How to create fsaverage bem folder and contents

šŸ’¬ Support & Discussions
1

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

Iā€™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 donā€™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 Iā€™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 ā€˜outer_skull.surfā€™, ā€˜outer_skin.surfā€™, and ā€˜inner_skull.surfā€™.
Subsequent to that, these files must be placed in a directory called ā€˜bemā€™ 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 havenā€™t yet had time to try them out!
Bianca, what would you use in yourMRIfilename.nii.gz for the fsaverage brain?

Megan

5

Is there a way to download what mne.datasets.fetch_fsaverage() generates? My environment is closed network so I need everything offline.

6

The data is stored on OSF; you can find the URLs in the MNE source code:

Best wishes
Richard

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