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.