<div dir="ltr"><div>Hi,</div><div>At first glance, no! The first step is indeed to check that you correctly read the projections, i.e. that your images are converted to line integrals (if needed). I would write to disk what you pass to FDK (with itk.imwrite) and check, e.g., that air is at 0.</div><div>Simon<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Jan 24, 2023 at 12:58 AM Keven Qiu <<a href="mailto:keven.qiu@ucalgary.ca">keven.qiu@ucalgary.ca</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="msg-7973956459539223703">
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<div><span style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">Hello Simon,</span></div>
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<div><span style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">We are trying to use OpenRTK to reconstruct some knee images from
cone beam CT. We have managed to run the example script in Python but haven't been able to reconstruct our knee images. We have all the geometry parameters but are still struggling to get it to work. Here is our pseudocode below:</span></div>
<div><span style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">```</span></div>
<div><span style="font-family:monospace;font-size:12pt">Load projection images from DICOM series using </span></div>
<div><span style="font-family:monospace;font-size:12pt">rtk.ProjectionsReader[ImageType] where ImageType = itk.Image[itk.F, 3]</span><br>
</div>
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</span></div>
<div><span style="font-family:monospace;font-size:12pt">We construct geometry object with SID, SDD, and gantry angle, and source offset X/Y, <span style="color:rgb(0,0,0);background-color:rgb(255,255,255);display:inline">as
well as the number of projections</span></span></div>
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</span></div>
<div><span style="font-family:monospace;font-size:12pt">We create a blank image</span></div>
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</span></div>
<div><span style="font-family:monospace;font-size:12pt">We pass the
<span style="color:rgb(0,0,0);background-color:rgb(255,255,255);display:inline">
projections</span>, blank image, and geometry into the FDK reconstruction method</span></div>
<div><span style="font-family:monospace;font-size:12pt"><br>
</span></div>
<div><span style="font-family:monospace;font-size:12pt">We then pass the projections, FDK return value from previous step and geometry into the field of view mask</span></div>
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</span></div>
<div><span style="font-family:monospace;font-size:12pt">Finally, we write the reconstructed image to file in NIfTI using rtk.ImageFileWriter[ImageType]</span></div>
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```</div>
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
We seem to be having a problem when we load any projection images instead of generating them like the FirstReconstruction example with the sphere. We get a blank image of 0's, or a grey image with a circle outline.</div>
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At first glance, is there anything we are missing?</div>
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Look forward to your response,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
Keven Q</div>
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</div></blockquote></div>