[Rtk-users] Fwd: Have you encountered this artifact?

[Simon Rit]

Hi,
You can try any iterative reconstruction, they can also handle short scans.
Start with a few iterations of rtksart or rtkconjugategradient. However,
the nature of the artifacts indicate more a problem in the geometry in my
opinion. I have seen such errors when, for example, rotating in the wrong
direction. I can have a look if you share the dataset.
Cheers,
Simon

On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen <
andreasg at phys.au.dk> wrote:

> Thanks for the suggestions, Simon and Cyril!
>
> I have been carefully looking though the geometry and from what I
> understand of the transformations matrices, the geometry looks correct/(as
> expected).
>
> HOWEVER: I found out that the reason for the Hnd to behave differently
> were because had used half-fan scans (full-arc).
> When I used a full-fan (half-arc) scan of Hnd projections the same
> artifacts occurs!
>
> Are there other (built-in) means of improving half-arc scans, than the
> parker short scan filter?
>
> Parker short scan does a decent job, but the result is still far from the
> quality of the Varian software reconstruction at least for the CatPhan.
>
> Best regards
> Andreas
>
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Department of Oncology,
>
> Aarhus University Hospital
>
> Nørrebrogade 44,
>
> 8000, Aarhus C
>
> Mail:     andreasg at phys.au.dk
>
> Cell:      +45 3165 8140
>
>
>
> 2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
>
>> One suggestion since it works with the Hnd projections:
>> You can run rtkprojections twice (with the Hnd projections, then with Xim
>> projections) and output two projection stack files and two geometry files,
>> then compare the projection stack files by subtracting one to the other
>> (with SimpleRTK or clitk) and the geometry files with diff. If they are
>> identical, then I do not see any reason why the reconstructions should be
>> different, so my guess is that you will find differences.
>>
>>
>> On 09/13/2016 10:18 PM, Simon Rit wrote:
>>
>>> Hi,
>>> I have almost never worked with Varian data but it looks like a
>>> geometry problem. Maybe the problem comes from a bad ordering of the
>>> projections which results in assigning a bad geometry to each
>>> projection. How did you name your projections? Maybe check that the
>>> order matches that of the RTK geometry file. Otherwise, there might be
>>> an issue in the creation of the geometry file itself.
>>> All this sounds good, happy bug hunt and don't hesitate to share your
>>> code when you feel it's ready.
>>> Simon
>>>
>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen
>>> <andreasg at phys.au.dk> wrote:
>>>
>>>> Dear RTK experts,
>>>>
>>>> I am reconstructing Varian ProBeam projections of the Xim image format.
>>>> I
>>>> have written the reader myself - very similar to the Hnd one already
>>>> available with RTK.
>>>> Links to my fork: [XimReader, XMLReader, GeometryReader]
>>>>
>>>> The reader apparently works (Images and angles displays as expected in
>>>> UI),
>>>> however when reconstructing with a regular FDK I get a reconstructed
>>>> image
>>>> that is smeared out around the high and low density areas [see attached
>>>> image]
>>>>
>>>> I'm using half arc, full fan images with no bow-tie filter from Scripps
>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m,
>>>> SDD=3m.
>>>>
>>>> For the Hnd projections the reconstruction works perfectly (Same
>>>> algorithm).
>>>> The reconstruction of the Xim projections performed on Varian software
>>>> works
>>>> perfectly.
>>>>
>>>> Without the Parker Short Scan Filter the first and last projections
>>>> creates
>>>> streaks across the reconstruction as if they were way too bright.
>>>> If the first few projections are excluded, the following projection
>>>> will act
>>>> the same way.
>>>>
>>>> The projections are corrected for beam hardening and all the projections
>>>> have the expected attenuation.
>>>> No "smearing" filters (like median) is used, and iterative
>>>> reconstruction
>>>> makes the same artifacts.
>>>>
>>>> Setting the value of the first and last projection to zero has the same
>>>> effect as excluding. Changing the ramp filter only changes noise, not
>>>> the
>>>> artifacts.
>>>>
>>>> Have any of you had a similar problem? Am I missing something?
>>>> Any suggestions are welcome I'm running out of ideas.
>>>>
>>>> Best regards
>>>> Andreas
>>>>
>>>> __________________________________
>>>>
>>>> Andreas Gravgaard Andersen
>>>>
>>>> Department of Oncology,
>>>>
>>>> Aarhus University Hospital
>>>>
>>>> Nørrebrogade 44,
>>>>
>>>> 8000, Aarhus C
>>>>
>>>> Mail:     andreasg at phys.au.dk
>>>>
>>>> Cell:      +45 3165 8140
>>>>
>>>>
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>>>
>>
>
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