<div dir="ltr"><div class="gmail_default" style="font-family:'trebuchet ms',sans-serif"><font color="#0000ff">Hi Chao,</font></div><div class="gmail_default" style="font-family:'trebuchet ms',sans-serif"><font color="#0000ff">Your explanation is very clear and helpful, thanks very much, Chao :)</font></div><div class="gmail_default" style="font-family:'trebuchet ms',sans-serif"><font color="#0000ff">As for the two ways you suggested to generated a 128^3 size volume with spacing =1, i prefer the second one( i.e. <span style="font-size:14px;font-family:arial,sans-serif">first create a dimension=128 but spacing=4 image file and subsequently change the spacing from 4 to 1.)</span></font></div><div class="gmail_default" style="font-family:'trebuchet ms',sans-serif"><font color="#0000ff"><span style="font-size:14px;font-family:arial,sans-serif">But the question is after i </span><span style="font-size:14px;font-family:arial,sans-serif">first create a dimension=128 with spacing=4 image file, i got a output(That's say A.mha) . how could use the A.mha as a input to generate a volume( B.mha) with spacing as 1? what command should i use</span></font></div><div class="gmail_default" style="font-family:'trebuchet ms',sans-serif"><span style="font-size:14px;font-family:arial,sans-serif"><font color="#0000ff"><br></font></span></div><div class="gmail_default" style="font-family:'trebuchet ms',sans-serif"><font color="#0000ff"><span style="font-size:14px;font-family:arial,sans-serif">BTW, Is it available to use RTK to generate </span><span style="font-size:14px;font-family:arial,sans-serif">SheppLogan phantom with different volume size automatically ?</span></font></div><div class="gmail_default" style="font-family:'trebuchet ms',sans-serif"><span style="font-size:14px;font-family:arial,sans-serif"><font color="#0000ff">Thanks again.</font></span></div><div class="gmail_default" style="font-family:'trebuchet ms',sans-serif"><span style="font-size:14px;font-family:arial,sans-serif"><font color="#0000ff">Best regards</font></span></div><div class="gmail_default" style="font-family:'trebuchet ms',sans-serif"><span style="font-size:14px;font-family:arial,sans-serif"><font color="#0000ff">Guangming</font></span></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><font style="line-height:23.32400131225586px" face="arial, helvetica, sans-serif" color="#674ea7"><b><i>Guangming Zang (Alex)</i></b></font><div style="line-height:23.32400131225586px"><font face="arial, helvetica, sans-serif"><b><i><font color="#0b5394">King Abdullah University of Science and Technology</font><font color="#073763">(KAUST)</font></i></b></font></div><div style="line-height:23.32400131225586px"><span style="font-family:arial;font-size:13px;line-height:20.020000457763672px"><font color="#0b5394"><b><i>University of Chinese Academy of Sciences(UCAS)</i></b></font></span><font face="arial, helvetica, sans-serif"><b><i><font color="#073763"><br></font></i></b></font></div><div style="line-height:23.32400131225586px"><span style="font-family:arial;font-size:13px;line-height:20.020000457763672px"><font color="#0b5394"><b><i><br></i></b></font></span></div><div style="line-height:23.32400131225586px"><span style="font-family:arial;font-size:13px;line-height:20.020000457763672px"><font color="#0b5394"><b><i><br></i></b></font></span></div><div style="line-height:23.32400131225586px"><br></div></div></div></div></div></div>
<br><div class="gmail_quote">2015-05-11 14:18 GMT+03:00 Chao Wu <span dir="ltr"><<a href="mailto:wuchao04@gmail.com" target="_blank">wuchao04@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Guangming,<div><br></div><div>Glad to see you get it work.</div><div><br></div><div>The size of the phantom is described in physical units (e.g. mm) in the txt file. The spacing of the image file is also in physical units (mm) and the dimension is in number of voxels. Therefore spacing * dimension gives you the physical size of the image volume. That's why if you want to have the same volume in mm^3 you need keep the spacing * dimension a constant.