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

[Simon Rit]

Hi,
Thanks for sharing. There still seems to be some streak artefacts, do you
see the same in the Varian reconstruction?
I'm looking forward to the pull-request, I think we should try to make the
bzip2 optional.
Simon

On Fri, Sep 16, 2016 at 10:37 PM, Andreas Gravgaard Andersen <
andreasg at phys.au.dk> wrote:

> Thanks for the fast response Simon!
>
> I flipped the angles (360 - angle[deg]) and it worked! Thanks, you were
> right all along!
> I just didn't get why it makes a difference. I think I do now, as the
> resulting image was flipped upside down and not left/right as I expected.
> [attached]
>
> The reconstruction is significantly better, I'll look into what should be
> included in the reader and what I should keep in my program to keep
> conformity with the other readers. Then I'll create a pull request.
>
> Just for the purpose of others hitting the same or a similar bug, I also
> attempted:
> I did the  SART reconstruction with 10 iterations, lambda=0.3, and Joseph
> back/forward projection, *but with no* significant improvement [attached]
>
> And:
> If you want you can download the data set from: [Dropbox link to 460MB zip
> <https://www.dropbox.com/s/hg2k50vw3f7bt4b/CatPhan.zip?dl=0> (I'll keep
> it up as long as Dropbox allows me)] Only the Acquisitions/subfolder is
> used along with the Scan.xml (Calibrations folder may be used in the future
> in my program, but I'm not sure if you can rely on the existence of the
> content).
>
> A MatLab XimReader is available: link
> <https://github.com/agravgaard/RTK/blob/master/code/ReadXim.m> (also
> available from Varian bitbucket along a with a python version and a
> C#->matlab plugin
> <https://bitbucket.org/dmoderesearchtools/ximreader/downloads>).
> Otherwise my fork with the RTK-style reader is available from the same
> repository (I have also added Hnc support, thanks to the Geoff Hugo fork,
> so bzip2 is a new dependancy).
>
> 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
>
>
>
> 2016-09-16 16:13 GMT+02:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:
>
>> 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
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>>> _______________________________________________
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>>>>>
>>>>
>>>
>>
>
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