[Mne_analysis] Discrepancy between visualization of freesurfer label and its vertices

[Pavan Ramkumar]

Thanks Hari! Your hunch is spot on and potentially saved me weeks.

> Hi Pavan,
>   I suspects this is as a result of the freesurfer indexing being zero
> based and MNE's being 1 based. If that were indeed the case, if you add
> 1 to the vertex numbers read by mne_read_label_file() before finding the
> common vertices that would resolve it..
>
> Regards,
> Hari
>
>
>
>
> On Wed, December 22, 2010 6:25 am, Pavan Ramkumar wrote:
>> Dear MNE users,
>>
>> I observed a discrepancy between
>>
>> (1) the visualization of Freesurfer generated anatomical labels (*.label
>> files) which can be loaded in mne_analyze with Labels --> Load Label
>>
>> AND
>>
>> (2) the actual vertices that the label contains. I visualize these
>> vertices by reading in the label file with mne_read_label_file() in
>> MATLAB
>> and writing out an *.stc file with all vertices common between the label
>> file and the vertices in the source space set to '1' and all the other
>> source space vertices set to '0'.
>>
>> To be specific, I'm having trouble with the 'S_central-lh.label' file
>> generated by Freesurfer 4.1.0. The visualizations (1) and (2) should
>> look
>> the same, but I notice that (2) also contains a couple of vertices on
>> the
>> medial wall.
>>
>> Has anyone else observed this before? How am I mistaken? Thanks for your
>> comments.
>>
>> Kind regards,
>> Pavan
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>>
>>
>>
>
>
> --
> Hari Bharadwaj
>
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