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

Fri May 25 16:37:05 EDT 2018

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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