[Rtk-users] Sophia beads reconstruction

[MG Vallet]

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>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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