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</o:shapelayout></xml><![endif]--></head><body bgcolor=white 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 Cyril,<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 a lot for your advices.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Thanks to your help, I did some trials and errors and finally succeeded.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Following is the final version of my instruction.<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'>p.s. To RTK developers<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Extracting phase signal from CBCT looks beautiful and very convenient! I really like it. Thanks for your hard works on this.<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 style='margin:0in;margin-bottom:.0001pt'><span style='font-size:20.0pt;font-family:"Calibri Light",sans-serif;color:black'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:black'>[ITK/RTK compile instruction to use FFTW: For windows7 with VS2013]<o:p></o:p></span></p><p style='margin:0in;margin-bottom:.0001pt'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:black'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><System used for this test><o:p></o:p></span></p><p class=MsoNormal style='vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>- Windows 7 64 bit<o:p></o:p></span></p><p class=MsoNormal style='vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>- Visual Studio 2013<o:p></o:p></span></p><p class=MsoNormal style='vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>- Cmake 3.1.0<o:p></o:p></span></p><p class=MsoNormal style='vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>- ITK 4.8.0<o:p></o:p></span></p><p class=MsoNormal style='vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>- CUDA v6.5<o:p></o:p></span></p><p class=MsoNormal style='vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>- RTK: Up-to-date (revision: 3346)<o:p></o:p></span></p><p style='margin:0in;margin-bottom:.0001pt'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:black'><o:p> </o:p></span></p><p style='margin:0in;margin-bottom:.0001pt'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:black'><Procedures><o:p></o:p></span></p><p style='margin:0in;margin-bottom:.0001pt'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:black'><o:p> </o:p></span></p><p class=MsoNormal style='margin-left:27.0pt;text-indent:-.25in;mso-list:l3 level1 lfo1;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Prepare fftw library files<o:p></o:p></span></p><p class=MsoNormal style='margin-left:.75in;text-indent:-.25in;mso-list:l3 level2 lfo2;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Download FFTW 3.3.4 from </span><a href="http://www.fftw.org/install/windows.html"><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>http://www.fftw.org/install/windows.html</span></a><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><o:p></o:p></span></p><p class=MsoNormal style='margin-left:.75in;text-indent:-.25in;mso-list:l3 level2 lfo2;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Unzip it in a proper directory (e.g. ~/lib/FFTW3.3.4/fftw-3.3.4-dll64)<o:p></o:p></span></p><p class=MsoNormal style='margin-left:.75in;text-indent:-.25in;mso-list:l3 level2 lfo2;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Find VS2013 command prompt short-cut (Start --> Program --> Visual Studio 2013 --> Tools -->VS2013 x64 Native Tools Command Prompt)<o:p></o:p></span></p><p class=MsoNormal style='margin-left:.75in;text-indent:-.25in;mso-list:l3 level2 lfo2;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Set "Start in" property of the shortcut to the directory where FFTW files are located and then run the shortcut<o:p></o:p></span></p><p class=MsoNormal style='margin-left:.75in;text-indent:-.25in;mso-list:l3 level2 lfo2;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Convert *.def files to *.lib files by typing following commands.<o:p></o:p></span></p><p style='mso-margin-top-alt:0in;margin-right:0in;margin-bottom:0in;margin-left:81.0pt;margin-bottom:.0001pt'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:black'>"lib /machine:x64 /def:libfftw3-3.def" (for double)<o:p></o:p></span></p><p style='mso-margin-top-alt:0in;margin-right:0in;margin-bottom:0in;margin-left:81.0pt;margin-bottom:.0001pt'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:black'>"lib /machine:x64 /def:libfftw3f-3.def" (for float)<br> <o:p></o:p></span></p><p class=MsoNormal style='margin-left:27.0pt;text-indent:-.25in;mso-list:l4 level1 lfo3;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Cmake for ITK<o:p></o:p></span></p><p class=MsoNormal style='margin-left:.75in;text-indent:-.25in;mso-list:l4 level2 lfo4;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Configure<o:p></o:p></span></p><p class=MsoNormal style='margin-left:.75in;text-indent:-.25in;mso-list:l4 level2 lfo4;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Turn on the following and reconfigure<o:p></o:p></span></p><p class=MsoNormal style='margin-left:81.0pt;text-indent:-81.0pt;mso-text-indent-alt:-.25in;mso-list:l4 level3 lfo5;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'><span style='font:7.0pt "Times New Roman"'> </span>i.