[Rtk-users] Preprocessing

[Simon Rit]

Good to hear! We have similar projects in Lyon, sometimes in collaboration
with other groups. We'll let you know when we have made significant
progresses.
Simon

On Tue, Dec 1, 2015 at 10:47 AM, Jonathan Mason <j.mason at ed.ac.uk> wrote:

> 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> 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>
>> 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> 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>:
>>>
>>>> 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.
>>
>>
>
>
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
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