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:     andre...@phys.au.dk

Cell:      +45 3165 8140



2016-09-14 9:10 GMT+02:00 Cyril Mory <cyril.m...@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
>> <andre...@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:     andre...@phys.au.dk
>>>
>>> Cell:      +45 3165 8140
>>>
>>>
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>>>
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>
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