[Rtk-users] rtkfdk and rtksart application input projection type and voxel value range

[Simon Rit]

Hi,
Be aware that since the "object scanned always occupies the entire
projection" you are dealing with the (difficult) interior problem. See,
e.g., http://doi.org/10.1109/MSP.2010.936743. It's not surprising for this
problem that FDK and SART give different answers.
Best regards,
Simon

On Fri, May 25, 2018 at 2:37 PM, <louis.godon at student.uliege.be> wrote:

> Hi Cyril,
>
> Thank you for your fast response.
>
> The images are from a custom device in development by the X-RIS company
> where I am currently doing an
> internship in relation with my master thesis. However, due to the scanner
> design (collimator and small field
> of view) and the application, the type of object scanned always occupies
> the entire projection. One aspect of
> the application is to reconstruct object that nearly fit the scanner field
> of view and therefore I do not have
> other projections to show you except other ones of this kind.
>
> Indeed, we did not apply pre-processing to the projection to obtain
> line-integrals. I will try this
> solution.
>
> Thank you very much for your help,
> Best regards,
>
> Louis
>
> ----- Mail original -----
> De: "Cyril Mory" <cyril.mory at creatis.insa-lyon.fr>
> À: rtk-users at public.kitware.com
> Envoyé: Vendredi 25 Mai 2018 17:43:41
> Objet: Re: [Rtk-users] rtkfdk and rtksart application input projection
> type and voxel value range
>
> Hi Louis,
>
> You first need to get the projections right. RTK has a filter
> "rtkProjectionsReader" to read projections exported from a scanner, and
> apply all the necessary processing, including log-transform, to obtain
> line-integrals. The reconstruction methods (rtkfdk, rtksart, ...) all
> use line integrals as inputs, but they embed an rtkProjectionsReader,
> which can do the conversion at runtime. However, if rtkProjectionsReader
> does not recognize your data and applies the wrong processing, the
> reconstruction methods will return garbage. So the safest way is to
> first call the rtkProjectionsReader (using the command line tool
> rtkprojections), look at its output, and make sure it looks like line
> integrals: it must have near-zero values in air, and higher values in
> dense objects. Only then can you start reconstructing.
>
> The diagram available here
> http://www.openrtk.org/Doxygen/classrtk_1_1ProjectionsReader.html shows
> which processing is applied to which kind of data. The files in .mha
> format are assumed to be line integrals already, and bypass all
> processing, so it is probably not the format you should use. I do not
> know which way .tif are processed, especially unsigned short .tif, but
> I've had a look at your data, and it looks as if no log-transform is
> applied on your projections. The borders of the projections, where
> probably the rays have only gone through air, have high values.
> Therefore, you're reconstructing a cylinder, as large as your
> projections, which probably isn't what you want.
>
> Are you getting these images from a custom device built at the
> university, or from a commercially available machine ?
>
> Do you have an acquisition where the object is clearly visible in the
> projections ? If so, can you send over one of these projections ?
>
> Hope that helps,
>
> Cyril
>
>
> On 25/05/2018 16:46, louis.godon at student.uliege.be wrote:
> > Hi,
> >
> > I am currently using RTK for my Electrician Master's thesis and I am
> finding some difficulties...
> >
> > We observed that reconstructed values range using fdk algorithm and sart
> are different. How can this range be interpreted depending on the algortihm
> used in order to compare the image quality between both algorithms?
> >
> > Furthermore, some voxels have negative value, is it possible to obtain
> negative values with rtkfdk or rtksart application? does it make sens and
> how can that be?
> >
> > And finally, last question, is there a specific projection file type
> (.tif, .mha, ...) and/or pixel type (unsigned short, float, ...) to use
> when using rtkfdk or rtksart?
> >
> > Here are some informations that may be useful:
> > Object scanned:
> >   Rock sample and homogeneous polymer cylinder
> > Projection are:
> >   -type: .tif (unsigned short) or .mha (float)
> >   -projection set: 360 seperated (.tif) files or 360 seperated (.mha)
> files or one single (.mha) file
> >
> > Reconstructed image:
> >   -type: .mha (float)
> >
> > Algorithm used:
> >   -rtkfdk (without ramp filter)
> >   -rtksart (3~5 iterations, 1 projections processed between each update
> of the reconstructed volume (1 for SART))
> >
> > Here is a link to download some projection and reconstructed image:
> > https://www.dropbox.com/sh/sgrzrylphe4dar2/
> AAAFW3hJYzyZGbPevf_CYteka?dl=0
> >
> > Thanks in advance for your help or advices.
> >
> > Best regards,
> >
> > Louis
> > _______________________________________________
> > Rtk-users mailing list
> > Rtk-users at public.kitware.com
> > https://public.kitware.com/mailman/listinfo/rtk-users
>
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