Hi David
we don't have anything that does this by default, sorry. If you don't
care about the location of the white surface you could try setting all
the voxels in the wm.mgz that are left or right hippo/amygdala in the aseg
to 255 then running from autorecon2-wm forward.
cheers
Bruce
On Wed, 15
Jun 2016, David Groppe wrote:
Dear Free Surfers,
I am using FreeSurfer's pial surface to map ECoG electrodes onto the
FreeSurfer average brain for group analyses via these two methods:
Dykstra, A. R., Chan, A. M., Quinn, B. T., Zepeda, R., Keller, C. J.,
Cormier, J., et al. (2011). Individualized localization and cortical
surface-based registration of intracranial electrodes. NeuroImage, 1–42.
http://doi.org/10.1016/j.neuroimage.2011.11.046
Yang, A. I., Wang, X., Doyle, W. K., Halgren, E., Carlson, C., Belcher, T.
L., et al. (2012). Localization of dense intracranial electrode arrays using
magnetic resonance imaging. NeuroImage, 63(1), 157–165.
http://doi.org/10.1016/j.neuroimage.2012.06.039
The methods work great. However, we've noticed that the pial surface
typically underestimates the extent of the amygdala and hippocampus (see
attached example images from FreeSurfer's demo Bert subject) where we often
have electrodes. I understand that FreeSurfer does this by design, since the
amygdala and hippocampus are not neocortex. However, is there a way to force
the pial surface to include those medial temporal lobe structures for our
purposes? I tried "mris_make_surfaces -fix_mtl" but that did the opposite of
what we need (i.e., it withdrew the pial surface so that it included none of
the amygdala or hippocampus).
much appreciated,
-David
P.S. Thanks for creating and maintaining such an amazing suite of freeware.
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