[Rtk-users] Sophia beads reconstruction

[Simon Rit]

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 
> <mailto: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
>     <mailto: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
>         <mailto: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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