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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Hi Simon,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Thank you very much for your suggestion.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>I’ve finally figured out that any conversion (btw. short and float) could be used as long as same equation is applied to both FDK and forward projection.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>I’ve tested orthodox way of conversion (HU =(mu – mu_w) / mu_w * 1000) by using a nominal mu_w value (= 0.027 mm-1) and I could get same FDK results as original CT image. (Of course, the previous “custom” formula is also working)<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>However, I’d better go for the previous one, since the orthodox way is generating very low intensity for my CT image, where I have very small room to process.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Thanks!<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Yang<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>From:</span></b><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> simon.rit@gmail.com [mailto:simon.rit@gmail.com] <b>On Behalf Of </b>Simon Rit<br><b>Sent:</b> Tuesday, March 03, 2015 10:57 AM<br><b>To:</b> Yang K Park<br><b>Cc:</b> Rune Slot Thing; rtk-users@openrtk.org<br><b>Subject:</b> Re: [Rtk-users] Obtaining HU number from RTK float data after CBCT reconstruction<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>Yes, what you've suggested before is fine but the 1/65536 and 65536 multiplications could be avoided. If you really want to do something in physical units, you need to convert hu to linear attenuation which requires the knowledge of the linear attenuation of water.<o:p></o:p></p></div><p class=MsoNormal>Simon<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>On Tue, Mar 3, 2015 at 3:34 PM, Yang K Park <<a href="mailto:theday79@gmail.com" target="_blank">theday79@gmail.com</a>> wrote:<o:p></o:p></p><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in'><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'>Hi Rune, </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'>That is a great tip. Thank you so much. (We’ve recently installed XVI5.0 so I’m better off trying to use that new feature.)</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'>My remaining question is, then, when you guys do a forward projection for clinical CT images (singed short) using rtk, which pre-processing do you do?</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'>I think some “short to float” conversion is needed and that conversion formula should be also working with FDK to restore the CT image with same HU values.</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'>Thanks.</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'>Yang</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'> </span><o:p></o:p></p><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b>From:</b> Rune Slot Thing [mailto:<a href="mailto:Rune.Slot.Thing@rsyd.dk" target="_blank">Rune.Slot.Thing@rsyd.dk</a>] <br><b>Sent:</b> Tuesday, March 03, 2015 3:29 AM<br><b>To:</b> 'Yang K Park'; <a href="mailto:rtk-users@openrtk.org" target="_blank">rtk-users@openrtk.org</a><br><b>Subject:</b> SV: [Rtk-users] Obtaining HU number from RTK float data after CBCT reconstruction<o:p></o:p></p></div></div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=DA style='color:#1F497D'>Hi Yang,</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=DA style='color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'>The short answer to your question is that the projection images you acquire on an Elekta CBCT unit are not normalized properly. If you perform the same scan with two different exposures (e.g. double the mAs value), you will get different projection images and hence different grey values in the reconstructed images, regardless of whether you use the XVI reconstruction or RTK. Since the Elekta system does not record your unattenuated signal anywhere, it is not possible to do the proper I/I_0 normalization that you need in order to get to the attenuation coefficients required for the HU definition, and hence you cannot get to proper HU values from the projection images alone. Due to detector drift and all the different sources of artefacts in CBCT imaging, it is a non-trivial problem to get this normalization right.</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'>With the latest release of the Elekta XVI 5.0 software, there is some calibration added on the software side to allow a pseudo-HU calibration of the CBCT grey values. Since we do not have the software in our clinic yet, I have not investigated how exactly this is incorporated. My guess is that it is more of an empirical mapping which works well on objects of similar size, shape and composition as the calibration phantom used, than it is a proper calibration of all projection images to the open field images that would give the correct normalization.</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'> </span><o:p></o:p></p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'>Hope this helps – otherwise feel free to ask again.</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'>Best regards,</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'>Rune Slot Thing</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'>PhD Student</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'>Institute of Clinical Research, University of Southern Denmark</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='color:#1F497D'>Laboratory of Radiation Physics, Odense University Hospital</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=DA style='color:#1F497D'><a href="mailto:rune.slot.thing@rsyd.dk" target="_blank">rune.slot.thing@rsyd.dk</a></span><o:p></o:p></p></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=DA style='color:#1F497D'> </span><o:p></o:p></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><span lang=DA style='font-size:10.0pt;font-family:"Tahoma",sans-serif'>Fra:</span></b><span lang=DA style='font-size:10.0pt;font-family:"Tahoma",sans-serif'> Rtk-users [<a href="mailto:rtk-users-bounces@public.kitware.com" target="_blank">mailto:rtk-users-bounces@public.kitware.com</a>] <b>På vegne af </b>Yang K Park<span style='color:#1F497D'> </span><br><b>Sendt:</b> 3. marts 2015 02:05<br><b>Til:</b> <a href="mailto:rtk-users@openrtk.org" target="_blank">rtk-users@openrtk.org</a><br><b>Emne:</b> [Rtk-users] Obtaining HU number from RTK float data after CBCT reconstruction</span><o:p></o:p></p></div></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span lang=DA> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Hi RTK users,<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>This could be a class question but I couldn’t have any chance to ask it so far.<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>After the RTK reconstruction, I can get float values for each voxel which might be linear attenuation coefficients (µ [mm-1]) coming from logarithm calculation.<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>In my experience, this value is quite different from that of helical CT.<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>For example, µ for water ~= 0.015 [mm-1] in RTK (measured in regions without scatter artifacts) <i>vs</i> ~0.027 [mm-1] in CT. And that µ value is also affected by mAs value as well.<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>My goal is to convert that float value to HU number with a reasonable explanation. <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>In our Elekta system, they seem to convert those float values to their own CBCT number ranging from “0-65535” by using a following formula:<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-indent:.5in'>Elekta CBCT number = µ * 65536 – 1024 (µ seems to be the float value identical to that comes from RTK reconstruction)<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>, which has no relationship to HU definition.<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>And I’m wondering why they are using the above formula instead of using classic HU definition ( HU = (µ - µ_w / µ_w)*1000). <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Of course I’m aware of that CBCT number should be quite different from CT number due to many artifact sources.<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>I’m just trying to get some physically reasonable conversion method between CBCT number to HU number.<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Thank you guys for your help in advance!<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Yang<o:p></o:p></p></div></div></div></div><p class=MsoNormal style='margin-bottom:12.0pt'><br>_______________________________________________<br>Rtk-users mailing list<br><a href="mailto:Rtk-users@public.kitware.com">Rtk-users@public.kitware.com</a><br><a href="http://public.kitware.com/mailman/listinfo/rtk-users" target="_blank">http://public.kitware.com/mailman/listinfo/rtk-users</a><o:p></o:p></p></blockquote></div><p class=MsoNormal><o:p> </o:p></p></div></div></body></html>