[Rtk-users] Sophia beads reconstruction

[MG Vallet]

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>
>> 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>
>>> 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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>>>>
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