[Rtk-users] Preprocessing

Jonathan Mason j.mason at ed.ac.uk
Tue Dec 1 04:47:14 EST 2015


Thanks Simon,

I have implemented both of the techniques you have mentioned. Nui
scatter correction does do a reasonable job, but I have found it leaves
significant artefacts when there is a substantial change in organ shape
or location between scans, and I hope that MC will allow me to
investigate the true effect of this technique when I have the scatter
ground truth.

WLS also has been outperforming LS in phantom experiments, but only when
photon flux is being starved, and has been difficult to get a reasonable
estimate of I0 from Varian data (also have yet to set up the scanner to
even produce such a low current).

I am doing my developments in MATLAB rather than RTK at the moment as I
find it quicker to test things out, and utilise Toolboxes, but it is my
hope to eventually move over once I have found more stability. I would
love to contribute to what is now a very comprehensive and powerful
software package.

Cheers,

Jonathan

On 01/12/15 08:58, Simon Rit wrote:
> Hi,
> For scatter and assuming you have the planning CT, you could consider
> the solution of Yang et al
> <http://www.openrtk.org/RTK/news/201507_press.php> (that he
> implemented from Niu et al) that is much simpler than Monte Carlo. I
> know two teams that have already implemented it using RTK and we will
> try to do our own in the future.
> For photon statistics, Cyril has recently been working on a weighted
> least square solution, see, e.g., this commit
> <https://github.com/SimonRit/RTK/commit/b133c0bb96bff6805dd28c7820a89310629ff031>.
> But I don't think it's mature yet.
> Note that we discussed pre-processing in July in Lyon, the minutes are
> here
> <http://wiki.openrtk.org/index.php/RTK/Meetings/TrainingNov15#Pre-processing>.
> Good luck, it's not an easy task,
> Simon
>
> On Tue, Dec 1, 2015 at 9:50 AM, Jonathan Mason
> <s1015431 at staffmail.ed.ac.uk <mailto:s1015431 at staffmail.ed.ac.uk>> wrote:
>
>     Thank you Simon and Chao,
>
>     I apologise for the confusion—I can see that my message was not
>     very clear. I am essentially trying to compensate for low photon
>     flux and scatter, but am finding it difficult with pre corrected
>     data. I will certainly take time to look through your suggested
>     publications, so thanks for that.
>
>     Without having access to low level physical data, I am considering
>     simulating a scanner with MC, where I will have the ground truth
>     for scatter field and photon statistics, and try to produce
>     reconstructions on this.
>
>     Many thanks,
>
>     Jonathan
>
>>     On 1 Dec 2015, at 07:27, Simon Rit
>>     <simon.rit at creatis.insa-lyon.fr
>>     <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>>
>>     Hi Jonathan,
>>     I'm not sure I fully get it either. What I can say is that I was
>>     a postdoc at the NKI until the end of 2009 where I was working on
>>     the Elekta reconstruction software. The way
>>     rtk::ProjectionsReader
>>     <http://www.openrtk.org/Doxygen/classrtk_1_1ProjectionsReader.html>
>>     works for Elekta projections is close to what they were doing at
>>     the time, i.e., Boellaard scatter correction, cropping and simple
>>     log to go to a line integral. I know they have been improving it
>>     since (with lag and scatter corrections) but I'm not sure what's
>>     commercialized what's not. In any case, they publish / present
>>     what they do (see publications of M. van Herk, J-J. Sonke and L.
>>     Ploeger).
>>     I'm not expert of Varian data but for sure, when you get
>>     pre-corrected projections, it's hard to know what part you're
>>     correcting (uncorrected problems or miscorrections). Instead of
>>     reverse engineering, which can be tough because Varian does a lot
>>     of stuff on the raw data I believe (look at the publications of
>>     J. Star-Lack), I would start from the raw data if you can access
>>     them.
>>     Good luck,
>>     Simon
>>
>>     On Mon, Nov 30, 2015 at 7:50 PM, Chao Wu <wuchao04 at gmail.com
>>     <mailto:wuchao04 at gmail.com>> wrote:
>>
>>         Hi Jonathan,
>>
>>         I do not quite understand your problem.
>>         I think most information can be retrieved by the relationship
>>         between flux (I) and attenuation (u):
>>         I = I0 * exp (- integral(u * dL) )
>>         Of course there are other effects like beam hardening and
>>         scattering involved but this model is the basic.
>>
>>         Regards,
>>         Chao
>>
>>         2015-11-30 17:29 GMT+01:00 Jonathan Mason <j.mason at ed.ac.uk
>>         <mailto:j.mason at ed.ac.uk>>:
>>
>>             Good afternoon RTK users,
>>
>>             I have access to "raw data" from a Varian OBI scanner,
>>             and have
>>             experimented with RTK for performing its reconstruction.
>>             However, it is
>>             not really "raw" in the sense that the coefficients are
>>             proportional to
>>             the photon flux recorded at a given sensor, but is
>>             instead proportional
>>             to the Hounsfield attenuation along that path. With this
>>             data, it means
>>             that one can reconstruct using FDK and other iterative
>>             techniques, which
>>             assume a linear model, but the connection to the
>>             underlying physics is
>>             abstract.
>>
>>             The problem I then have when trying to develop reconstruction
>>             techniques, is that I do not know whether I am really
>>             correcting for
>>             physical distortions or just correcting for Varian's
>>             preprocessing,
>>             which has been finely tuned for its own FDK method.
>>
>>             My question is whether anybody has dug into the steps
>>             that manufacturers
>>             such as Varian or Elekta perform to arrive at these
>>             projection images?
>>             And if they think that if reverse engineered, could
>>             provide a richer set
>>             of information to facilitate advanced strategies.
>>
>>             Best wishes,
>>
>>             Jonathan Mason
>>
>>             --
>>             The University of Edinburgh is a charitable body,
>>             registered in
>>             Scotland, with registration number SC005336.
>>
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>>
>>
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>
>
>     The University of Edinburgh is a charitable body, registered in
>     Scotland, with registration number SC005336.
>
>

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