[Simnibs-discuss] compact bone tissue effect on magnitudes

[Alexandru Ciobanu]

Hi SimNIBS Team,

We are running SimNIBS 4 simulations for TMS with `map_to_vol` option enabled, to obtain the `.nii.gz` file of the field.

For a typical TMS coil position (simlar to FCz), we see that including the compact bone (7) tissue in the `tissues_in_niftis` result in the range of magnitude values increasing a lot, because there are a few voxels with high values. So if at the grey matter surface we get around 1-2 V/m maximum, at the areas around the orbital bones we see up to 10 V/m values.

See attached image orbital_bones.png.

It seems these very "hot" areas are around the orbital bones, far from coil location.

Do you think this is a numerical artifact from the simulation (e.g. due to very thin bone) or something else?

Maybe there are ways to filter such values that are both very far from the coil and very high?


See the attached images showing the results for various selections of tissues:
 - tissues_2.png -- for grey matter only.
 - tissues_all.png -- for `all` tissues
 - tissues_all_except_7.png -- for `[1,2,3,4,5,6,8,9,10]` tissues, i.e. everything except compact bone tissue

We reproduce this with our own segmentations, but also with the standard Ernie segmentation. 

See the included demo python script for easy reproduction of this effect. Just point it to the Ernie segmentation file:

  $ simnibs_python demo.py YOURPATH/m2m_ernie/ernie.msh

and then examine the output `.nii.gz` file in `/tmp/result/subject_volumes`.


sincerely,
Alex Ciobanu



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