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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 Matt,<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 so much for your advice.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Recently I have revisited this project and tried to compile ITK with those options on as you suggested.<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 tried to use the up-to-date version of FFTW (3.3.4), but it seems that it doesn’t work with RTK. <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>There were some link errors like: <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:black'>rtkextractshroudsignal.obj : error LNK2019: unresolved external symbol __imp_fftw_execute referenced in function "protected: virtual void __cdecl itk::FFTWComplexToComplexFFTImageFilter<class itk::Image<class std::complex<double>,1> >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@?<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'>May I ask you which version of fftw you are successfully using in which system(Windows or Linux)?<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><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><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'> Matthew J. Riblett [mailto:riblettmj@mymail.vcu.edu] <br><b>Sent:</b> Friday, September 18, 2015 6:56 PM<br><b>To:</b> Yang K Park <theday79@gmail.com><br><b>Subject:</b> Re: [Rtk-users] Generating signal data from Amsterdam Shroud<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Yang,<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>One ITK requirement of the new RTK version is the inclusion of the Fast Fourier Transform components. This requires compilation with the ITK_USE_FFTWF and the<o:p></o:p></p></div><p class=MsoNormal>ITK_USE_FFTWD options. I know, I didn’t compile that way initially, and it took a little bit of time to figure out.<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal>Hope that helps,<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>— Matt<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p><div><div><div><p class=MsoNormal><span style='color:black'>__<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'>Matthew J. Riblett<br>Virginia Commonwealth University<br>Department of Radiation Oncology<br>Medical Physics Graduate Program<br><br>Office: Sanger Hall, Room B1-013<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'>401 College Street | P.O. Box 980058<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'>Richmond, Virginia 23298<br><br>VCU Email:<span class=apple-tab-span> </span> <a href="mailto:riblettmj@vcu.edu">riblettmj@vcu.edu</a><br>MCV Office Phone:<span class=apple-tab-span> </span> +1.804.628.4858<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div></div></div><p class=MsoNormal><o:p> </o:p></p><div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal>On Sep 18, 2015, at 4:55 PM, Yang K Park <<a href="mailto:theday79@gmail.com">theday79@gmail.com</a>> wrote:<o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Hi Matt,</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>That sounds great! I really appreciate your advice.</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>I’m now compiling itk-4.8 to use that feature since I’ve found my itk version is a bit obsolete (4.4).</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Thanks!</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Yang</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p></div><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><div><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>From:</span></b><span class=apple-converted-space><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> </span></span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Matthew J. Riblett [<a href="mailto:riblettmj@mymail.vcu.edu">mailto:riblettmj@mymail.vcu.edu</a>]<span class=apple-converted-space> </span><br><b>Sent:</b><span class=apple-converted-space> </span>Friday, September 18, 2015 4:31 PM<br><b>To:</b><span class=apple-converted-space> </span>Yang K Park <<a href="mailto:theday79@gmail.com">theday79@gmail.com</a>><br><b>Subject:</b><span class=apple-converted-space> </span>Re: [Rtk-users] Generating signal data from Amsterdam Shroud</span><o:p></o:p></p></div></div></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal>Hi Yang,<o:p></o:p></p></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal>Nice to hear from you! I have had some success since my initial posting – in fact I’m currently working on a new method for accomplishing this task in certain challenging cases.<o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal>The most recent version of RTK provides an update to the rtkextractshroudsignal application which provides a phase signal output when called using the ‘-p’ flag at runtime:<o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal><b><i>rtkextractshroudsignal -i shroud.mhd -o raw_signal.txt -p phase_signal.txt --method LINEAR_BETWEEN_MINIMA</i></b><o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal>From what I’ve experienced, this generally provides a good signal [0,1) characterizing the respiratory phase using the default settings. Occasionally, I’ve run into issues where the default ‘unsharpness’ parameter needs to be adjusted to give a clear signal (by appending the<span class=apple-converted-space> </span><b>--unsharp ##</b><span class=apple-converted-space> </span>flag to the command). On more challenging shroud images – notably, those with little detectable signal from background – additional contrast-enhancement by pre-processing of the shroud has assisted in signal extraction.<o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal>I hope that helps – and please let me know how it works out for you.