Question about MCX for tPBM - Fang/Cassano Paper
Tara Ahmed
Qianqian Fang
see my replies below
Hi,
I'm trying to replicate the MCX simulation that was done in this paper: "Selective photobiomodulation for emotion regulation: model-based dosimetry study" using the Colin27 atlas. I'm still a little new to MCX so I had a few questions that I was wondering you could answer for me:
1. Regarding the domain section in the JSON code, how do you assign the location of the different mediums (air, gray matter etc)2. Is there any way to edit the array zip data? I'm not sure how to even read it.
answer both questions above: mcx uses a 3D label (integer) array to represent medium - a voxel value of 1 means the tissue is type 1, value 2 means the tissue is type 2, and so on; the tissue type to optical property look up table is the Domain.Media field; where the first entry is label 0 (background), 2nd entry is medium 1 etc.
the Shapes field in the JSON file is simply a compressed and base64 encoded text string representing the binary data of the 3D label array.
you can not edit it directly. you must read this data in Python
(use jdata module) or MATLAB (use jsonlab) and decode this data
into a 3D array, modify it, and save it back.
3. Is it possible to have more than one light source entering the model? How would you configure that?
mcx newer than v2024.2 supports multiple sources, but at the
time, it did not
4. Is there a legend that describes what the different colors are?
I don't know what color you were referring to
5. Could you walk me through which parameters were changed and how for the Cassano/Fang paper?
I am also not sure what "change" you were referring to - why you
think it was changed? compared to what?
if you were referring to the built-in colin27 example script, it
was meant o replicate the Fig. 6 in my original MCX paper
(https://opg.optica.org/oe/fulltext.cfm?uri=oe-17-22-20178), it
has nothing to do with the PBM paper as the source settings are
entirely different.
If you want to understand our PBM study in details, please
carefully read our paper first. it was an accumulation of over 2
years of work from a former student. It is not easy to "walk you
through", but everything we did were described clearly in the
paper.
Best,Tara--
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