</div><div><br></div><div>If you want to have a 128^3 dimension spacing=1 SheppLogan phantom with the <b>same</b> <b>content, not same physical size</b>, you are actually looking for a smaller phantom: 128 * 1 is 1/4 of 256 * 2, so it is 4 times smaller in length. You can get this phantom by changing the size description in the txt file, or you can first create a dimension=128 but spacing=4 image file and subsequently change the spacing from 4 to 1.</div><div><br></div><div>Regards,</div><div>Chao</div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">2015-05-11 13:05 GMT+02:00 Guangming Zang <span dir="ltr"><<a href="mailto:guangming.zang@kaust.edu.sa" target="_blank">guangming.zang@kaust.edu.sa</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_default" style="font-family:'trebuchet ms',sans-serif"><p class="MsoNormal" style="color:rgb(0,0,255)"> </p>
<p class="MsoNormal"><font color="#0000ff">Hi Chao,</font></p>
<p class="MsoNormal"><font color="#0000ff">Thanks for your help.</font></p>
<p class="MsoNormal"><font color="#0000ff">Yes, it works. But I am still a little confused.</font></p>
<p class="MsoNormal"><font color="#0000ff"> I<a href="http://wiki.openrtk.org/index.php/RTK/Examples/ADMMTVReconstruction" target="_blank">n the example in wiki,</a>the only input for command rtkdrawgeometricphantom is SheppLogan.txt, in which , after I checked,
the geometry information is not included. So I thought I can generated any size
of volume as I want. (for example, 64^3 volume dimension with spacing 1 or 1024^3
volume dimension with spacing 10) why should the dimension
*spacing (1*512=2*256=512) should be fixed as a constant???</font></p>
<p class="MsoNormal"><br></p><font color="#0000ff">Briefly speaking,my question is , by using command <span style="font-family:monospace,monospace;font-size:14px;line-height:1.2em;background-color:rgb(249,249,249)">rtkadmmtotalvariation or </span><span style="font-family:monospace,monospace;font-size:14px;line-height:1.2em;background-color:rgb(249,249,249)">rtkdrawgeometricphantom, </span><span style="font-family:monospace,monospace;font-size:14px;line-height:1.2em;background-color:rgb(249,249,249)"><br></span></font></div><div class="gmail_default" style="font-family:'trebuchet ms',sans-serif"><font color="#0000ff">how can i generated a 128^3 dimension SheppLogan volume with spacing as 1 . Is it possible for the SheppLogan.txt provided by this example to make it ??? </font></div><div class="gmail_default" style="font-family:'trebuchet ms',sans-serif">
<p class="MsoNormal"><font color="#0000ff">So could you help me to find the solution??</font></p><p class="MsoNormal"><font color="#0000ff">Thanks for your help, Chao.</font></p><span><p class="MsoNormal"><font color="#0000ff">With my best regards </font></p><p class="MsoNormal"><font color="#0000ff">Guangming </font></p></span></div></div><div class="gmail_extra"><span><br clear="all"><div><div><div dir="ltr"><div><div dir="ltr"><font style="line-height:23.32400131225586px" face="arial, helvetica, sans-serif" color="#674ea7"><b><i>Guangming Zang (Alex)</i></b></font><div style="line-height:23.32400131225586px"><font face="arial, helvetica, sans-serif"><b><i><font color="#0b5394">King Abdullah University of Science and Technology</font><font color="#073763">(KAUST)</font></i></b></font></div><div style="line-height:23.32400131225586px"><span style="font-family:arial;font-size:13px;line-height:20.020000457763672px"><font color="#0b5394"><b><i>University of Chinese Academy of Sciences(UCAS)</i></b></font></span><font face="arial, helvetica, sans-serif"><b><i><font color="#073763"><br></font></i></b></font></div><div style="line-height:23.32400131225586px"><span style="font-family:arial;font-size:13px;line-height:20.020000457763672px"><font color="#0b5394"><b><i><br></i></b></font></span></div><div style="line-height:23.32400131225586px"><span style="font-family:arial;font-size:13px;line-height:20.020000457763672px"><font color="#0b5394"><b><i><br></i></b></font></span></div><div style="line-height:23.32400131225586px"><br></div></div></div></div></div></div>
