[Rtk-users] Sophia beads reconstruction

[Simon Rit]

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>
>>> 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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