Hello,
I have a few questions about the coordinate systems MNE uses.
1) When I use the Matlab toolbox functions mne_read_bem_surfaces,
fiff_read_mri, and mne_read_surfaces, the resulting structures are all
in the same coordinate system? If so, the transformation matrix in
result.trans.trans is all that needs to be used to take these
structures to the head coordinate system? If not, how can I take these
structures from the MRI coordinates to head coordinates? (I'm assuming
that the matlab functions to read the MEG data already return the data
in the head frame, but let me know if I'm wrong about that too).
2) mne_analyze has a great tool to align the MEG data to MRIs using
the digitized points. I figure that the transformation matrix after
the aligning process is stored in the COR* files in the subject's
folder. In this case, if I open that COR*.fif file in matlab with
fiff_read_mri, can I just use the trans.trans matrix that comes with
it to take the MRI to the head coordinate system?
3) When I use mne_read_surfaces I get an array with two surfaces, one
for each hemisphere. Is there a quick way to plot them together as one
connected brain (e.g. as it is done in mne_analyze visualizer)? If I
just plot both arrays they get plotted on top of each other...
Thanks,
Gus