[Rtk-users] Rtkfdk Geometry Question

[Ali Yazdanpanah]

Simon,
Thank you. I think now I understand how the whole geometry is defined in
RTK. The projection is based on one experiment I am doing using different
simulation techniques.
Again thank you for your help.
Best,
Ali

On Wed, Jul 8, 2015 at 11:23 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> 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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>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
>>
>
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