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