I have an application outside freesurfer/mne where I need the scalp/face surface from the MRI file. I was able to generate the scalp surface through mne analysis pipeline in the bem folders, but when I read the subject-outer_skin.surf file in matlab using the read_surf command I see that the facial features (nose, eyes, lips, chin) are not clear. But when I viewed the MRI file using mrilab I can see the facial features clearly. So I was wondering if there is a way to get good face shape from the MRI file. I'm also up for any suggestions/hints.
I am copying from mne manual, method to get high resolution head surfaces
7.16.1Using a high-resolution head surface tessellation
The newest version of FreeSurfer contains a script called mkheadsurfwhich
can be used for coordinate alignment purposes. For more information,
try mkheadsurf --help. This script produces a file called
surf/lh.smseghead, which can be converted into a fif file using
mne_surf2bem.
Suggested usage:
1.Set the SUBJECTS_DIR correctly.
2.Run mkheadsurf: mkheadsurf -subjid <subject>.
3.Goto the directory $SUBJECTS_DIR/<subject>/bem.
4.Convert the head surface file: mne_surf2bem --surf ../surf/lh.smseghead
--id 4 --check --fif <subject>-head-dense.fif
5.Rename the existing head surface file to <subject>-head-sparse.fif
6.Copy <subject>-head-dense.fif to <subject>-head.fif
7.Click Reload in the viewer window.
After this you can switch between the dense and smooth head surface
tessellations
by copying either <subject>-head-dense.fif or <subject>-
head-sparse.fif to <subject>-head.fif.
Important: While the dense head surface tessellation may help in coordinate
frame alignment, it will slow down the operation of the viewer window
considerably. Furthermore, it cannot be used in forward modelling due to
the huge number of triangles. For the BEM, the dense tessellation does not
provide much benefit because the potential distributions are quite smooth
and widespread on the scalp.