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>ITK_USE_SYSTEM_FFTW (mandatory to make the following options appear)<o:p></o:p></span></p><p class=MsoNormal style='margin-left:.75in;text-indent:-.25in;mso-list:l4 level2 lfo5;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Set proper paths for FFTW_INCLUDE_PATH, FFTWD_LIB and FFTW_LIB values<o:p></o:p></span></p><p style='mso-margin-top-alt:0in;margin-right:0in;margin-bottom:0in;margin-left:.75in;margin-bottom:.0001pt'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:black'>e.g.)<o:p></o:p></span></p><p class=MsoNormal style='margin-left:81.0pt;text-indent:-81.0pt;mso-text-indent-alt:-.25in;mso-list:l2 level1 lfo6;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'><span style='font:7.0pt "Times New Roman"'> </span>i.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>FFTW_INCLUDE_PATH = H:/lib/FFTW/fftw-3.3.4-dll64<o:p></o:p></span></p><p class=MsoNormal style='margin-left:81.0pt;text-indent:-81.0pt;mso-text-indent-alt:-.25in;mso-list:l0 level1 lfo7;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'><span style='font:7.0pt "Times New Roman"'> </span>ii.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>FFTWD_LIB = H:/lib/FFTW/fftw-3.3.4-dll64/libfftw3-3.lib<o:p></o:p></span></p><p class=MsoNormal style='margin-left:81.0pt;text-indent:-81.0pt;mso-text-indent-alt:-.25in;mso-list:l0 level1 lfo7;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'><span style='font:7.0pt "Times New Roman"'> </span>iii.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>FFTWF_LIB = H:/lib/FFTW/fftw-3.3.4-dll64/libfftw3f-3.lib<o:p></o:p></span></p><p class=MsoNormal style='margin-left:81.0pt;text-indent:-81.0pt;mso-text-indent-alt:-.25in;mso-list:l0 level1 lfo7;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'><span style='font:7.0pt "Times New Roman"'> </span>iv.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>FFTWD_THREADS_LIB and FFTWF_THREAD_LIB may remain blank.<o:p></o:p></span></p><p class=MsoNormal style='margin-left:.75in;text-indent:-.25in;mso-list:l1 level1 lfo8;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>d.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>"BUILD_SHARED_LIBS" can be turned off (no effect on FFTW), BUILD_EXAMPLE can be turned off<o:p></o:p></span></p><p class=MsoNormal style='margin-left:.75in;text-indent:-.25in;mso-list:l1 level1 lfo8;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>e.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Reconfigure, Generate<o:p></o:p></span></p><p style='mso-margin-top-alt:0in;margin-right:0in;margin-bottom:0in;margin-left:27.0pt;margin-bottom:.0001pt'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:black'> <o:p></o:p></span></p><p class=MsoNormal style='margin-left:27.0pt;text-indent:-.25in;mso-list:l5 level1 lfo9;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Build ITK with Visual Studio<o:p></o:p></span></p><p class=MsoNormal style='margin-left:.75in;text-indent:-.25in;mso-list:l5 level2 lfo10;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>In both Debug and Release<o:p></o:p></span></p><p style='mso-margin-top-alt:0in;margin-right:0in;margin-bottom:0in;margin-left:.75in;margin-bottom:.0001pt'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:black'> <o:p></o:p></span></p><p class=MsoNormal style='margin-left:27.0pt;text-indent:-.25in;mso-list:l6 level1 lfo11;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Cmake for RTK<o:p></o:p></span></p><p class=MsoNormal style='margin-left:.75in;text-indent:-.25in;mso-list:l6 level2 lfo12;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Default settings were used.<o:p></o:p></span></p><p class=MsoNormal style='margin-left:.75in;text-indent:-.25in;mso-list:l6 level2 lfo12;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>"BUILD_SHARED_LIBS" can be turned off (no effect on FFTW)<o:p></o:p></span></p><p style='margin:0in;margin-bottom:.0001pt'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:black'> <o:p></o:p></span></p><p class=MsoNormal style='margin-left:27.0pt;text-indent:-.25in;mso-list:l7 level1 lfo13;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Build RTK using Visual Studio<o:p></o:p></span></p><p class=MsoNormal style='margin-left:27.0pt;text-indent:-.25in;mso-list:l7 level1 lfo13;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>6.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Copy dll files to RTK bin folders<o:p></o:p></span></p><p class=MsoNormal style='margin-left:.75in;text-indent:-.25in;mso-list:l7 level2 lfo14;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>a.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Which files?: libfftw3-3.dll, libfftw3f-3.dll<o:p></o:p></span></p><p class=MsoNormal style='margin-left:.75in;text-indent:-.25in;mso-list:l7 level2 lfo14;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>b.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>To where?: (~RTK)\bin\Release and (~RTK)\bin\Debug<o:p></o:p></span></p><p class=MsoNormal style='margin-left:.75in;text-indent:-.25in;mso-list:l7 level2 lfo14;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>c.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><o:p> </o:p></span></p><p class=MsoNormal style='margin-left:27.0pt;text-indent:-.25in;mso-list:l7 level1 lfo14;vertical-align:middle'><![if !supportLists]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><span style='mso-list:Ignore'>7.