[FieldTrip] MNE cortical sheet parcellation with AAL atlas

Xu, Weiyong weiyong.w.xu at jyu.fi
Mon Nov 28 15:21:31 CET 2016

Dear all,

After MNE source analysis with the template MRI(Colin27),  I want to do parcellation with the AAL atlas.  So first I checked how well the template cortical sheet and AAL atlas fit with the following code:


aal = ft_read_atlas('C:\MyTemp\Toolbox\fieldtrip\fieldtrip_git\template\atlas\aal\ROI_MNI_V4.nii');


cfg = [];

cfg.interpmethod = 'nearest';

cfg.parameter = 'tissue';

mne_sourcemodel_with_label = ft_sourceinterpolate(cfg, aal, mne_sourcemodel);


for i=1:length(mne_sourcemodel_with_label.tissue)

    if mne_sourcemodel_with_label.tissue(i)==0;







The result looks like that the parcellation of the sulci are not very good.  Also parts of the cerebellum are included after interpolation.

So I want to ask if there are surface-based atlas available (preferably also based on the Colin27)?

And also I noticed the freesurfer pipeline creates cortical parcellation  such as the Destrieux atlas, could I somehow utilize this in creating surface-based atlas for my MNE source model?

Thanks in advance.


Weiyong Xu

Ph.D. student
Department of Psychology
University of Jyväskylä
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