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Hi Simon,</div>
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Do we need to read the raw projections or the sinogram images? Currently, we are reading the sinogram images and the air is at 0. Can you confirm which one we are supposed to load in? We have only tried loading in the sinogram images.</div>
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If this is not the problem, any other suggestions to reconstruct the images?</div>
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Are there also other projections readers in RTK that we could use instead of ProjectionsReader?</div>
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Raw projection:</div>
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<img style="max-width:100%" class="ContentPasted1 w-512 h-512" size="352863" contenttype="image/png" data-outlook-trace="F:1|T:1" src="cid:cb2c9fb4-772c-4a11-bc86-02cfffdcbd5f"><br>
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Sinogram</div>
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<img style="max-width:100%" class="ContentPasted0 w-2722 h-2704" size="2030291" contenttype="image/png" data-outlook-trace="F:1|T:1" src="cid:060efe66-4246-4d75-9427-0c0bbf1b519f"><br>
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Thanks,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="elementToProof">
Keven</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Simon Rit <simon.rit@creatis.insa-lyon.fr><br>
<b>Sent:</b> Tuesday, January 24, 2023 12:14 AM<br>
<b>To:</b> Keven Qiu <keven.qiu@ucalgary.ca><br>
<b>Cc:</b> Tadiwa Waungana <tadiwa.waungana@ucalgary.ca>; rtk-users@openrtk.org <rtk-users@openrtk.org><br>
<b>Subject:</b> Re: Cone Beam Reconstruction using Open RTK</font>
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<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>
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<div dir="ltr" class="x_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>
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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>
<div><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255)"><br>
</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)">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>
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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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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>
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Keven Q</div>
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