[FieldTrip] Import Freesurfer atlas to ft

Mikkel Vinding mikkel at cnru.dk
Tue Dec 4 20:20:45 CET 2018

Dear FieldTrip list

Has anyone here imported individual atlases from Freesurfer into FieldTrip?
It should be possible with ft_read_atlas. From the documentation of

*  For individual surface-based atlases from FreeSurfer, you should specify
two *

*  filenames as a cell-array: the first points to the file that contains

*  with respect to the parcels' labels, the second points to the file that
defines the*

*  mesh on which the parcellation is defined.*

Ft_read_atlas require a struct containing the filename of the atlas file
and the cortical surface/mesh. However, I keep getting errors that
ft_read_atlas cannot read Freesurfers “annot” files: “ *unrecognized
filetype 'freesurfer_annot'.*“ I get a similar error when I try to read
Freesurfer “label” files.

The problem seems to be because ft_read_atlas calls ft_read_mri which does
not support the type 'freesurfer_annot'. My question is how to read in
Freesurfer annotations or labels? Do I need to convert the Freesurfer files
first or is there another step I need to do first? If anyone has managed to
read Freesurfer labels in FieldTrip, I will be delighted to hear the answer.

Best regards


Mikkel C. Vinding
NatMEG, Karolinska Institutet
Nobels väg 9
171 77 Stockholm, Sweden
Email: mikkel.vinding at ki.se
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