[Rtk-users] Sophia beads reconstruction

Thu Jan 28 16:27:15 EST 2016

Louie,
I played with sdd and sid, following your advise. But they have few effect,
clearly less effect than proj_iso_x. And none of these parameters can
significantly improve my result.

Simon,
I carefully checked every input data and I cant see what I did wrong. I
want first to reproduce your output. You said earlier it's easy to convert
a series of tiff image into a mha file using SimpleRTK. Do you mean by
writing a short program, or is it possible from the command line ?

MG

2016-01-26 17:17 GMT-05:00 louie L <ghostcz at hotmail.com>:

> 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
>
>
>
> Sent from Mail <http://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
>
> *From: *Simon Rit <simon.rit at creatis.insa-lyon.fr>
> *Sent: *Tuesday, January 26, 2016 13:24
> *To: *MG Vallet <mgvallet.pro at gmail.com>
> *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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