[Rtk-users] Conjugate Gradient Artefact

Tue Jun 2 14:21:46 EDT 2015

Hi Jonathan,

Please try to keep the discussions on RTK on the mailing list, so that 
everyone can benefit from the questions and answers.
About the disk artifact you observe, could you try another iterative 
algorithm, like for example SART (same parameters, only less iterations, 
4 is sufficient), and let us know whether the same artifact is present 
in your results ? If the artifact is only present in the CG result, then 
I'll have to take a deep dive into the CG code and the way the weighting 
is performed.

Regarding PICCS, many things come to my mind:
- it mostly depends on the algorithm you would like to use to minimize 
the PICCS cost function. If you want to maximize re-use of available RTK 
code, I recommend you adopt an alternating scheme : minimize the data 
attachment term, then the TV of the volume, then the TV of the 
difference between volume and prior, and repeat. You can do that with 
the SART filter and a TotalVariationDenoisingBPDQ filter. If, on the 
other hand, you want a more theoretically solid minimization algorithm, 
you will need more implementation work
- that being said, my personal experience with PICCS, on 4D C-arm CT of 
the human heart, was disappointing. If you intend to use PICCS to 
reconstruct either beating heart or free-breathing thorax data, I would 
recommend you try rtkfourdrooster (and maybe read the paper that 
compares ROOSTER with PICCS, called "Cardiac C-arm computed tomography 
using a 3D + time ROI reconstruction method with spatial and temporal 
regularization", http://www.ncbi.nlm.nih.gov/pubmed/24506624)
- if you do implement PICCS, it would be a valuable addition to RTK, so 
I encourage you to submit it :)

All the best,
Cyril

On 2015-06-02 09:04, Jonathan Mason wrote:
> Hi Cyril,
> 
> Thank you for your response. It indeed seems as though the artefact is
> due to the geometry mismatch, and I believe it originates from a
> calibration issue with the machine, so when I get access again I will
> try to fix this. You are also correct about my blurry reconstruction,
> and running for a decent number of iterations generates an image more
> comparable to FDK, though still with the disk present. In the mean 
> time,
> I have been exploring more of the software package on some synthetic 
> data.
> 
> I would like to implement a PICCS like reconstruction by incorporating
> prior image regularisation. What would you recommend the best approach
> to this task. Would it be possible to realise it with an application
> calling RTK functions, or would I need to construct new templates for 
> it?
> 
> Many thanks,
> 
> Jonathan
> On 07/05/15 15:25, mory wrote:
>> Hi Jonathan,
>> 
>> Welcome to RTK !
>> The artefact you see is indeed caused by the offset detector, but from
>> the documentation and the code, it seems that the "displaced detector
>> filter" should do its job in rtkconjugategradient, so I'm kind of
>> puzzled.
>> Your conjugate gradient reconstruction is very blurry. I guess you
>> used a very small number of iterations. Can you re-run it with 30
>> iterations and see what happens ?
>> 
>> Best regards,
>> Cyril
>> 
>> On 2015-05-07 14:38, Simon Rit wrote:
>>> Hi,
>>> Probably an offset detector artefact. Look at this conversation:
>>> http://public.kitware.com/pipermail/rtk-users/2015-March/000713.html
>>> [2]
>>> Maybe try one of the algorithms that properly uses the offset 
>>> detector
>>> filter? For the FOV, the option --displaced will provide the full 
>>> FOV.
>>> I hope this helps,
>>> Simon
>>> 
>>> On Thu, May 7, 2015 at 1:40 PM, Jonathan Mason <j.mason at ed.ac.uk>
>>> wrote:
>>> 
>>>> Hello RTK users,
>>>> 
>>>> I have been using RTK for a couple of weeks now, and really like
>>>> the
>>>> software. The extensive number of tools available is really
>>>> impressive
>>>> and helpful, so thanks!
>>>> 
>>>> I have been experiencing an cylindrical artefact in using conjugate
>>>> gradient reconstruction — illustrated in the attached images
>>>> along with
>>>> FDK with no artefact — of which I am unsure of its origin. The
>>>> data is a
>>>> scan of a thorax phantom from a Varian on-board imager. At first I
>>>> suspected it was due to the specimen extending beyond the
>>>> reconstruction
>>>> volume, but extending this unfortunately did not help. Something
>>>> else I
>>>> have noticed is that the FOV filter isolates just this pale
>>>> cylindrical
>>>> artefact around the centre of rotation.
>>>> 
>>>> Do you know of the cause of this effect, or how it could be
>>>> remedied?
>>>> 
>>>> Best wishes,
>>>> 
>>>> Jonathan
>>>> 
>>>> --
>>>> The University of Edinburgh is a charitable body, registered in
>>>> Scotland, with registration number SC005336.
>>>> 
>>>> _______________________________________________
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>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users [1]
>>> 
>>> 
>>> 
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>>> [2] 
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>>> 
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>> 