How to create fsaverage bem folder and contents

💬 Support & Discussions
1

Hi all,
I am using freesurfer 7.2, I have mne1.0 working.

I’ve used an old script that I inherited for the freesurfer processing, but if I try to follow some examples (like this one), but I am missing the fsaverage/bem/ folder. I now have all the files and folders I need for the freesurfer MRI processing of my subject data, but not the fsaverage in my project directory. I did a quick search of the mne documentation, but I don’t see how this is created. Can anyone point me in the right direction?

fsaverage does have the following directories
label mri mri.2mm scripts surf xhemi
and I’ve used it for other things, for example the labels and surf files.

Thanks,
Megan

2

Hey Megan,

I usually use the mri_watershed algorithm from FreeSurfer to compute the bem surfaces (see here:https://surfer.nmr.mgh.harvard.edu/fswiki/mri_watershed).

Simply generate them using

mri_watershed -surf [lh] yourMRIfilename.nii.gz BEMoutput

The BEMoutput directory should then appear in your subjects directory.
To be able to use them with MNE I simply rename the files to ‘outer_skull.surf’, ‘outer_skin.surf’, and ‘inner_skull.surf’.
Subsequent to that, these files must be placed in a directory called ‘bem’ into the Freesurfers recon-all -all output directory.

I hope this is helpful,
Bianca

3

There is also mne.datasets.fetch_fsaverage()
https://mne.tools/stable/overview/datasets_index.html#fsaverage

4

Hi all,
Thank you for your suggestions. I haven’t yet had time to try them out!
Bianca, what would you use in yourMRIfilename.nii.gz for the fsaverage brain?

Megan