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<div>Thanks all! I think I have all of the demo simulations running now. </div>
<div>Best, </div>
<div>Bennett</div>
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<p class="MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt;"><b><font size="2" face="Calibri"><span style="font-size: 10pt;">Bennett Landman, Ph.D., </span></font></b><a href="mailto:bennett.landman@vanderbilt.edu" target="_blank" style="color: rgb(149, 79, 114);"><b><font size="2" color="blue"><span style="font-size: 10pt;">bennett.landman@vanderbilt.edu</span></font></b></a><b><font size="2"><span style="font-size: 10pt;"></span></font></b><o:p></o:p></p>
<p class="MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt;"><b><font size="2" face="Calibri"><span style="font-size: 10pt;">Assistant Professor</span></font></b><o:p></o:p></p>
<p class="MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt;"><i><font size="2" face="Calibri"><span style="font-size: 10pt;"> Electrical Engineering (primary),<o:p></o:p></span></font></i></p>
<p class="MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt;"><b><font size="2" face="Calibri"><span style="font-size: 10pt;"> </span></font></b><i><font size="2"><span style="font-size: 10pt;">Computer Science, Biomedical Engineering,</span></font></i><o:p></o:p></p>
<p class="MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt;"><b><font size="2" face="Calibri"><span style="font-size: 10pt;"> </span></font></b><i><font size="2"><span style="font-size: 10pt;">Radiology and Radiological Sciences<o:p></o:p></span></font></i></p>
<p class="MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt;"><i><font size="2" face="Calibri"><span style="font-size: 10pt;"> Vanderbilt University</span></font></i><i><o:p></o:p></i></p>
<p class="MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt;"><b><font size="2" face="Calibri"><span style="font-size: 10pt;">Director of the Center for Computational Imaging<o:p></o:p></span></font></b></p>
<p class="MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt;"><b><font size="2" face="Calibri"><span style="font-size: 10pt;"> </span></font></b><i><font size="2"><span style="font-size: 10pt;">Vanderbilt University Institute of Image Science</span></font></i><o:p></o:p></p>
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<span style="font-weight:bold">From: </span>Alonso Ramírez <<a href="mailto:alram@cimat.mx">alram@cimat.mx</a>><br>
<span style="font-weight:bold">Date: </span>Monday, November 2, 2015 at 7:02 PM<br>
<span style="font-weight:bold">To: </span>Bennett Landman <<a href="mailto:bennett.landman@vanderbilt.edu">bennett.landman@vanderbilt.edu</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [Camino-users] More questions on units with the diffusion simulator: Irregularly Packed, Distributed Radius Cylinders<br>
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<div dir="ltr">Hello,
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<div>i'm not sure about that 'pdf' matlab function you used, but I checked exactly the same some months ago with the following commands in matlab:</div>
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<div>R = gamrnd(1.84037, 7.8E-7,10000,1);</div>
<div>figure; hist(R,1000)</div>
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<div>I got radius around 1 micrometer as expected.</div>
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<div>Best!</div>
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<div>Alonso Ramírez M.<br>
Centro de Investigación en Matemáticas A.C.<br>
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<div>Tel. +52 (473) 73 271 55<br>
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<div>Off. H1, Ext. 4494</div>
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<div class="gmail_quote">2015-11-02 10:35 GMT-06:00 Landman, Bennett A <span dir="ltr">
<<a href="mailto:bennett.landman@vanderbilt.edu" target="_blank">bennett.landman@vanderbilt.edu</a>></span>:<br>
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<div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px">I’m looking at the example: </div>
<div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px"><code style="color:rgb(80,80,80)">datasynth -walkers 100000 -tmax 1000 -voxels 1 -p 0.0 -schemefile my.scheme -initial uniform -substrate inflammation -increments 1 -gamma 1.84037 7.8E-7
-substratesize 3.5E-5 -numcylinders 100 > gammacyls.bfloat </code><br style="color:rgb(80,80,80);font-family:Arial,Verdana,Helvetica,sans-serif;font-size:13px">
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<div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px">From <a href="http://cmic.cs.ucl.ac.uk/camino/index.php?n=Tutorials.MCSimulator#toc10" target="_blank">http://cmic.cs.ucl.ac.uk/camino/index.php?n=Tutorials.MCSimulator#toc10</a></div>
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<div>If I construct a gamma PDF using matlab assuming a=1.84037 and b=7.8E-7, I see a median radius of about 176. It is not clear to me how to interpret these units. </div>
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<div>I do not see where the system would output the actual radii of the cylinders used in a particular simulation, so I don’t know how to double check units. However, the documentation seems to imply that the simulations are conducted on a 35x35um array, so
176 does seem to match a reasonable unit. </div>
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<div>Here is the line of Matlab code that I am using to see the PDF: </div>
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<div>x=linspace(0,1000,1000); px = pdf('gamma',x,'a',1.84037,'b',7.8E-7); plot(x,px)</div>
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<div>Documented here: <a href="http://www.mathworks.com/help/stats/pdf.html" target="_blank">http://www.mathworks.com/help/stats/pdf.html</a></div>
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<div>Thanks,</div>
<div>Bennett</div>
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<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:11pt"><b><font size="2" face="Calibri"><span style="font-size:10pt">Bennett Landman, Ph.D., </span></font></b><a href="mailto:bennett.landman@vanderbilt.edu" style="color:rgb(149,79,114)" target="_blank"><b><font size="2" color="blue"><span style="font-size:10pt">bennett.landman@vanderbilt.edu</span></font></b></a><b><font size="2"><span style="font-size:10pt"></span></font></b><u></u><u></u></p>
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:11pt"><b><font size="2" face="Calibri"><span style="font-size:10pt">Assistant Professor</span></font></b><u></u><u></u></p>
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:11pt"><i><font size="2" face="Calibri"><span style="font-size:10pt"> Electrical Engineering (primary),<u></u><u></u></span></font></i></p>
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:11pt"><b><font size="2" face="Calibri"><span style="font-size:10pt"> </span></font></b><i><font size="2"><span style="font-size:10pt">Computer Science, Biomedical Engineering,</span></font></i><u></u><u></u></p>
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:11pt"><b><font size="2" face="Calibri"><span style="font-size:10pt"> </span></font></b><i><font size="2"><span style="font-size:10pt">Radiology and Radiological Sciences<u></u><u></u></span></font></i></p>
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:11pt"><i><font size="2" face="Calibri"><span style="font-size:10pt"> Vanderbilt University</span></font></i><i><u></u><u></u></i></p>
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:11pt"><b><font size="2" face="Calibri"><span style="font-size:10pt">Director of the Center for Computational Imaging<u></u><u></u></span></font></b></p>
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:11pt"><b><font size="2" face="Calibri"><span style="font-size:10pt"> </span></font></b><i><font size="2"><span style="font-size:10pt">Vanderbilt University Institute of Image Science</span></font></i><u></u><u></u></p>
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