[Camino-users] More questions on units with the diffusion simulator: Irregularly Packed, Distributed Radius Cylinders

[Landman, Bennett A]

Thanks all! I think I have all of the demo simulations running now.
Best,
Bennett

------------------------------------------------------------------------------
Bennett Landman, Ph.D., bennett.landman at vanderbilt.edu<mailto:bennett.landman at vanderbilt.edu>
Assistant Professor
     Electrical Engineering (primary),
     Computer Science, Biomedical Engineering,
     Radiology and Radiological Sciences
     Vanderbilt University
Director of the Center for Computational Imaging
     Vanderbilt University Institute of Image Science


From: Alonso Ramírez <alram at cimat.mx<mailto:alram at cimat.mx>>
Date: Monday, November 2, 2015 at 7:02 PM
To: Bennett Landman <bennett.landman at vanderbilt.edu<mailto:bennett.landman at vanderbilt.edu>>
Subject: Re: [Camino-users] More questions on units with the diffusion simulator: Irregularly Packed, Distributed Radius Cylinders

Hello,

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:

R = gamrnd(1.84037, 7.8E-7,10000,1);
figure; hist(R,1000)

I got radius around 1 micrometer as expected.

Best!



Alonso Ramírez M.
Centro de Investigación en Matemáticas A.C.
Tel. +52 (473) 73 271 55
Off. H1, Ext. 4494

2015-11-02 10:35 GMT-06:00 Landman, Bennett A <bennett.landman at vanderbilt.edu<mailto:bennett.landman at vanderbilt.edu>>:
I’m looking at the example:
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

>From http://cmic.cs.ucl.ac.uk/camino/index.php?n=Tutorials.MCSimulator#toc10

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.

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.

Here is the line of Matlab code that I am using to see the PDF:

x=linspace(0,1000,1000); px = pdf('gamma',x,'a',1.84037,'b',7.8E-7); plot(x,px)

Documented here: http://www.mathworks.com/help/stats/pdf.html

Thanks,
Bennett

------------------------------------------------------------------------------
Bennett Landman, Ph.D., bennett.landman at vanderbilt.edu<mailto:bennett.landman at vanderbilt.edu>
Assistant Professor
     Electrical Engineering (primary),
     Computer Science, Biomedical Engineering,
     Radiology and Radiological Sciences
     Vanderbilt University
Director of the Center for Computational Imaging
     Vanderbilt University Institute of Image Science


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