[Rtk-users] Sophia beads reconstruction

[louie L]

Hi MG,

Sometimes, the progressive deformation from the center of rotation to the edge of the image is caused by wrong sdd/sid ratio. Such as change in the geometry will lead to distortion of the image and wrong magnification.
Maybe you can play with that parameter and report your result. 

Cheers,
Louie

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From: Simon Rit
Sent: Tuesday, January 26, 2016 13:24
To: MG Vallet
Cc: rtk-users at public.kitware.com
Subject: Re: [Rtk-users] Sophia beads reconstruction

Hi,
I think it's likely a problem with parameters. The best would be to obtain them from the Matlab code they provide.
Good luck,
Simon

On Mon, Jan 25, 2016 at 5:48 PM, MG Vallet <mgvallet.pro at gmail.com> wrote:
Hi Simon,

this was a point I missed. I had to do the log mapping.

I must say, I do not use RTK from shell. I just plugged the objects
FDKConeBeamReconstructionFilter and ThreeDCircularProjectionGeometry from RTK into a visualisation software. That's the reason I'm not absolutely sure about the length parameter setting.

Anyway, I'm now pretty close to your result. I believe the only difference is the progressive deformation of beads with the distance to center.

What's your opinion : is there another step I might have missed, or is it more likely a problem with parameters ?

MG

2016-01-21 14:22 GMT-05:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:
Not exactly. rtk::FDKConeBeamProjectionFilter assumes that you pass the line integral (ln(I0/I)). But rtkfdk uses the ProjectionsReader to read the projections and converts them depending on the type: for mha or mhd, it just reads it and nothing else. For tif, it assumes that I is passed, try to guess I0 (or gets it from the cmd line) and computes ln(I0/I).
So from each tif projection, instead of letting them go through the ProjectionsReader in RTK, directly use the ImageReader, stack them and pass it to the reconstruction algorithm. In other words, if you use SimpleRTK, use ImageSeriesReader instead of ProjectionsReader.
Regarding the geometry, it would be nice to be confident in the geometry parameters, maybe from their Matlab code?
Simon

On 21/01/2016 20:02, MG Vallet wrote:
Hi Simon and Cyril, 

I really appreciate your insight.

By examining the parameters of the acquisition, I saw that the center must effectively be offset (4.8 mm in both directions). For the attached image, I also increases sdd and sid by a factor 1000, just in case I would be wrong in units. It reduces the first default I pointed out in my first message. Also note that my input dataset was SophiaBeads_512_averaged.

Regarding the pre-processing mentioned by Simon, I need more help. Is it as simple as the FDK filter assumes that the input is intensity, but the dataset provides -ln(I/I0) ?

Regards,
mg

2016-01-20 3:33 GMT-05:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:
Hi,
I quickly checked SophiaBeads_64_averaged.zip. First, it seems that what is provided is directly the line integral. RTK will process the tif images as if it were a photon count so I converted the tif projections to mha to avoid this. For the conversion, I used another piece of software but you can easily do the same thing with SimpleRTK.
Second, I used the enclosed script which gives me a much better result. I have however a geometry problem. I think they provide a Matlab piece of code to get the center of rotation. If you can run it and find out what is this center, then you can use it to configure the geometry better with the options --proj_iso_x and --proj_iso_y.
Good luck,
Simon

On Tue, Jan 19, 2016 at 8:02 PM, MG Vallet <mgvallet.pro at gmail.com> wrote:
Thanks Cyril! 
going to carefully check my inputs and I give you some news.
mgv

2016-01-19 10:33 GMT-05:00 Cyril Mory <cyril.mory at uclouvain.be>:
Hi, 

It looks like the geometry is wrong indeed, because I have never seen such artifacts.

Hope that helps,
Cyril 

Le 19/01/2016 16:19, MG Vallet a écrit :
Dear rtk-users, 

I applied the FDKConeBeamReconstructionFilter to a data set from https://zenodo.org/record/16539. 
This is a plastic tube filled with glass beads that has been scanned.

Attached is a view of the reconstructed central slice. It is found that:
1. the beads are quickly deformed outside the center
2. each one has a halo, or a shadow (dont know the proper term)
My question is if these are simply expected artifacts. I am not 100% sure I properly set the geometry parameters.

Regards,
mgv

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