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

[MORY, CYRIL]

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<mailto: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> [mailto:rtk-users-bounces at openrtk.org<mailto:rtk-users-bounces at openrtk.org>] De la part de emaddox at planet.nl<mailto:emaddox at planet.nl>
Envoyé : lundi 26 août 2013 11:48
À : rtk-users at openrtk.org<mailto: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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