[Rtk-users] Question about the geometry

[Chao Wu]

Hi Arvid,

Since you know how important a correct geometry is, you should understand
why you need projection origin and spacing.
CT geometry has more parameters than sid and sdd. How big the detector
pixel size (spacing) and how the detector is places w.r.t. the central ray
(origin) also play a role in the geometry. And in-plane/out-of-plane
rotations etc.
In your dataset the correct spacing and origin information is not stored
correctly in the projection data, so the total geometry is wrong.

I have tested your data with the following command line and it gives
meaningful image. The newspacing and neworigin arguments force rtkfdk to
accept spacing and origin information of projections from command line
instead of from the data. Also I change the spacing of the volume from 2 to
0.2 because your object is small.

rtkfdk -p c:\Work\out_dir\ -r cylinder-a.mha -o
c:\Work\out_dir\cylinder_a_recon.mha
-g c:\Work\out_dir\geometry_real.xml --spacing=0.2 --dimension=256
 --newspacing=0.2 --neworigin=-20,-20

Apparently there is still some misalignment between this guessed geometry
and the real geometry, which you need to figure out with your own hardware.

Regards,
Chao


2015-10-16 13:15 GMT+02:00 Arvid Piehl Lauritsen Böttiger <
bottiger at gmail.com>:

> Hi Chao.
>
> Thank you for the reply. However, I'm not quite sure what you mean by
> origin and spacing.
> A pixel on the detector is ~200 microns, and the sample is magnified
> around 1.3 times.
>
> I do understand that having a correct geometry is important to get an
> output image with correct dimensions, but I do not understand it's so
> difficult for me to make a single successful reconstruction (possibly
> with a dummy geometry).
>
> best
>
> Arvid
>
> PS: Just to validate the data I'm testing on I installed Octave and
> created a sinogram I then ran through its iradon implementation. It
> seemed to work quite nicely (see attachments).
>
> On Fri, Oct 16, 2015 at 12:09 PM, Chao Wu <wuchao04 at gmail.com> wrote:
> > Hi Arvid,
> >
> > Is the origin and spacing of your projection data correct? What is your
> > projection pixel size?
> >
> > Regards, Chao
> >
> > 2015-10-16 9:12 GMT+02:00 Arvid Piehl Lauritsen Böttiger
> > <bottiger at gmail.com>:
> >>
> >> Dear all. Hello again.
> >>
> >> I writing to you again because I need some help to understand how to
> >> declare the geometry of the system.
> >>
> >> Cyril redirected me towards this document (
> >> http://www.creatis.insa-lyon.fr/~srit/geometry.pdf ) which helped a
> >> lot, but unfortunately it has not been enough to make me reconstruct a
> >> tomogram.
> >>
> >> I have attached a drawing of my setup (setup.jpg). The
> >> source-to-detector distance is around 1600 mm. I just rotate the
> >> sample instead of the source, and the sample-detector distance is 15
> >> cm which makes the isocenter distance 1450. The field of view is
> >> around 2 cm.
> >>
> >> The aligned projections are located here:
> >> https://www.dropbox.com/s/ycg41qkeym61kec/cylinder-a.mha?dl=0
> >> and the raw tiffs are here:
> >> https://www.dropbox.com/s/hb67pkueyb3zcc3/tiffs.zip?dl=0
> >>
> >> I would say the input data looks as nice, but when reconstructing I'm
> >> still just getting noise:
> >>
> >> This is how I perform my "reconstruction"
> >>
> >> # 361 projections from 0 to 360 degrees. The source-detector distance
> >> is 1.6 m and the
> >> # sample-detector distance is 15 cm
> >> # I have tried with many variations of --ssd and --sid but I think
> >> they all look the same
> >> rtksimulatedgeometry.exe -f 0 -n 361 -a 360 --sdd 1600 --sid 1450 -o
> >> c:\Work\out_dir\geometry_real.xml
> >>
> >> # make a mha file out of the tiff files
> >> rtkprojections.exe --path c:\Work\tomography_data\tiffs\ --output
> >> c:\Work\out_dir\cylinder-a.mha --regexp .tif
> >>
> >> # "Reconstruct" the data.
> >> rtkfdk.exe -p c:\Work\out_dir\ -r cylinder-a.mha -o
> >> c:\Work\out_dir\cylinder_a_recon.mha -g
> >> c:\Work\out_dir\geometry_real.xml --spacing 2 --dimension 256
> >>
> >> The result can be viewed in the recon_result.PNG attachment.
> >> The reconstrcution can be found here:
> >> https://www.dropbox.com/s/cbwwnbbzvhqiyvy/cylinder_a_recon.mha?dl=0
> >>
> >> Can someone please help me what I am doing wrong?
> >>
> >> best
> >>
> >> Arvid
> >>
> >> _______________________________________________
> >> Rtk-users mailing list
> >> Rtk-users at public.kitware.com
> >> http://public.kitware.com/mailman/listinfo/rtk-users
> >>
> >
>
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