Surface based field maps for mag and grad channels

💬 Support & Discussions
1

Hi everyone,

I am trying to understand how surface based field maps are implemented in MNE.
example code/script:

https://mne.tools/stable/auto_examples/visualization/mne_helmet.html#sphx-glr-auto-examples-visualization-mne-helmet-py

##########################
test codes with slight modification:
aim:
to plot surface based field topography # plot the maps for individual channel types and combination
#########################
import os.path as op
import mne

sample_path = mne.datasets.sample.data_path()
subjects_dir = op.join(sample_path, ‘subjects’)
fname_evoked = op.join(sample_path, ‘MEG’, ‘sample’, ‘sample_audvis-ave.fif’)
fname_inv = op.join(sample_path, ‘MEG’, ‘sample’,
‘sample_audvis-meg-oct-6-meg-inv.fif’)
fname_trans = op.join(sample_path, ‘MEG’, ‘sample’,
‘sample_audvis_raw-trans.fif’)
inv = mne.minimum_norm.read_inverse_operator(fname_inv)
evoked = mne.read_evokeds(fname_evoked, baseline=(None, 0),
proj=True, verbose=False, condition=‘Left Auditory’)

channels= [‘grad’, ‘mag’, ‘comb’]

for ch in channels:
if ch==‘comb’:
meg=True
else:
meg= ch
evk = evoked.copy().pick_types(eeg=False, meg=meg)
#evk.plot()
maps = mne.make_field_map(evk, trans=fname_trans, ch_type=‘meg’,meg_surf=‘head’,
subject=‘sample’, subjects_dir=subjects_dir)
time = 0.083
fig = mne.viz.create_3d_figure((256, 256))
mne.viz.plot_alignment(
evk.info, subject=‘sample’, subjects_dir=subjects_dir, fig=fig,
trans=fname_trans, meg=False, eeg=False, surfaces=‘white’,
coord_frame=‘mri’)
evk.plot_field(maps, time=time, fig=fig, time_label=None)
mne.viz.set_3d_view(fig, azimuth=40, elevation=87, focalpoint=(0., -0.01, 0.04), roll=-25,
distance=0.55)

Results:

surface_maps
surface_maps4234×2428 1.03 MB

scale: I have used vmax as absolute max() of the mapped data.

Questions:

  1. Gradiometer topography looks quite symmetric to magnetometer, I am not sure if the coil definitions have been changed/transform to magnetometer to reconstruct these grad maps. I looked at the codes but I found only change has been done i.e., ch_def to head coordinates since its surface based mapping. Plus, I looked at the vmax value and its in e-12 range, is it in ft/cm for grad in this case?

  2. When you do a combination of channels mapping, how do you combine the channel data without using the any conversion factor like, ft/cm to ft or similar? Can you provide me some info on it?

  3. feature request: a global scaling/color range for multiple time points comparison. I am interested in looking at the surface based topography at different time points to understand the source pattern at the sensor level. A color normalization would help instead of looking the float values with different scale. I tried z-scoring normalization earlier but somehow the maps shows only positive pattern. (but honestly, I have to check again). Any other suggestions would be helpful.

best,
Dip

2

hi Dip,

I think this code is “projecting” the magnetic field onto the skin as if it was measured directly
at the surface of the head.

Matti should be able to say more.

Alex