Using mne_annot2labels

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1

Hi folks,

    I am trying to convert freesurfer parcellation data into labels using
mne_annot2labels(Page 241 of Manual) command. The command ran, however
the
converted label files when opened in text editor showed a row of 4 zeros
next to each vertex (meaning it did not look like a typical label file
which has the 3 coordinates corresponding to the vertex). Any help on
successful use of this command will be appreciated.

Our aim is to load these converted labels using mne_analyze and also to
compute the lead field matrices for each of these labels using
mne_forward_solution script. My expectation was that converted labels
using this command could be viewed in the same way as manually created
labels (described in 7.13.4 of manual). Is this correct?

I ran the command from the directory labels which had the
following files
lh.aparc.a2005s.annot lh.test_aparc.annot rh.aparc.annot
lh.aparc.annot rh.aparc.a2005s.annot
The command was used after correctly setting the SUBJECTS_DIR and SUBJECT
env variables was
mne_annot2labels --parc aparc

Here is what it returned

2

Do not worry about the zeros, they are immaterial to MNE, only the
vertex numbers (first column) count. It is normal that
mne_annot2labels writes these zeros.

Incidentally, the FreeSurfer parcellation most probably too coarse to
be used as parcels of the source space.

- Matti