[Rtk-users] Preprocessing
Jonathan Mason
j.mason at ed.ac.uk
Tue Dec 1 10:47:14 CET 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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>
>
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
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