[Rtk-users] Rtkfdk Geometry Question

[Simon Rit]

Hi,
We can try to help but we need to understand your geometry... Where does it
come from by the way? If I understand your geometry correctly, I would say :
- sid, sdd, nproj, arc are correct,
- voxel size is wrong. For the detector, if your detector is 7200x9200 mm2
and you have 36x100 pixels, then the pixel size is [200,92,1] (last
dimension is not used so anything). For the volume, if your volume is
5000^3 mm^3 and you have 500^3 voxels, then pixel size is [10,10,10] and
not 0.1.
- offset of projections is probably wrong. If you want to have a centered
projections, you'll need something like (-3500, -554, 0). You can set is to
0 and put those values in proj_iso_x and proj_iso_y.
Regarding mha file, you can write mha files in many ways, using SimpleRTK,
matlab or writing an ITK code.
Good luck!
Simon

On Thu, Jul 9, 2015 at 4:26 AM, Ali Yazdanpanah <ali.yazdanpanah at gmail.com>
wrote:

> Hi,
>
> I have a question from you about the CT reconstruction, I would really
> appreciate if you can help me with this.
>
> I have the geometry as described in following and I am trying to run the
> rtkfdk code from RTK.
>
>
> % parameters % % % % % % %
>
> param.nx = 500; % number of voxels
> param.ny = 500;
> param.nz = 500;
>
>
> param.sx = 5000; % mm (real size)
> param.sy = 5000; % mm
> param.sz = 5000; % mm
>
>
> %The real detector panel pixel density (number of pixels)
> param.nu = 36; % number of pixels
> param.nv = 100;
>
> % Detector setting (real size)
> param.su = 7200; % mm (real size)
> param.sv = 9200; % mm
>
>
> % X-ray source and detector setting
> param.DSD = 32900; % Distance source to detector
> param.DSO = 27400; % X-ray source to object axis distance
>
>
> % angle setting
> param.dir = +1; % gantry rotating direction (clock wise/ counter clockwise)
> param.dang = 5; % angular step size (deg)
> param.deg = 0:param.dang:360-1; % you can change
> param.deg = param.deg*param.dir;
> param.nProj = length(param.deg);
>
> param.parker = 0; % data with 360 deg -> param.parker = 0 , data less than
> 360 deg -> param.parker=1
>
> param.filter='ram-lak'; % high pass filter
>
>
> param.dx = param.sx/param.nx; % single voxel size
> param.dy = param.sy/param.ny;
> param.dz = param.sz/param.nz;
> param.du = param.su/param.nu;
> param.dv = param.sv/param.nv;
> param.off_u = 0; param.off_v = 0; % detector rotation shift (real size)
>
>
> % Geometry calculation % % %
> param.xs = [-(param.nx-1)/2:1:(param.nx-1)/2]*param.dx;
> param.ys = [-(param.ny-1)/2:1:(param.ny-1)/2]*param.dy;
> param.zs = [-(param.nz-1)/2:1:(param.nz-1)/2]*param.dz;
> param.us = (-(param.nu-1)/2:1:(param.nu-1)/2)*param.du + param.off_u;
> param.vs = (-(param.nv-1)/2:1:(param.nv-1)/2)*param.dv + param.off_v;
>
>
>
> So basically my final projection array has 36 * 100 * 72(=angles: 0 : 5 :
> 360).
> But I got confused how to set the geometry parameters in RTK
> I followed the rtkfdk tutorial but I can’t get any result using this method
>
> I did the following:
>
> 1-       Create geometry.xml using these parameters:
>
>   nproj = 72 ;
>   first_angle = 0 ;
>   arc = 360 ;
>   sid = 27400 ;
>   sdd = 32900 ;
>   proj_iso_x = 0;
>   proj_iso_y = 0;
>   out_angle = 0 ;
>   in_angle = 0 ;
>   source_x = 0;
>   source_y = 0 ;
>
> 2-       Create my own mha file (WriteMhaFile.m) from my projection array
> (36*100*72) using a matlab code with following properties:
> Voxel size = [0.1 0.1 0.1]
> Offset = [1 1 1]
>
>
> 3-       Then run the:
> rtkfdk -p . -r projections.mha -o fdk.mha -g geometry.xml --spacing 0.1
> --dimension 500
>
>
> Could you please tell me if I am setting the geometry correctly?
> Also, is there any other way to create my own mha file?
>
> Thank you in advance and looking forward to hear back from you.
>
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