[FieldTrip] Import Freesurfer atlas to ft

[Schoffelen, J.M. (Jan Mathijs)]

Dear Mikkel,

I did not look into it in detail, but from your description it seems that the code takes a wrong turn somewhere, and thinks that the fileformat is of type freesurfer_volume (and for this reason it ends up on a line that tries to use ft_read_mri). I read in the code that the default allocation of the fileformat based on an educated guess from the filename  is implemented in a slightly clunky way. Soooo, perhaps you could try and overrule this default allocation by explicitly specifying it in your call to ft_read_atlas:

ft_read_atlas({filename_annotation filename_mesh}, ‘format’, ‘freesurfer_*’);

where the * should be the appropriate choice of ‘a2009s’ ‘aparc’, or ‘ba’.

Best wishes,
Jan-Mathijs

On 4 Dec 2018, at 20:20, Mikkel Vinding <mikkel at cnru.dk<mailto:mikkel at cnru.dk>> wrote:

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 ft_read_atlas:

  For individual surface-based atlases from FreeSurfer, you should specify two
  filenames as a cell-array: the first points to the file that contains information
  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

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