thanks for the great HCP tutorial and for brainstorm in general, it’s just fantastic!
Instead of a “Cortex surface” source model I would like to have an “MRI volume” source model to also estimate source activity in subcortical regions. I’m wondering whether this endeavour would be as easy as selecting “MRI volume” instead of “Cortex surface” or whether there are additionally steps that need to be done.
Importantly, after source estimation I would like to aggregate source time series for each subcortical region using either the subcortical segmentation of FreeSurfer or HCP’s MMP atlas.
I’m asking because in the tutorial the unprocessed MRI image is used, which might interfere with Atlas alignment.
Also, HCP provides readily computed 2d (cortex) and 3d (volume) source models (e.g. _MEG_anatomy_sourcemodel_3d4mm.mat). I wonder if these could be used within brainstorm?
From the HCP dataset, you don’t have access to surface or volume based atlases like you would when using FreeSurfer (http://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer). I am not sure how to deal with your atlas problem. If you process the T1 with FreeSurfer, you would get all the atlases, but FreeSurfer rewrites the input volume, so the anatomy would not be registered with the MEG sensors anymore, and they don’t provide the digitized head shapes of the subjects so we can’t recompute this registration.