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

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 Gravgaard Andersen

Department of Oncology,

Aarhus University Hospital

Nørrebrogade 44,

8000, Aarhus C


Cell:      +45 3165 8140

2016-09-14 9:10 GMT+02:00 Cyril Mory <>:

> 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
>> <> 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:
>>> Cell:      +45 3165 8140
>>> _______________________________________________
>>> Rtk-users mailing list
>>> _______________________________________________
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