Question of MCXLAB creating single vessel model

[Yu Sun]

Hi Dr. Fang,

I am trying to use mcxlab to simulate a single vessel inside a 2  cubic domain, which vessel is inside the top layer. Here is my code:

cfg.unitinmm = 0.1;

cfg.nphoton=1e7; 

cfg.issrcfrom0 = 1;

cfg.srctype='disk';

cfg.srcparam1=[3 0 0 0 ];% radium and half angle in radian

cfg.srcdir=[0 0 1];

cfg.vol=uint8(ones(300,300,150));

cfg.shapes='{"Shapes":[{"Cylinder":{"Tag":2,"C0": [0.0,150.0,10.0], "C1":[300.0,150.0,10.0],"R":5.0}}]}';

cfg.vol(:,:,30:end) = 3;

x = size(cfg.vol,1)/2;

y = size(cfg.vol,2)/2;

z = 0; 

cfg.srcpos=[x y z];

cfg.tstart=0;

cfg.tend=5e-9;

cfg.tstep=5e-9;

cfg.autopilot=1;

cfg.gpuid=1;

cfg.isnormalized = 1;

cfg.issaveref = 1; %

cfg.issaveexit = 1;

cfg.debuglevel='P';

cfg.detpos = [x+10.4  y+0   z  3];

cfg.prop=[0 0 1 1;

     0.1089 0.7094 0.9 1.37

     0.23 1.421 0.9 1.37

     0.1549 0.5275 0.9 1.37];

[flux,detp,vol,seeds]=mcxlab(cfg);

I have 2 questions;

1. Did I use the cfg.shape correctly? What does the C0 &C1 control? In the demo_mcxyz_skinvessel, it also used the shape  'ZLayers'. Could you explain these different shape functions a little bit?

2. How could I show the cfg data? I tried to use the function 'mcxpreview(cfg)', however, the plot only showed 2 cubic layers without the cylinder. Did I make a mistake on model creation?

Thank you!

Best,

Yu

[Qianqian Fang]

hi Yu,

a few comments -

first, the mcxpreview function failed with your domain due to a combination of several things - first, although mcx accepts both cfg.vol and cfg.shapes, the mcxpreview function could not handle it; secondly, the mcxplotshapes function used to handle cfg.shapes does not support cfg.unitinmm, thus, even it can be plotted, it will be in a different scale if your cfg.unitinmm is not 1.

I have fixed both, see the below bug tracker, and now your cfg should be displayed correct

https://github.com/fangq/mcx/issues/131

for your question on the C0/C1 and ZLayers shape constructs, you can find more info in the "MCX_Shape_Command_Help" section of the README: https://github.com/fangq/mcx#using-json-formatted-shape-description-files

for a two-layered domain, you can use "ZLayers" in cfg.shapes, such as

cfg.shapes='{"Shapes":[{"ZLayers":[[1,29,1],[30,150,3]]},{"Cylinder":{"Tag":2,"C0": [0.0,150.0,10.0], "C1":[300.0,150.0,10.0],"R":5.0}}]}';

if you define the above shapes, you could remove the cfg(...30:end) line - but even you don't, the results will be the same because the shape constructs overlays on top of cfg.vol.

let me know if you have further questions.

Qianqian

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