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

[Chao Wu]

Hi Louis,

For projections in unsigned short TIF format, by default the applications
expect intensities as pixel values, and the embedded
rtk::LUTbasedVariableI0RawToAttenuationImageFilter will perform the log
transform to convert intensities to line itergral of attenuation. However
an I0 value (intensity of ray passing through air only) must be specified
for the log transform if this value cannot be well determined by the other
embedded filter rtk::I0EstimationProjectionFilter. This is likely to be the
case since you seem to have (nearly) an interior problem in your geometry.

Regards,
Chao

2018-05-25 22:37 GMT+02:00 <louis.godon at student.uliege.be>:

> 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
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://public.kitware.com/pipermail/rtk-users/attachments/20180528/6f400dbd/attachment.html>