<br></span><div><div><div class="gmail_quote">2015-05-11 11:06 GMT+03:00 Chao Wu <span dir="ltr"><<a href="mailto:wuchao04@gmail.com" target="_blank">wuchao04@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Guangming,<div><br></div><div>If you half the spacing you need twice the dimension (in length, or 8 times in volume) to cover the same area, i.e. --spacing 1 --dimension 512.</div><div>Is this what you want?</div><div><br></div><div>Regards,</div><div>Chao</div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div>2015-05-10 22:50 GMT+02:00 Guangming Zang <span dir="ltr"><<a href="mailto:guangming.zang@kaust.edu.sa" target="_blank">guangming.zang@kaust.edu.sa</a>></span>:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr"><div class="gmail_default" style="font-family:'trebuchet ms',sans-serif"><font color="#0000ff">Hi all.</font></div><div class="gmail_default" style="font-family:'trebuchet ms',sans-serif"><font color="#0000ff">I have implemented SART algorithm with some optimizations.and i wanna to make a comparison with the implementations in our RTK.</font></div><div class="gmail_default" style="font-family:'trebuchet ms',sans-serif"><font color="#0000ff">My questions are:</font></div><div class="gmail_default" style="font-family:'trebuchet ms',sans-serif"><font color="#0000ff">1. how to use RTK to generate the initial volume(i.e., ground Truth )to make the comparison?</font></div><div class="gmail_default" style="font-family:'trebuchet ms',sans-serif"><font color="#0000ff">2. My answer to the question 1 is that maybe i can use <span style="font-family:monospace,monospace;font-size:14px;line-height:1.2em;background-color:rgb(249,249,249)">rtkdrawgeometricphantom to generate a reference volume. However, </span></font></div><div class="gmail_default" style="font-family:'trebuchet ms',sans-serif"><font color="#0000ff">I noticed that in the <a href="http://wiki.openrtk.org/index.php/RTK/Examples/ADMMTVReconstruction" target="_blank">ADMMTV example in RTK wiki page,</a> when i use the default demand, it works well (both for <span style="font-family:monospace,monospace;font-size:14px;line-height:1.2em;background-color:rgb(249,249,249)">rtkadmmtotalvariation and </span><span style="font-family:monospace,monospace;font-size:14px;line-height:16.7999992370605px;background-color:rgb(249,249,249)">rtkdrawgeometricphantom)</span><span style="font-family:monospace,monospace;font-size:14px;line-height:16.7999992370605px;background-color:rgb(249,249,249)"> </span><span style="font-family:monospace,monospace;font-size:14px;line-height:1.2em;background-color:rgb(249,249,249)"><br></span></font></div><div class="gmail_default" style="font-family:'trebuchet ms',sans-serif"><font color="#0000ff">. But when i change the spacing from 2 to 1, and dimension as 128. i.e. the commands</font><br></div><div class="gmail_default"><font color="#0000ff" face="trebuchet ms, sans-serif">from </font></div><div class="gmail_default"><font face="trebuchet ms, sans-serif"><span style="color:rgb(0,0,0);font-size:14px;line-height:1.2em;background-color:rgb(249,249,249)">rtkdrawgeometricphantom </span><span style="color:rgb(0,0,0);font-size:14px;line-height:1.2em">--spacing</span><span style="color:rgb(0,0,0);font-size:14px;line-height:1.2em;background-color:rgb(249,249,249)"> </span><span style="font-size:14px;line-height:1.2em"><font color="#ff0000">2</font></span><span style="color:rgb(0,0,0);font-size:14px;line-height:1.2em;background-color:rgb(249,249,249)"> </span><span style="color:rgb(0,0,0);font-size:14px;line-height:1.2em">--dimension</span><span style="font-size:14px;line-height:1.2em;background-color:rgb(249,249,249)"><font color="#000000"> </font><font color="#ff0000">256</font></span><span style="color:rgb(0,0,0);font-size:14px;line-height:1.2em">--phantomfile</span><span style="color:rgb(0,0,0);font-size:14px;line-height:1.2em;background-color:rgb(249,249,249)"> SheppLogan.txt </span><span style="color:rgb(0,0,0);font-size:14px;line-height:1.2em">-o</span><span style="color:rgb(0,0,0);font-size:14px;line-height:1.2em;background-color:rgb(249,249,249)"> ref.mha</span></font></div><div class="gmail_default"><span style="font-size:14px;line-height:1.2em;background-color:rgb(249,249,249)"><font color="#0000ff" face="trebuchet ms, sans-serif">to </font></span></div><div