FsAverage Scale

Hello all,

I am using the fsaverage brain for subjects for which no structural MRIs are available. During coregistration I noticed that quite a few subjects have a head that is much smaller than the fsaverage head. Is there a possibility to scale the fsaverage brain to fit a subject's head shape better? If this is not implemented, would it be possible to implement it in Python with mne-python/PySurfer? (i.e., which files would have to be modified/created?) Or is this scale difference not a real problem?

Thank you,


hi Christian,

sorry but I am not aware of anybody working with MNE using a template brain.

I don't know how this could work, but if you hack something let us know.


hi Christian,

You can always use SPM or brainstorm for wrapping the fsaverage to subject



Hi Sheraz,

Thanks for your suggestion! I am not familiar with SPM and brainstorm, would they allow to import bem files, scale them to fit the digitization data in a fiff file, and export them again as a bem? Or would I have to do the whole source estimation in the respective package?



They both are Matlab base packages and support import/export of
surface/volume data, using freesurfer and mne matlab toolboxes you can
easily exchange data between the packages.



i had to look into this lately and it turns out there now a solution and super simple using the scale_mri function.

you can simply do something like:

mne.coreg.scale_mri("fsaverage", "fsaverage_small", scale=0.9, subjects_dir=subjects_dir, annot=True, overwrite=True)

and this will create a new subject with a head 90% the size of fsaverage.