[Rtk-users] FirstReconstruction questions

[Lai Yao Hao]

Hi,
I cannot send the projections via email as the projections are too big in size. Instead, I am sharing the files on Drive, with the hyperlink as below. In the folder, there is a subset of 100 projections out of the 800 projections, with the angle between each projection being 3.6 degrees. There are other details on the projects as listed in report.txt file in the folder.

Google drive share link:
https://drive.google.com/drive/folders/1wMRo3Rmr6HszUVil0vEsLPtLSLftFyfQ?usp=sharing

Regards
lyh
________________________________
From: Simon Rit <simon.rit at creatis.insa-lyon.fr>
Sent: Tuesday, January 5, 2021 5:21 PM
To: Lai Yao Hao <yao_hao777 at hotmail.com>
Cc: rtk-users at public.kitware.com <rtk-users at public.kitware.com>
Subject: Re: [Rtk-users] FirstReconstruction questions

Hi,
I think the issue is that your projection images are given in the TIFF file format which does not contain important meta information such as the origin and the spacing of the projections. You should use ChangeInformationFilter<https://itk.org/Doxygen/html/classitk_1_1ChangeInformationImageFilter.html> to set these. I'm guessing that the origin is currently (0,0) and since you do not set any offsets when using AddProjection, it comes down to having the corner of your projection aligned with the central ray (line defined by the source and the center of rotation).
You can share projections or a subset of them if you'd like us to give it a try with your code.
Good luck!
Simon

On Mon, Jan 4, 2021 at 4:35 PM Lai Yao Hao <yao_hao777 at hotmail.com<mailto:yao_hao777 at hotmail.com>> wrote:
Hi,

The code is as attached. Just for further reference, I am given images as attached, and there are 800 of them, with 0.45 degrees separating each frame. The naming of the screenshots depicts the frame that it is in.

Thanks in advance for the advice and help!! I really appreciate this community 🙂

Regards
lyh
________________________________
From: Simon Rit <simon.rit at creatis.insa-lyon.fr<mailto:simon.rit at creatis.insa-lyon.fr>>
Sent: Wednesday, December 30, 2020 9:35 PM
To: Lai Yao Hao <yao_hao777 at hotmail.com<mailto:yao_hao777 at hotmail.com>>
Cc: rtk-users at public.kitware.com<mailto:rtk-users at public.kitware.com> <rtk-users at public.kitware.com<mailto:rtk-users at public.kitware.com>>
Subject: Re: [Rtk-users] FirstReconstruction questions

Hi,
RTK cone beam reconstruction filters expect line integrals but the projection that you are showing seems to have the highest value in air. RTK automatically processes such projections with log and normalization if the pixels are unsigned short. Otherwise, you need to do it yourself.
It is not clear if the geometry is correct from the reconstruction screen shot. The best would be to share your code if you want us to have a look.
Simon

On Mon, Dec 28, 2020 at 8:34 AM Lai Yao Hao <yao_hao777 at hotmail.com<mailto:yao_hao777 at hotmail.com>> wrote:
Dear Simon and the RTK community

Really thank you for the answer, and really sorry for the late reply. I am trying to reconstruct a 3d model using 800 images, rotating an object 360 degrees using rtk::ThreeDCircularProjectionGeometry, rtk::ConstantImageSource and rtk:: FDKConeBeamReconstructionFilter from the FirstReconstruction example as well as itk::ImageSeriesReader.

However, the reconstruction created is shown above in the screenshot and after checking all the parameters, I have no idea on how to move forward from here. From reading the forums, I think that I should do one more image filter before applying the cone beam reconstruction? However, I am not too sure. Please advise on the next steps that can enable me to get the 3d reconstruction.

Thanks so much in advance and look forward to everyone's reply!!

PS: the tif file is just 1 of the 800 images I am given to reconstruct the object

Regards
lyh

________________________________
From: Simon Rit <simon.rit at creatis.insa-lyon.fr<mailto:simon.rit at creatis.insa-lyon.fr>>
Sent: Wednesday, December 9, 2020 4:23 PM
To: Lai Yao Hao <yao_hao777 at hotmail.com<mailto:yao_hao777 at hotmail.com>>
Cc: rtk-users at public.kitware.com<mailto:rtk-users at public.kitware.com> <rtk-users at public.kitware.com<mailto:rtk-users at public.kitware.com>>
Subject: Re: [Rtk-users] FirstReconstruction questions

Hi,
constantImageSource creates a constant volume. In the example, one is used as input of the simulation of projections of an ellipsoid (rei) and one as input of the reconstruction algorithm (feldkamp). fieldofview masks out (i.e., set to 0) voxels which are not in the field of view.
I don't understand your screenshot either but if you use the tiff format, make sure you use a viewer capable of dealing with 3D tiff images (e.g., vv<http://vv.creatis.insa-lyon.fr> or ImageJ).
Simon

On Wed, Dec 9, 2020 at 8:59 AM Lai Yao Hao <yao_hao777 at hotmail.com<mailto:yao_hao777 at hotmail.com>> wrote:
Hi to all the rtk-users

I am a new user of rtk, and I have some questions regarding the FirstReconstruction example given in github. I have generated an image as attached, with 4 tiny ball-like drawing hanging from the top. Can anyone explain to me why do I get such image and what are the implications of constantImageSource, rei, constantImageSource2, feldkamp and fieldofview?

Your explanation will be much appreciated. Thanks in advance!

Regards
lyh
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