plotting vertices/sources in the brain

I have a list of locations in an array (of the shape array([[-56.452962, -47.393728, 3.289199], etc) that I’m trying to plot on a 3D brain using mne.viz.Brain.

The code is as follows:

from mne.datasets import fetch_fsaverage
import os.path
fs_dir = fetch_fsaverage(verbose=True)
subjects_dir = os.path.dirname(fs_dir)
subject = 'fsaverage'
import mne
subjects_dir = mne.datasets.sample.data_path() + '/subjects'
Brain = mne.viz.get_brain_class()
brain = Brain('sample', hemi='both', surf='pial',cortex='classic',
              subjects_dir=subjects_dir, alpha = 0.2, size=(800, 600))
brain.add_foci(data, hemi='rh',color='blue')

I have two questions:

  1. I’m not sure what coordinate space my data is in and judging by the plots, it might be wrong but I’m not sure how to adjust it.
  2. the “data” array has locations in both hemispheres, but I can only add the foci if I specify left or right, why can’t I specify “both” hemispheres?

Hello @vss245 and welcome to the forum!

I don’t understand the question. To convert your data into a different coordinate system, you will have to apply some sort of transformation. Without knowing the source coordinate system, there’s no way to know if and which transform to apply.

I believe this is a limitation inherited from FreeSurfer, which treats the hemispheres separately.

Have you had a look at the Label class? I believe this could be what you need.

hi Richard, thanks for the answers. I assumed that MNE might account for some standard coordinate spaces (e.g. MNI, Talaraich) that I can explicitly set when plotting, but I will try to find out the coordinate system of my data by cross-checking it against atlases or something like that. thanks for the answer on the hemispheres point and I will try the Label class!

MNE-Python internally stores everything in SI units, which for source locations means the units are meters. The coordinate frame is usually “head” which is a Right-Anterior-Superior frame defined by the cardinal anatomical points (nasion, left- and right-preauricular points). Much more info can be found here: