<div dir="ltr"><span style="font-size:12.8000001907349px">Simon,</span><div style="font-size:12.8000001907349px">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.</div><div style="font-size:12.8000001907349px">Again thank you for your help.</div><div style="font-size:12.8000001907349px">Best,</div><div style="font-size:12.8000001907349px">Ali </div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jul 8, 2015 at 11:23 PM, Simon Rit <span dir="ltr"><<a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank">simon.rit@creatis.insa-lyon.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div><div>Hi,<br></div>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 :<br></div>- sid, sdd, nproj, arc are correct,<br></div><div>- 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. <br></div>- 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.<br></div>Regarding mha file, you can write mha files in many ways, using SimpleRTK, matlab or writing an ITK code.<br></div><div>Good luck!<br></div>Simon<br></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="h5">On Thu, Jul 9, 2015 at 4:26 AM, Ali Yazdanpanah <span dir="ltr"><<a href="mailto:ali.yazdanpanah@gmail.com" target="_blank">ali.yazdanpanah@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div dir="ltr"><div dir="ltr"><span style="font-size:12.8000001907349px">Hi,</span><div><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px">I have a question from you about the CT reconstruction,</span><span style="font-size:12.8000001907349px"> I would really appreciate if you can help me with this.</span><br style="font-size:12.8000001907349px"><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px">I have the geometry as described in following and I am trying to run the rtkfdk code from RTK.</span><div><br></div><div><br></div><div>% parameters % % % % % % %<br></div><div><div><br></div><div>param.nx = 500; % number of voxels</div><div>param.ny = 500;</div><div><a href="http://param.nz/" target="_blank">param.nz</a> = 500;</div><div><br></div><div><br></div><div>param.sx = 5000; % mm (real size)</div><div><a href="http://param.sy/" target="_blank">param.sy</a> = 5000; % mm</div><div><a href="http://param.sz/" target="_blank">param.sz</a> = 5000; % mm</div><div><br></div><div><br></div><div>%The real detector panel pixel density (number of pixels)</div><div><a href="http://param.nu/" target="_blank">param.nu</a> = 36; % number of pixels</div><div>param.nv = 100;</div><div><br></div><div>% Detector setting (real size)<br></div><div><a href="http://param.su/" target="_blank">param.su</a> = 7200; % mm (real size)</div><div><a href="http://param.sv/" target="_blank">param.sv</a> = 9200; % mm</div><div><br></div><div><br></div><div>% X-ray source and detector setting</div><div>param.DSD = 32900; % Distance source to detector </div><div>param.DSO = 27400; % X-ray source to object axis distance</div><div><br></div><div><br></div><div>% angle setting</div><div>param.dir = +1; % gantry rotating direction (clock wise/ counter clockwise)</div><div>param.dang = 5; % angular step size (deg)</div><div>param.deg = 0:param.dang:360-1; % you can change</div><div>param.deg = param.deg*param.dir;</div><div>param.nProj = length(param.deg);</div><div><br></div><div>param.parker = 0; % data with 360 deg -> param.parker = 0 , data less than </div><div>360 deg -> param.parker=1 <br></div><div><br></div><div>param.filter='ram-lak'; % high pass filter<br></div><div><br></div><div><br></div><div>param.dx = param.sx/param.nx; % single voxel size</div><div>param.dy = <a href="http://param.sy/param.ny" target="_blank">param.sy/param.ny</a>;<br></div><div><a href="http://param.dz/" target="_blank">param.dz</a> = <a href="http://param.sz/param.nz" target="_blank">param.sz/param.nz</a>;<br></div><div>param.du = <a href="http://param.su/param.nu" target="_blank">param.su/param.nu</a>;<br></div><div>param.dv = <a href="http://param.sv/param.nv" target="_blank">param.sv/param.nv</a>;<br></div><div>param.off_u = 0; param.off_v = 0; % detector rotation shift (real size)<br></div><div><br></div><div><br></div><div>% Geometry calculation % % %</div><div>param.xs = [-(param.nx-1)/2:1:(param.nx-1)/2]*param.dx;<br></div><div>param.ys = [-(param.ny-1)/2:1:(param.ny-1)/2]*param.dy;<br></div><div>param.zs = [-(param.nz-1)/2:1:(param.nz-1)/2]*<a href="http://param.dz/" target="_blank">param.dz</a>;<br></div><div><a href="http://param.us/" target="_blank">param.us</a> = (-(param.nu-1)/2:1:(param.nu-1)/2)*param.du + param.off_u;<br></div><div>param.vs = (-(param.nv-1)/2:1:(param.nv-1)/2)*param.dv + param.off_v;<br></div></div><div><br></div><div><br></div><div><br></div><div><span style="font-size:12.8000001907349px">So basically my final projection array has 36 * 100 * 72(=angles: 0 : 5 : 360).</span><br></div><div><span style="font-size:12.8000001907349px">But I got confused how to set the geometry parameters in RTK</span><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px">I followed the rtkfdk tutorial but I can’t get any result using this method</span><br style="font-size:12.8000001907349px"><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px">I did the following:</span><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px"> </span><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px">1- Create geometry.xml using these parameters:</span><br style="font-size:12.8000001907349px"><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px"> nproj = 72 ;</span><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px"> first_angle = 0 ;</span><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px"> arc = 360 ;</span><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px"> sid = 27400 ;</span><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px"> sdd = 32900 ;</span><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px"> proj_iso_x = 0;</span><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px"> proj_iso_y = 0;</span><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px"> out_angle = 0 ;</span><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px"> in_angle = 0 ;</span><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px"> source_x = 0;</span><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px"> source_y = 0 ;</span><br style="font-size:12.8000001907349px"><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px">2- Create my own mha file (WriteMhaFile.m) from my projection array (36*100*72) using a matlab code with following properties:</span><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px">Voxel size = [0.1 0.1 0.1]</span><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px">Offset = [1 1 1]</span><br style="font-size:12.8000001907349px"><br style="font-size:12.8000001907349px"><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px">3- Then run the:</span><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px">rtkfdk -p . -r projections.mha -o fdk.mha -g geometry.xml --spacing 0.1 --dimension 500</span><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px"> </span><br style="font-size:12.8000001907349px"><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px">Could you please tell me if I am setting the geometry correctly?</span><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px">Also, is there any other way to create my own mha file?</span><br style="font-size:12.8000001907349px"><br style="font-size:12.8000001907349px"><span style="font-size:12.8000001907349px">Thank you in advance and looking forward to hear back from you.</span></div></div></div></div>
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