FsAverage Scale

✉️ Mailing List Archive (read-only)
1

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,

Christian

2

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.

Best,
Alex

3

hi Christian,

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

http://neuroimage.usc.edu/brainstorm/Tutorials/TutWarping

Sheraz

4

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?

Thanks!

Christian

5

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.

Sheraz

6

hi,

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.

Alex

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