[Simnibs-discuss] Headreco vs Charm

[Oula Puonti]

Hi Ville,

You can copy the settings.ini file from inside the m2m-folder and edit
the following field:

# Define thickness-dependent element sizes
# 	"range": upper and lower cut-offs for element sizes
# 	"slope": the smaller the finer the mesh
# 	"standard": applies to all tissues not defined otherwise
elem_sizes = {"standard": {"range": [1, 5], "slope": 1.0},
                     "1": {"range": [1, 7], "slope": 1.0},
                     "2": {"range": [1, 2], "slope": 1.0},
                     "5": {"range": [1, 5], "slope": 0.6}}

where the element sizes are in mm. If you want smaller elements you can
either change the lower and upper bounds or the slope or both. 

The mesh resolution will still be spatially adaptive depending on the
thicknesses of the various tissues, which are calculated automatically
in charm. 

Once you've modified the settings.ini file you can do a new charm run
with the additional flag "--usesetting settings.ini", or, if you
already have a charm run, you can remesh the upsampled tissue labeling
using the meshmesh function, see here:

https://simnibs.github.io/simnibs/build/html/documentation/command_line/meshmesh.html?highlight=meshmesh

If you want fine-level spatial control of the density, the meshmesh
function also accepts a sizing field as an input. In a standard charm
run the sizing field is based on the automatically calculated tissue
thicknesses.

Best,
Oula



On Tue, 2023-01-24 at 19:10 +0000, Rimpilainen, Ville wrote:
> Dear SimNIBS Team,
> 
> In headreco it was possible to influence the density of nodes in the
> mesh by using the attribute -v. Now, I did not find similar feature
> in charm. Could you please advice whether charm has this feature, and
> if it has, then how to use it. Thank you!
> 
> Best wishes,
> Ville
> 
> Dr. Ville Rimpilainen
> Lecturer - Academic Manager
> University of Liverpool 
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