<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:dt="uuid:C2F41010-65B3-11d1-A29F-00AA00C14882" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:"Malgun Gothic";
panose-1:2 11 5 3 2 0 0 2 0 4;}
@font-face
{font-family:"Calibri Light";
panose-1:2 15 3 2 2 2 4 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:"\@Malgun Gothic";
panose-1:2 11 5 3 2 0 0 2 0 4;}
@font-face
{font-family:Consolas;
panose-1:2 11 6 9 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman",serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p
{mso-style-priority:99;
mso-margin-top-alt:auto;
margin-right:0in;
mso-margin-bottom-alt:auto;
margin-left:0in;
font-size:12.0pt;
font-family:"Times New Roman",serif;}
pre
{mso-style-priority:99;
mso-style-link:"HTML Preformatted Char";
margin:0in;
margin-bottom:.0001pt;
font-size:10.0pt;
font-family:"Courier New";}
span.HTMLPreformattedChar
{mso-style-name:"HTML Preformatted Char";
mso-style-priority:99;
mso-style-link:"HTML Preformatted";
font-family:Consolas;}
span.EmailStyle20
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri",sans-serif;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</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'>I’ve just tried to build it without FFTW library, as you have asked.<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 have encountered an error as shown in the attached pictures in running “rtkextractshroudsignal” application.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>It seems that ITK_FFT cannot find the peak signals successfully, making FFTW mandatory.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>(I guess Matt had experienced same issue in Linux environment.)<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'>Hope it helps.<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><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> Monday, October 05, 2015 1:45 AM<br><b>To:</b> Yang K Park <theday79@gmail.com><br><b>Cc:</b> Cyril Mory <cyril.mory@uclouvain.be>; 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><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>Thanks a lot Yang for the detailed report, I'm sure that will be helpful to many people. For my personal information, did you try to compile FFTW from ITK as well? If it didn't work, could you let us know what was the problem?<o:p></o:p></p></div><p class=MsoNormal>Simon<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div></div><div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>On Thu, Oct 1, 2015 at 11:33 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='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Hi Cyril,</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Thanks a lot for your advices.</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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.</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Following is the final version of my instruction.</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;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='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;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='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>p.s. To RTK developers</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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.</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></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]</span><o:p></o:p></p><p style='margin:0in;margin-bottom:.0001pt'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:black'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'><System used for this test></span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>- Windows 7 64 bit</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>- Visual Studio 2013</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>- Cmake 3.1.0</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>- ITK 4.8.0</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>- CUDA v6.5</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>- RTK: Up-to-date (revision: 3346)</span><o:p></o:p></p><p style='margin:0in;margin-bottom:.0001pt'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:black'> </span><o:p></o:p></p><p style='margin:0in;margin-bottom:.0001pt'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:black'><Procedures></span><o:p></o:p></p><p style='margin:0in;margin-bottom:.0001pt'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:black'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:27.0pt;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>1.</span><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Prepare fftw library files</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.75in;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>a.</span><span style='font-size:7.0pt'> </span><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" target="_blank"><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>http://www.fftw.org/install/windows.html</span></a><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.75in;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>b.</span><span style='font-size:7.0pt'> </span><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)</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.75in;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>c.</span><span style='font-size:7.0pt'> </span><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)</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.75in;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>d.</span><span style='font-size:7.0pt'> </span><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</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.75in;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>e.</span><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Convert *.def files to *.lib files by typing following commands.</span><o:p></o:p></p><p style='mso-margin-top-alt:5.0pt;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)</span><o:p></o:p></p><p style='mso-margin-top-alt:5.0pt;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> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:27.0pt;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>2.</span><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Cmake for ITK</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.75in;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>a.</span><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Configure</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.75in;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>b.</span><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Turn on the following and reconfigure</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:81.0pt;vertical-align:middle'><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>i.</span><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>ITK_USE_SYSTEM_FFTW (mandatory to make the following options appear)</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.75in;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>c.</span><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Set proper paths for FFTW_INCLUDE_PATH, FFTWD_LIB and FFTW_LIB values</span><o:p></o:p></p><p style='mso-margin-top-alt:5.0pt;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.)</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:81.0pt;vertical-align:middle'><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>i.</span><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>FFTW_INCLUDE_PATH = H:/lib/FFTW/fftw-3.3.4-dll64</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:81.0pt;vertical-align:middle'><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>ii.</span><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>FFTWD_LIB = H:/lib/FFTW/fftw-3.3.4-dll64/libfftw3-3.lib</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:81.0pt;vertical-align:middle'><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>iii.</span><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>FFTWF_LIB = H:/lib/FFTW/fftw-3.3.4-dll64/libfftw3f-3.lib</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:81.0pt;vertical-align:middle'><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>iv.</span><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>FFTWD_THREADS_LIB and FFTWF_THREAD_LIB may remain blank.</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.75in;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>d.</span><span style='font-size:7.0pt'> </span><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</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.75in;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>e.</span><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Reconfigure, Generate</span><o:p></o:p></p><p style='mso-margin-top-alt:5.0pt;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'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:27.0pt;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>3.</span><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Build ITK with Visual Studio</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.75in;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>a.</span><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>In both Debug and Release</span><o:p></o:p></p><p style='mso-margin-top-alt:5.0pt;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'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:27.0pt;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>4.</span><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Cmake for RTK</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.75in;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>a.