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<p>Hi Lorenza,</p>
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<p>Glad you're finding the simulation useful! If you're using a square packing, the arrangement is a regular grid of cylinders which extends periodically out to infinity. The number of cylinders in this case is just enough to define a unit cell with periodic
boundaries -- spins leave one side and wander into an identical cell next door. Under these circumstances there's no option to change the number of cylinders since the packing is so regular.</p>
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<p>This applies to the regular packings, but not the random packings. If you want to look at those you can specify the squashy inflammation substrate, a size (using -substratesize, a number of cylinders (-numcylinders) and paramters for the size distribution
(-gamma <scale> <shape>). You'll need to watch out that the substrate is large enough to hold all the cylinders -- it'll generate a warning if it can't place them all.</p>
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<p>Hope this helps,</p>
<p>Matt.<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> camino-users-bounces@www.nitrc.org <camino-users-bounces@www.nitrc.org> on behalf of Lorenza Brusini <lorenza.brusini@univr.it><br>
<b>Sent:</b> 29 September 2016 09:50:11<br>
<b>To:</b> camino-users@www.nitrc.org<br>
<b>Subject:</b> [Camino-users] Changing number of cylinders in MC simulation</font>
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<div dir="ltr">Hello, I'd like to ask a question about synthesis using Monte-Carlo diffusion simulator.<br>
<br>
I did a simple simulation using: <br>
<br>
datasynth -walkers 100000 -tmax 1000 -geometry cylinder -packing SQUARE -cylinderrad 0.5E-6 -cylindersep 1.1E-6 -p 0.0 -initial uniform -voxels 1 -schemefile scheme.scheme | float2txt > out.txt<br>
<br>
Now I would like to change the number of the cylinders that, if I understood well when I read the documentation on the web site, is set to 20 as default. Moreover, I would like to keep constant the dimensions of the voxel thus to change the volume fractions
only due to the number of cylinders. <br>
How could I do? I tried with option -latticesize and -numcylinders that I found in the ActiveAx tutorial, but nothing seems function.<br>
<br>
Another question is if is it possible to simulate myelinated cylinders or still not.<br>
<br>
Thanks in advance. Regards.<br>
<br>
Lorenza<br>
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