[FieldTrip] Brain segmentation has strange spikes in it

Thomas Radman radman.thomas at gmail.com
Tue May 22 00:53:03 CEST 2018


I am trying to segment an individual subject's MRI following this tutorial:

However, when plotting the mesh of the scalp segmentation I get these
horrible disfigurations that are not in the original MRI.  Here is a

These are the steps I'm taking
mri=ft_read_mri( '/data/radmantc/projects/T1_mni.nii')

cfg = [];
cfg.resolution = 1;
mri_resliced = ft_volumereslice(cfg, mri);
ft_sourceplot([], mri_resliced);

%volume conduction model
cfg           = [];
cfg.output    = {'brain', 'skull', 'scalp'};
mri_segmented = ft_volumesegment(cfg, mri_resliced);

% copy the anatomy into the segmented mri
mri_segmented.anatomy = mri_resliced.anatomy;

%reconstruct the three triangulated meshes.
cfg = [];
cfg.method = 'projectmesh';
cfg.tissue = 'brain';
cfg.numvertices = 3000;
mesh_eeg(1) = ft_prepare_mesh(cfg, mri_segmented);

cfg.tissue = 'skull';
cfg.numvertices = 2000;
mesh_eeg(2) = ft_prepare_mesh(cfg, mri_segmented);

cfg.tissue = 'scalp';
cfg.numvertices = 1000;
mesh_eeg(3) = ft_prepare_mesh(cfg, mri_segmented);

ft_plot_mesh(mesh_eeg(1), 'edgecolor', 'none', 'facecolor', 'r')
ft_plot_mesh(mesh_eeg(2), 'edgecolor', 'none', 'facecolor', 'g')
ft_plot_mesh(mesh_eeg(3), 'edgecolor', 'none', 'facecolor', 'b')  %this is
the only mesh that is distorted
alpha 0.3

Also, can someone tell me how to respond to any replies I might get.  In
previous posts, I only see the replies in the listserv digest emails.  Do I
create a new email with the subject line of this case intact?  I don't get
an email directly from the person sending the reply to my email, I only see
it in the digest.

Thank you for the help,
Thomas Radman
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