<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Build RTK with Visual Studio<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><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;color:windowtext'>From:</span></b><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext'> Cyril Mory [mailto:cyril.mory@uclouvain.be] <br><b>Sent:</b> Thursday, October 01, 2015 4:02 AM<br><b>To:</b> Yang K Park <theday79@gmail.com>; 'Matthew J. Riblett' <riblettmj@mymail.vcu.edu>; rtk-users@public.kitware.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><p class=MsoNormal>Hi Yang,<br><br>First, a quick explanation: ITK embeds FFTW. On linux, you just have to activate it in the CMake options. On Windows, you cannot do that. I do not have a clue why, but you cannot. You have to install FFTW separately.<br><br>Now, a solution: The quickest way is to download the precompiled DLLs from <a href="http://www.fftw.org/install/windows.html">http://www.fftw.org/install/windows.html</a><br>On that same page, follow the indications on how to create the .lib files (that is absolutely necessary). You may have to run the "lib.exe" program from the VS developer prompt instead of the standard windows cmd.exe prompt. Specify you CPU architecture explicitly, just to be sure.<br><br>Then in the CMake options of ITK, set the following:<br>FFTWF_LIB = TheRelevantFolderOnYourSystem/libfftw3f-3.lib<br>FFTW_INCLUDE_PATH = TheRelevantFolderOnYourSystem/<br><br>Let the rest of the FFTW options blank. Compile ITK, then RTK, and you should be fine. I have successfully compiled this with BUILD_SHARED_LIBS = ON (on both ITK and RTK), I don't know if it matters.<br><br>If it works for you, then you might want to play around with the other FFTW .lib files, and send on this mailing list a more complete set of CMAKE options that works. I have tried some other combinations without success, so I'd be happy to learn more.<br><br>Hope it helps,<br>Cyril<o:p></o:p></p><div><p class=MsoNormal>On 09/30/2015 11:12 PM, Yang K Park wrote:<o:p></o:p></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Hi Matt,</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Thank you so much for your help, again.</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Unfortunately, I’m using windows system (windows7 64 with VS 2013) and I guess this could be a challenging issue to me.</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Hi RTK users,</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Is there anyone who successfully compiled RTK with “ITK + FFTW” in windows system?</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>I’m just trying to use <b>rtkextractshroudsignal</b> and it seems to require FFTW library externally.</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>When I tried to use FFTW 3.3.4, I’ve encountered link errors as shown below.</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Any help will be highly appreciated.</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Yang</span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> </span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;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><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 [<a href="mailto:riblettmj@mymail.vcu.edu">mailto:riblettmj@mymail.vcu.edu</a>] <br><b>Sent:</b> Wednesday, September 30, 2015 5:01 PM<br><b>To:</b> Yang K Park <a href="mailto:theday79@gmail.com"><theday79@gmail.com></a><br><b>Subject:</b> Re: [Rtk-users] Generating signal data from Amsterdam Shroud</span><o:p></o:p></p></div></div><p class=MsoNormal> <o:p></o:p></p><p class=MsoNormal>Yang,<o:p></o:p></p><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal>I’m running on Ubuntu 14.04 LTS and used the distribution library (FFTW 3.3.3). If you’re running on a Debian-based linux system, you can also install the full development library set using the following command: <b><i>sudo apt-get install libfftw3-3 libfftw3-dev</i></b>. Then just make sure that these libraries are being used by rerunning CCMake. <o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal>I’m not quite sure about the error being thrown in your build, but perhaps one of the main developers would be able to provide some more insight into the issue.<o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal>Hope this helps,<o:p></o:p></p></div><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>__<o:p></o:p></p></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><p class=MsoNormal>401 College Street | P.O. Box 980058<o:p></o:p></p></div><div><p class=MsoNormal>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></p></div></div></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></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 30, 2015, at 4:44 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'>Thank you so much for 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'>Recently I have revisited this project and tried to compile ITK with those options on as you suggested.</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'>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.<span class=apple-converted-space> </span></span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>There were some link errors like:<span class=apple-converted-space> </span></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'>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@?