</span><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Default settings were used.</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.75in;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>b.</span><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>"BUILD_SHARED_LIBS" can be turned off (no effect on FFTW)</span><o:p></o:p></p><p style='margin:0in;margin-bottom:.0001pt'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:black'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:27.0pt;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>5.</span><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Build RTK using Visual Studio</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:27.0pt;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>6.</span><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Copy dll files to RTK bin folders</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.75in;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>a.</span><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Which files?: libfftw3-3.dll, libfftw3f-3.dll</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.75in;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>b.</span><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>To where?: (~RTK)\bin\Release and (~RTK)\bin\Debug</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.75in;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>c.</span><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:27.0pt;vertical-align:middle'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>7.</span><span style='font-size:7.0pt'> </span><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Build RTK with Visual Studio</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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'> Cyril Mory [mailto:<a href="mailto:cyril.mory@uclouvain.be" target="_blank">cyril.mory@uclouvain.be</a>] <br><b>Sent:</b> Thursday, October 01, 2015 4:02 AM<br><b>To:</b> Yang K Park <<a href="mailto:theday79@gmail.com" target="_blank">theday79@gmail.com</a>>; 'Matthew J. Riblett' <<a href="mailto:riblettmj@mymail.vcu.edu" target="_blank">riblettmj@mymail.vcu.edu</a>>; <a href="mailto:rtk-users@public.kitware.com" target="_blank">rtk-users@public.kitware.com</a></span><o:p></o:p></p><div><div><p class=MsoNormal><br><b>Subject:</b> Re: [Rtk-users] Generating signal data from Amsterdam Shroud<o:p></o:p></p></div></div></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'>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" target="_blank">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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Hi Matt,</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;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='font-size:11.0pt;font-family:"Calibri",sans-serif'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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" target="_blank">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" target="_blank"><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 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><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Hope this helps,<o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>— Matt<o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>__<o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>401 College Street | P.O. Box 980058<o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Richmond, Virginia 23298<br><br>VCU Email: <a href="mailto:riblettmj@vcu.edu" target="_blank">riblettmj@vcu.edu</a><br>MCV Office Phone: <a href="tel:%2B1.804.628.4858" target="_blank">+1.804.628.4858</a><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></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>On Sep 30, 2015, at 4:44 PM, Yang K Park <<a href="mailto:theday79@gmail.com" target="_blank">theday79@gmail.com</a>> wrote:<o:p></o:p></p></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>There were some link errors like: </span><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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" target="_blank">mailto:riblettmj@mymail.vcu.edu</a>] <br><b>Sent:</b> Friday, September 18, 2015 6:56 PM<br><b>To:</b> Yang K Park <<a href="mailto:theday79@gmail.com" target="_blank">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></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><div><div><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='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Hope that helps,<o:p></o:p></p></div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>— Matt<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></div><div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>__<o:p></o:p></p></div></div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>401 College Street | P.O. Box 980058<o:p></o:p></p></div></div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>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">+1.804.628.4858</a><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></div></div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div></div></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>On Sep 18, 2015, at 4:55 PM, Yang K Park <<a href="mailto:theday79@gmail.com" target="_blank"><span style='color:purple'>theday79@gmail.com</span></a>> wrote:<o:p></o:p></p></div></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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" target="_blank"><span style='color:purple'>mailto:riblettmj@mymail.vcu.edu</span></a>] <br><b>Sent:</b> Friday, September 18, 2015 4:31 PM<br><b>To:</b> Yang K Park <<a href="mailto:theday79@gmail.com" target="_blank"><span style='color:purple'>theday79@gmail.com</span></a>><br><b>Subject:</b> Re: [Rtk-users] Generating signal data from Amsterdam Shroud</span><o:p></o:p></p></div></div></div></div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Hi Yang,<o:p></o:p></p></div></div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>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 <b>--unsharp ##</b> 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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>— Matt<o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div></div><div><div><div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>__<o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>401 College Street | P.O. Box 980058<o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>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">+1.804.628.4858</a><o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div></div></div></div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div><div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>On Sep 18, 2015, at 4:12 PM, Yang K Park <<a href="mailto:theday79@gmail.com" target="_blank"><span style='color:purple'>theday79@gmail.com</span></a>> wrote:<o:p></o:p></p></div></div></div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div><div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Thanks. </span><o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Tel: <a href="tel:%2B1-617-726-0186" target="_blank">+1-617-726-0186</a></span><o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Fax: <a href="tel:%2B1-617-726-3603" target="_blank">+1-617-726-3603</a></span><o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><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'> Rtk-users [<a href="mailto:rtk-users-bounces@public.kitware.com" target="_blank"><span style='color:purple'>mailto:rtk-users-bounces@public.kitware.com</span></a>] <b>On Behalf Of </b>Joel Beaudry<br><b>Sent:</b> Tuesday, March 17, 2015 5:25 PM<br><b>To:</b> Matthew J. Riblett <<a href="mailto:riblettmj@mymail.vcu.edu" target="_blank"><span style='color:purple'>riblettmj@mymail.vcu.edu</span></a>><br><b>Cc:</b> <a href="mailto:rtk-users@public.kitware.com" target="_blank"><span style='color:purple'>rtk-users@public.kitware.com</span></a><br><b>Subject:</b> Re: [Rtk-users] Generating signal data from Amsterdam Shroud</span><o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div></div><div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'>Hi Matthew, <o:p></o:p></p></div><p class=MsoNormal style='mso-margin-top-alt:auto;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? <o:p></o:p></p></div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Hope that helps,<o:p></o:p></p></div></div></div></div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Joel<o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div></div><div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Hello fellow RTK users,<o:p></o:p></p></div></div></div><div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Thanks!<o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>— Matt<o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div></div><div><div><div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>__<o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>401 College Street | P.O. Box 980058<o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div></div></div></div><p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'><br>_______________________________________________<br>Rtk-users mailing list<br><a href="mailto:Rtk-users@public.kitware.com" target="_blank"><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 style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div><p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'><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" target="_blank">Rtk-users@public.kitware.com</a><o:p></o:p></pre><pre><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></pre></blockquote><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <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>