[Mne_analysis] a junior question on mne_setup_source_space

[peng]

Dear MNE users,

 I am new to MNE software. I wish to establish source space based on the
brain surface. I first run recon-all in freesurfer (latest version) to
generate potentially necessary files for MNE. Then I run
===
mne_setup_source_space --subject <my subject> --ico 4 --overwrite
===
to generate the source locations for a particular subject (<my subject>).

Then I had many files in the /bem folder, including an xxx-rh.pnt file,
which I assume is the coordinates of these locations in the right
hemisphere. I then used freeview (part of freesurfer) to load the brain
image (/mri/brain.mgz) of this subject; and overlap xxx-rh.pnt as dot sets.
I surprisingly found these dots are not located one the surface of the
white matter as expected, but much lower (several centimeters).
If I changed <my subject> with fsaverage (template from freesurfer), and
re-run the above command, the new generated dots seemed to be on the
correct place.
Third, I changed <my subject> with an icbm152 asym template, the result was
similar to <my subject> : the dots were lower than the image.

So I am a little confused. Shall I do some coordinates transformation to
align these dots to the mri image? Or it is just a display problem of
freeview? I quickly browsed the manual and had not find a direct answer
yet. Thanks a lot for any hint!

best
Peng
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