[FieldTrip] MNE cortical sheet parcellation with AAL atlas

[Xu, Weiyong]

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');

mne_sourcemodel=ft_read_headshape('cortex_8196.surf.gii');



cfg = [];

cfg.interpmethod = 'nearest';

cfg.parameter = 'tissue';

mne_sourcemodel_with_label = ft_sourceinterpolate(cfg, aal, mne_sourcemodel);



disp(mne_sourcemodel_with_label.tissuelabel')



for i=1:length(mne_sourcemodel_with_label.tissue)

    if mne_sourcemodel_with_label.tissue(i)==0;

       mne_sourcemodel_with_label.tissue(i)=200;

    end;

end;



ft_plot_mesh(mne_sourcemodel_with_label,'vertexcolor',mne_sourcemodel_with_label.tissue,'edgecolor','black')

colorbar

---------------------------------------------------------



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.


Best,


Weiyong Xu

Ph.D. student
Department of Psychology
University of Jyväskylä
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20161128/e7eec75a/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: parcellation_with_AAL.pdf
Type: application/pdf
Size: 454680 bytes
Desc: parcellation_with_AAL.pdf
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20161128/e7eec75a/attachment-0001.pdf>