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

Martin Schaefer martin.schaefer at ki.se
Thu Apr 7 17:23:09 CEST 2022

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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