc.). You can check the complex graph
in the detailed description to find out what it does:
http://www.openrtk.org/Doxygen/classrtk_1_1ProjectionsReader.html. If you
just have a stack of projections and want to process it, just use
ImageFileReader to use them as is, without processing.
I'm not sure I understand the problem with the raw projections, it seems to
be an ITK I/O issue. Does ImageFileReader work for them? And the sinogram
does not seem right to me, air is brighter than the rest...
Simon

On Wed, Jan 25, 2023 at 10:26 PM Keven Qiu <keven.qiu at ucalgary.ca> wrote:

> Hi Simon,
>
> Do we need to read the raw projections or the sinogram images? Currently,
> we are reading the sinogram images and the air is at 0. Can you confirm
> which one we are supposed to load in? We have only tried loading in the
> sinogram images.
>
> If this is not the problem, any other suggestions to reconstruct the
> images?
>
> Are there also other projections readers in RTK that we could use instead
> of ProjectionsReader?
>
> Raw projection:
>
>
> Sinogram
>
>
> Thanks,
> Keven
> ------------------------------
> *From:* Simon Rit <simon.rit at creatis.insa-lyon.fr>
> *Sent:* Tuesday, January 24, 2023 12:14 AM
> *To:* Keven Qiu <keven.qiu at ucalgary.ca>
> *Cc:* Tadiwa Waungana <tadiwa.waungana at ucalgary.ca>; rtk-users at openrtk.org
> <rtk-users at openrtk.org>
> *Subject:* Re: Cone Beam Reconstruction using Open RTK
>
> [△EXTERNAL]
>
> Hi,
> At first glance, no! The first step is indeed to check that you correctly
> read the projections, i.e. that your images are converted to line integrals
> (if needed). I would write to disk what you pass to FDK (with itk.imwrite)
> and check, e.g., that air is at 0.
> Simon
>
> On Tue, Jan 24, 2023 at 12:58 AM Keven Qiu <keven.qiu at ucalgary.ca> wrote:
>
> Hello Simon,
>
> We are trying to use OpenRTK to reconstruct some knee images from cone
> beam CT. We have managed to run the example script in Python but haven't
> been able to reconstruct our knee images. We have all the geometry
> parameters but are still struggling to get it to work. Here is our
> pseudocode below:
> ```
> Load projection images from DICOM series using
> rtk.ProjectionsReader[ImageType] where ImageType = itk.Image[itk.F, 3]
>
> We construct geometry object with SID, SDD, and gantry angle, and source
> offset X/Y, as well as the number of projections
>
> We create a blank image
>
> We pass the projections, blank image, and geometry into the FDK
> reconstruction method
>
> We then pass the projections, FDK return value from previous step and
> geometry into the field of view mask
>
> Finally, we write the reconstructed image to file in NIfTI using
> rtk.ImageFileWriter[ImageType]
> ```
>
> We seem to be having a problem when we load any projection images instead
> of generating them like the FirstReconstruction example with the sphere. We
> get a blank image of 0's, or a grey image with a circle outline.
>
> At first glance, is there anything we are missing?
>
> Look forward to your response,
> Keven Q
>
>
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