[Rtk-users] how can I get a good 3d image?

[Simon Rit]

Can you be more specific about "not happy"? I think the geometry is now
correct although a cylinder is not the best way to check. What you can
improve is the conversion to attenuation by having the flood field images
(projection without object in the FOV, see Cyril's link for its use),
pre-processing the projections to remove noise (there is a median filter in
RTK but you have to add it in the code), windowing during filtering to
remove noise (see --hann option), etc. But you'll have to play with your
data to find the best combination.
Simon


On Mon, Aug 26, 2013 at 2:11 PM, emaddox at planet.nl <emaddox at planet.nl>wrote:

> Hi,
>
> Thanks for the fast feedback.
>
> Below the commands that do the job. I am not yet happy with the image
> quality
> compared to our normal reconstruction, but it is a start. Any suggestions
> how to improve
> continue?
>
>
> C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtksimulatedgeometry.e
> xe -n 103 -a 201.96 --sdd 255 --sid 200 -o geometry1.xml
> --proj_iso_x=-21.63 --p
> roj_iso_y=-54.08
>
> C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtkfdk.exe -g
> geometry
> 1.xml -p water -r .*.tif -o water.mha --spacing=0.169
> --dimension=256,640,256
>
> Kind regards,
> Erik Maddox.
>
> ----Original Message----
> From : Cyril.Mory at philips.com
> Date : 26/08/2013 13:39
> To : simon.rit at creatis.insa-lyon.fr
> Cc : emaddox at planet.nl, rtk-users at openrtk.org
> Subject : RE: [Rtk-users] how can I get a good 3d image?
>
>
>  Oups. My bad, I didn’t know that. ****
>
> Thanks for your correction.****
>
> ** **
>
> *De :* simon.rit at gmail.com [mailto:simon.rit at gmail.com] *De la part de*Simon Rit
> *Envoyé :* lundi 26 août 2013 13:33
> *À :* MORY, CYRIL
> *Cc :* emaddox at planet.nl; rtk-users at openrtk.org
> *Objet :* Re: [Rtk-users] how can I get a good 3d image?****
>
> ** **
>
> Hi,****
>
> Just a correction on Cyril's comment: there is a conversion to attenuation
> with tif images, see
> http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html
> ****
>
> It assumes that the maximum possible value is I0. You can check the result
> with
> rtkprojections -p. -r .*.tif -o proj.mha****
>
> I think that the problem is that you don't define the position of your
> rotation center with the --proj_iso_x and --proj_iso_y options in
> rtksimulatedgeometry. If you don't set those, the rotation center on the
> projection image is assumed to be the point of coordinate (0,0), i.e., the
> first pixel of the image with tif images. The two above-mentioned options
> allow to translate this point.
> Simon****
>
> ** **
>
> On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL <Cyril.Mory at philips.com>
> wrote:****
>
> Hi Erik,
>
> Judging from the projection image you sent, you seem to be missing a
> crucial step.
>
> The area around your water cylinder is white and the cylinder itself is
> black. This is the raw data you obtain from a scanner. It is (more or less)
> the power received by each
> pixel of the detector. Before you backproject this, you have to convert it
> to attenuations.
>
> Check out the Wikipedia page
> http://en.wikipedia.org/wiki/Tomographic_reconstruction.
> Currently your images represent I, and you have to extract p. Only then
> can you hope to get something coherent from an FDK reconstruction.
>
> Best regards,
> Cyril
>
> -----Message d'origine-----
> De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org]
> De la part de emaddox at planet.nl
> Envoyé : lundi 26 août 2013 11:48
> À : rtk-users at openrtk.org
> Objet : [Rtk-users] how can I get a good 3d image?****
>
>
> Hi,
>
> I tried to reconstruct with RTK an example CT data set of a water phantom
> but so far no success.
> I carefully checked all hints on the website and looked to the examples
> which I could  run on my system.
>
> My data is acquired in a cone beam CT system.
>
> My projections are tif images, 103 images each rotated by 1.98 degree
> steps.
> The images are 640 by 512 pixels.
>
> Distances: source to detector is 255 mm, source to centre object is 200 mm
>
> commands I used:
>
> rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o
> geometry.xml
>
> rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169
>
> (I tried --dimension with single slice and all slices (640))
>
> my projections:
>
> http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb)
>
> can someone tell me if I can (and how to) get a good reconstruction with
> RTK of this water phantom?
>
> Kind regards,
> Erik Maddox.
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> ** **
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