<o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal>— Matt<o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><div><div><div><p class=MsoNormal>__<o:p></o:p></p></div></div><div><div><p class=MsoNormal>Matthew J. Riblett<br>Virginia Commonwealth University<br>Department of Radiation Oncology<br>Medical Physics Graduate Program<br><br>Office: Sanger Hall, Room B1-013<o:p></o:p></p></div></div><div><div><p class=MsoNormal>401 College Street | P.O. Box 980058<o:p></o:p></p></div></div><div><div><p class=MsoNormal>Richmond, Virginia 23298<br><br>VCU Email:<span class=apple-tab-span> </span><span class=apple-converted-space> </span> <a href="mailto:riblettmj@vcu.edu"><span style='color:purple'>riblettmj@vcu.edu</span></a><br>MCV Office Phone:<span class=apple-tab-span> </span><span class=apple-converted-space> </span> +1.804.628.4858<o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><div><p class=MsoNormal>On Sep 18, 2015, at 4:12 PM, Yang K Park <<a href="mailto:theday79@gmail.com"><span style='color:purple'>theday79@gmail.com</span></a>> wrote:<o:p></o:p></p></div></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Hi Matthew,</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Hello, I found you in the RTK-thread.</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Recently, I’ve encountered exactly same issue and it would be highly appreciated if you can share with me your updates on this issue.</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Thanks.<span class=apple-converted-space> </span></span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Yang</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>_______________________________________________</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Yang-Kyun Park, Ph.D., DABR</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Assistant physicist & Instructor</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Department of Radiation Oncology</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Massachusetts General Hospital & Harvard Medical School</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>55 Fruit Street, Boston, MA 02114</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Tel: +1-617-726-0186</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Fax: +1-617-726-3603</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>From:</span></b><span class=apple-converted-space><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> </span></span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Rtk-users [<a href="mailto:rtk-users-bounces@public.kitware.com"><span style='color:purple'>mailto:rtk-users-bounces@public.kitware.com</span></a>]<span class=apple-converted-space> </span><b>On Behalf Of<span class=apple-converted-space> </span></b>Joel Beaudry<br><b>Sent:</b><span class=apple-converted-space> </span>Tuesday, March 17, 2015 5:25 PM<br><b>To:</b><span class=apple-converted-space> </span>Matthew J. Riblett <<a href="mailto:riblettmj@mymail.vcu.edu"><span style='color:purple'>riblettmj@mymail.vcu.edu</span></a>><br><b>Cc:</b><span class=apple-converted-space> </span><a href="mailto:rtk-users@public.kitware.com"><span style='color:purple'>rtk-users@public.kitware.com</span></a><br><b>Subject:</b><span class=apple-converted-space> </span>Re: [Rtk-users] Generating signal data from Amsterdam Shroud</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><div><div><p class=MsoNormal style='margin-bottom:12.0pt'>Hi Matthew,<span class=apple-converted-space> </span><o:p></o:p></p></div><p class=MsoNormal style='margin-bottom:12.0pt'>I'm not sure of what was used in the Matlab script, but I've had good success with using a Hilbert function in python (scipy). I'm sure that Matlab has an equivalent function, and maybe that is what was used?<span class=apple-converted-space> </span><o:p></o:p></p></div><div><div><p class=MsoNormal>Hope that helps,<o:p></o:p></p></div></div></div><div><div><p class=MsoNormal>Joel<o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><div><p class=MsoNormal>On Wed, Mar 11, 2015 at 2:40 PM, Matthew J. Riblett <<a href="mailto:riblettmj@mymail.vcu.edu" target="_blank"><span style='color:purple'>riblettmj@mymail.vcu.edu</span></a>> wrote:<o:p></o:p></p></div></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0in;margin-bottom:5.0pt'><div><div><div><p class=MsoNormal>Hello fellow RTK users,<o:p></o:p></p></div></div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal>I was wondering if anyone has a straightforward method of going from the results of the rtkamsterdamshroud and rtkextractshroudsignal applications to a [0,1) phase signal for performing motion-compensated reconstruction. I’ve been following along with the MC-CBCT Reconstruction example (<a href="http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction" target="_blank"><span style='color:purple'>http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction</span></a>), and there is an indication that Matlab is used to process the should signal prior to feeding it back into the reconstruction application, but there is no mention of how this is accomplished. I’m trying to implement this into an automated workflow and I’d love to know how this was accomplished.<o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal>Thanks!<o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal>— Matt<o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><div><div><div><p class=MsoNormal>__<o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal>Matthew J. Riblett<br>Virginia Commonwealth University<br>Department of Radiation Oncology<br>Medical Physics Graduate Program<br><br>Office: Sanger Hall, Room B1-013<o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal>401 College Street | P.O. Box 980058<o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal>Richmond, Virginia 23298<br><br>VCU Email: <a href="mailto:riblettmj@vcu.edu" target="_blank"><span style='color:purple'>riblettmj@vcu.edu</span></a><br>MCV Office Phone: <a href="tel:%2B1.804.628.4858" target="_blank"><span style='color:purple'>+1.804.628.4858</span></a><o:p></o:p></p></div></div></div></div></div><div><div><p class=MsoNormal> <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"><span style='color:purple'>Rtk-users@public.kitware.com</span></a><br><a href="http://public.kitware.com/mailman/listinfo/rtk-users" target="_blank"><span style='color:purple'>http://public.kitware.com/mailman/listinfo/rtk-users</span></a><o:p></o:p></p></blockquote></div></div></div></blockquote></div></div></div></blockquote></div><p class=MsoNormal><o:p> </o:p></p></div></div></body></html>