[Rtk-users] Cone Beam Reconstruction using Open RTK

[Keven Qiu]

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:
[cid:cb2c9fb4-772c-4a11-bc86-02cfffdcbd5f]

Sinogram
[cid:060efe66-4246-4d75-9427-0c0bbf1b519f]

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<mailto: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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.creatis.insa-lyon.fr/pipermail/rtk-users/attachments/20230125/8e189979/attachment-0001.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 2030291 bytes
Desc: image.png
URL: <http://www.creatis.insa-lyon.fr/pipermail/rtk-users/attachments/20230125/8e189979/attachment-0002.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 352863 bytes
Desc: image.png
URL: <http://www.creatis.insa-lyon.fr/pipermail/rtk-users/attachments/20230125/8e189979/attachment-0003.png>