Hello, I am reaching out after several unsuccessful attempts to realign head and MRI coordinates to my CTF 275 MEG recordings with the objective of performing a sources reconstruction. I think my issue might be somehow related to #4727.
I don’t have access to the individualized MRI scans of my subjects, hence at first I’ve tried to perform the sources reconstruction based either on a pre-made head model (e.g. ‘fsaverage’) or lately, on a sphere head model ( i.e. based on the the 3 cardinal fiducial points plus 29 other extra digitization points from my raw files) assuming it was easier to align it in space.
The steps I normally use for my datasets consist of a standard Pre-processing pipeline (e.g. Filtering, Finding events, Making a montage, Choosing Picks (meg + ref_meg), Epoching, Auto-reject, ICA), to later proceed to do the sources reconstruction. Nonetheless, I’ve got stuck several times trying to create the forward solution always with the same error message:
“Found N sensors inside the outermost sphere shell / scalp surface”
Here are some images of how the plot_alignment outputs look like at different runs:
In my last attempts I have thought that the problem was based on the origin coordinates I was passing to the make_sphere_model commnad through fit_sphere_to_headshape. Therefore, I have tried to copy the “origin device coordinates” (i.e. output in my bash window) manually to the sphere hoping that was going to work, but it was not the case. I have also tried to then look for those origin coordinates of my different frames of reference (e.g. head/MEG), but I haven’t been able to pull the coordinates from: mne-python/constants.py at main · mne-tools/mne-python · GitHub
I have also tried to empirically calculate the real MEG origin coordinates from data.info[‘dev_head_t’][‘trans’], hoping that would help me to compensate manually for the RunTimeWarning that says that (x,y) fit is more than 20 mm from head frame origin, but I was not quite sure on how to accurately compensate spatially those 20 mm that are mismatching.
Long story short, I feel I am running in circles from one possibility to another just in order to overcome what it seems to be a simple geometric problem. Thus, any advice to move forward (pun intended) in my analysis would be very much appreciated.
Thanks in advance for your inputs.
- MNE version: 1.0.3
- operating system: CentOS Linux 7