[FieldTrip] ft_prepare_mesh seems to change segmentation layers to alphabetical order

Schoffelen, J.M. (Jan Mathijs) janmathijs.schoffelen at donders.ru.nl
Mon Apr 11 11:41:25 CEST 2022

Dear Martin,

I would assume that the order of the tissuelabel is what’s in the data, i.e. the hexahedral elements that get a value of ‘1’ in your data example will be the csf compartment. I would visualize the segmentation to verify this. Not sure whether ft_sourceplot is capable of this out of the box, but I would assume that the ’tissue’ field should be reshapeable into a 3D volume, and visualized along with the anatomical image.

Anyway, I think that the order of the conductivity values in the cfg should be the same as the order of the tissuelabel in the mesh. The low-level simbio code does not do an extra check on this. Perhaps the simbio folks can chime in here, because they know the relevant code better than I do.

I think that it might be worthwile to consider building in an extra sanity check at a higher level in the code, where the cfg into ft_prepare_headmodel also informs the code about which conductivity value is to be associated with a particular tissue compartment. @the simbio/duneuro folks: what do you think?

Best wishes,

On 7 Apr 2022, at 17:23, Martin Schaefer via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Dear mailinglist,

I noticed that the function ft_prepare_mesh seems to change the order of the segmentation layers to alphabetical, rather than keeping the order chosen during ft_volumesegment.
This seems like it could potentially lead to a to a mismatch with the conductivity values chosen during ft_prepare_headmodel, which uses the layer order from ft_prepare_mesh.

For example, I run
cfg                       = [];
cfg.output          = {'gray','white','csf','skull','scalp'};
mri_segmented = ft_volumesegment(cfg, mri_resliced);
​followed by
cfg                 = [];
cfg.shift        = 0.3;
cfg.method  = 'hexahedral';
mesh            = ft_prepare_mesh(cfg,mri_segmented);
​When I then look at mesh.tissuelabel the order has changed to: {'csf'}    {'gray'}    {'scalp'}    {'skull'}    {'white'}

And if I continue to run
cfg                          = [];
cfg.method          = 'simbio';
cfg.conductivity  = [0.33 0.14 1.79 0.01 0.43];  % {'gray'  'white'  'csf'  'skull'  'scalp'}
headmodel_eeg = ft_prepare_headmodel(cfg, mesh_fem);
headmodel_eeg.tissuelabel has the same order as the mesh:  {'csf'}    {'gray'}    {'scalp'}    {'skull'}    {'white'}
And I assume this means the conductivity values are mismatched.

Can someone check this?

I use the fieldtrip version from 1st of April 2022.

Best regards,

Martin Schaefer | PhD Student
Department of Clinical Neuroscience (CNS), K8
Karolinska Institutet | 17 177 Stockholm | Nobels väg 9
martin.schaefer at ki.se<mailto:artin.arshamian at ki.se>
Karolinska Institutet – a Medical University

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