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

[Simon Rit]

Dear Andreas,
Today we had the RTK training and some users were looking for a XIM file
reader. I pointed to your contributions but any chance to have it put in
RTK soon?
Thanks in advance,
Simon

On Mon, Sep 19, 2016 at 9:26 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> 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
>>>>>>>
>>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
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>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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