</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'>May I ask you which version of fftw you are successfully using in which system(Windows or Linux)?</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><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 6:56 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><div><p class=MsoNormal>Yang,<o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><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></div><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><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><p class=MsoNormal>Hope that helps,<o:p></o:p></p></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><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 4:55 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 Matt,</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'>That sounds great! I really appreciate your advice.</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'>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><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'>Thanks!</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;color:#1F497D'> </span><o:p></o:p></p></div></div><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><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'>Matthew J. Riblett [<a href="mailto:riblettmj@mymail.vcu.edu"><span style='color:purple'>mailto:riblettmj@mymail.vcu.edu</span></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"><span style='color:purple'>theday79@gmail.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><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal>Hi Yang,<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>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><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></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><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></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><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></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><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></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><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><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:<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><div><div><p class=MsoNormal> <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><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><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><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><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><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><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><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><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><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><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><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><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><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><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><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><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><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><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><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><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><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><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><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><div><div><p class=MsoNormal> <o:p></o:p></p></div></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><div><p class=MsoNormal>Hope that helps,<o:p></o:p></p></div></div></div></div><div><div><div><p class=MsoNormal>Joel<o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></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></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><div><p class=MsoNormal>Hello fellow RTK users,<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><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><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal>Thanks!<o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal>— Matt<o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div><div><div><div><div><div><div><p class=MsoNormal>__<o:p></o:p></p></div></div></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><div><div><p class=MsoNormal>401 College Street | P.O. Box 980058<o:p></o:p></p></div></div></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><div><div><p class=MsoNormal> <o:p></o:p></p></div></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></div></div></blockquote></div><p class=MsoNormal> <o:p></o:p></p></div><p class=MsoNormal><br><br><br><o:p></o:p></p><pre>_______________________________________________<o:p></o:p></pre><pre>Rtk-users mailing list<o:p></o:p></pre><pre><a href="mailto:Rtk-users@public.kitware.com">Rtk-users@public.kitware.com</a><o:p></o:p></pre><pre><a href="http://public.kitware.com/mailman/listinfo/rtk-users">http://public.kitware.com/mailman/listinfo/rtk-users</a><o:p></o:p></pre></blockquote><p class=MsoNormal><o:p> </o:p></p></div></body></html>