[Mne_analysis] Guidance on FreeSurfer integration with MNE

Parth Chholak parthchholak at gmail.com
Tue Dec 22 06:29:45 EST 2020
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Dear all,

I don't have individual MRI scans for a MEG study and only have
digitization points collected via a Polhemus tracker. Hence, I would like
to use 'fsaverage' as a standard anatomy and transform it for each subject
using digitised points. All MNE tutorials assume that the complete anatomy
files would already be prepared using FreeSurfer.

All I could find on FreeSurfer documentation was to use this command:
recon-all -i path_to_T1.mgz -subjid subject_name

In one of the MNE workshops in winter last year, I remember a demonstration
to do the whole thing by Alex. It involved using the FreeSurfer GUI and
feeding in the FIF file to provide the channel and digitization data. I
somehow even managed to repeat the whole process myself in the summer but
unfortunately didn't document it. And now, I can't seem to make that
miracle happen again.

I hope it is a valid question to ask on this forum given the strong
dependency of MNE on this processing step. Any help or direction would be
greatly appreciated.

Kind regards,

*Parth Chholak*
Doctoral Candidate
Centre for Biomedical Technology
Technical University of Spain
+34 618689339979278
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