[FieldTrip] Brain segmentation has strange spikes in it

[Simon Homolle]

Dear Thomas,

unfortunately I cannot see the figure you send. But from the title of the email I think i have some suggestions for you.

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


for this segment you can play around with to make the the tissues more smooth
%   cfg.brainsmooth    = 'no', or scalar, the FWHM of the gaussian kernel in voxels, (default = 5)
%   cfg.scalpsmooth    = 'no', or scalar, the FWHM of the gaussian kernel in voxels, (default = 5)
%   cfg.skullsmooth    = 'no', or scalar, the FWHM of the gaussian kernel in voxels, (default = 5)

Or you can change the thresholds for the tissues
%   cfg.brainthreshold = 'no', or scalar, relative threshold value which is used to threshold the
%                       tpm in order to create a volumetric brainmask (see below), (default = 0.5)
%   cfg.scalpthreshold = 'no', or scalar, relative threshold value which is used to threshold the
%                        anatomical data in order to create a volumetric scalpmask (see below),
%                        (default = 0.1)
%   cfg.skullthreshold = 'no', or scalar, relative threshold value which is used to threshold the
%                        anatomical data in order to create a volumetric scalpmask (see below),
%                        (default = 0.5). this parameter is only used when
%                        the segmetnation contains 6 tissue types,
%                        including 'bone’,

> %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);


If the previous steps to not solve your problems, you can also try to change something in the method
%   cfg.method      = string, can be 'interactive', 'projectmesh', 'iso2mesh', 'isosurface',
%                     'headshape', 'hexahedral', 'tetrahedral', 'cortexhull'

Cheers,

Simon Homölle
PhD Candidate
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Phone: +31-(0)24-36-65059

> On 22 May 2018, at 00:53, Thomas Radman <radman.thomas at gmail.com> wrote:
> 
> Hello,
> 
> I am trying to segment an individual subject's MRI following this tutorial:
> http://www.fieldtriptoolbox.org/tutorial/natmeg/dipolefitting <http://www.fieldtriptoolbox.org/tutorial/natmeg/dipolefitting>
> 
> However, when plotting the mesh of the scalp segmentation I get these horrible disfigurations that are not in the original MRI.  Here is a screenshot:
> 
> 
> 
> These are the steps I'm taking
> mri=ft_read_mri( '/data/radmantc/projects/T1_mni.nii')
> mri.coordsys='mni'
> 
> cfg = [];
> cfg.resolution = 1;
> mri_resliced = ft_volumereslice(cfg, mri);
> figure
> 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);
> 
> figure
> 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
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20180523/010e18ed/attachment-0002.html>