class="gmail_default"><pre style="font-size:14px;padding:0px;border:0px none white;line-height:1.2em;font-stretch:normal;margin-top:0px;margin-bottom:0px;vertical-align:top;background-image:none;background-color:rgb(249,249,249);background-repeat:initial"><font face="trebuchet ms, sans-serif"><font color="#000000">rtkdrawgeometricphantom </font><span style="color:rgb(0,0,0)">--spacing</span><font color="#000000"> </font><span><font color="#ff0000">1</font></span><font color="#000000"> </font><span style="color:rgb(0,0,0)">--dimension</span><font color="#000000"> </font><font color="#ff0000">128 </font><span style="color:rgb(0,0,0)">--phantomfile</span><font color="#000000"> SheppLogan.txt </font><span style="color:rgb(0,0,0)">-o</span><font color="#000000"> ref.mha</font></font></pre><pre style="font-size:14px;padding:0px;border:0px none white;line-height:1.2em;font-stretch:normal;margin-top:0px;margin-bottom:0px;vertical-align:top;background-image:none;background-color:rgb(249,249,249);background-repeat:initial"><font face="trebuchet ms, sans-serif"><font color="#0000ff">the volume's visualization(</font><span style="color:rgb(0,0,0);line-height:1.2em">ref.mha</span><span style="color:rgb(0,0,255);line-height:1.2em">) is wired .</span></font></pre><pre style="font-size:14px;padding:0px;border:0px none white;line-height:1.2em;font-stretch:normal;margin-top:0px;margin-bottom:0px;vertical-align:top;background-image:none;background-color:rgb(249,249,249);background-repeat:initial"><font color="#0000ff" face="trebuchet ms, sans-serif">So can you help me to find what's going on or tell me a better way to make the comparison between RTK method and my implementations.</font></pre><pre style="font-family:monospace,monospace;font-size:14px;padding:0px;border:0px none white;color:rgb(0,0,0);line-height:1.2em;font-stretch:normal;margin-top:0px;margin-bottom:0px;vertical-align:top;background-image:none;background-color:rgb(249,249,249);background-repeat:initial"><br></pre><pre style="font-family:monospace,monospace;font-size:14px;padding:0px;border:0px none white;line-height:1.2em;font-stretch:normal;margin-top:0px;margin-bottom:0px;vertical-align:top;background-image:none;background-color:rgb(249,249,249);background-repeat:initial"><font color="#0000ff">Thanks in advance and with my best regards</font></pre><pre style="font-family:monospace,monospace;font-size:14px;padding:0px;border:0px none white;line-height:1.2em;font-stretch:normal;margin-top:0px;margin-bottom:0px;vertical-align:top;background-image:none;background-color:rgb(249,249,249);background-repeat:initial"><font color="#0000ff">Guangming</font></pre><pre style="font-family:monospace,monospace;color:rgb(0,0,0);font-size:14px;padding:0px;border:0px none white;line-height:1.2em;font-stretch:normal;margin-top:0px;margin-bottom:0px;vertical-align:top;background-image:none;background-color:rgb(249,249,249);background-repeat:initial"><br></pre></div><div><div><div dir="ltr"><div><div dir="ltr"><font style="line-height:23.3240013122559px" face="arial, helvetica, sans-serif" color="#674ea7"><b><i>Guangming Zang (Alex)</i></b></font><div style="line-height:23.3240013122559px"><font face="arial, helvetica, sans-serif"><b><i><font color="#0b5394">King Abdullah University of Science and Technology</font><font color="#073763">(KAUST)</font></i></b></font></div><div style="line-height:23.3240013122559px"><span style="font-family:arial;font-size:13px;line-height:20.0200004577637px"><font color="#0b5394"><b><i>University of Chinese Academy of Sciences(UCAS)</i></b></font></span><font face="arial, helvetica, sans-serif"><b><i><font color="#073763"><br></font></i></b></font></div><div style="line-height:23.3240013122559px"><span style="font-family:arial;font-size:13px;line-height:20.0200004577637px"><font color="#0b5394"><b><i><br></i></b></font></span></div><div style="line-height:23.3240013122559px"><span style="font-family:arial;font-size:13px;line-height:20.0200004577637px"><font color="#0b5394"><b><i><br></i></b></font></span></div><div style="line-height:23.3240013122559px"><br></div></div></div></div></div></div>
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