[FieldTrip] coordinate off with ft_prepare_mesh

Danny Huang dannyhuangyuhao at gmail.com
Fri Sep 6 02:40:01 CEST 2019

Hi there,

I am following the protocol (
here and intending to plot subcortical segmentation along with the brain
surface mesh.

However, I am noticing that when I convert the subcortical volume into a
mesh using the code below, the mesh seems to be in a different coordinate
space than the native freesurfer space, such that my electrodes and lh.pial
rendering don't line up with the subcortical mesh.

Would anyone be able to advise why this is happening?

Stanford University

seg = keepfields(atlas, {'dim',
'unit','coordsys','transform'});seg.brain = mask_rha;cfg             =
[];cfg.method      = 'iso2mesh';cfg.radbound    = 2;cfg.maxsurf     =
0;cfg.tissue      = 'brain';cfg.numvertices = 1000;cfg.smooth      =
3;cfg.spmversion  = 'spm12';mesh_rha = ft_prepare_mesh(cfg, seg);
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