Topoplot

✉️ Mailing List Archive (read-only)
1

MNE group,

When I plot the time frequency display, I predominantly get beta desynchrony with a strong negative z-score (using power.plot_topo). When I plot that same data using the topomap (power.plot_topomap) and selecting the appropriate frequencies and time latencies the data appears as a positive Z-score. Is there a sign flip during the topomap plotting and is there a flag to set to prevent the flip?

Attached are the outputs of the code below. The data frequencies are 20-25Hz to highlight the difference in plots. Data is from a Neuromag system - using the gradiometers only.

Some code:
freqs = np.logspace(*np.log10([20, 25]), num=20)
n_cycles = freqs / 2. # different number of cycle per frequency
power_3, itc = tfr_morlet(epochs['3'], freqs=freqs, n_cycles=n_cycles, use_fft=True,
                        return_itc=True, decim=3, n_jobs=-1)
power_2, itc = tfr_morlet(epochs['2'], freqs=freqs, n_cycles=n_cycles, use_fft=True,
                        return_itc=True, decim=3, n_jobs=-1)

power_minus=copy.copy(power_3)
power_minus._data=power_3._data - power_2._data
##### TOPOPLOT#######
tf_plot=power_minus.plot_topo(baseline=(-0.5, 0), mode='zscore', title='Average power', vmin=-10, vmax=10, tmin=-.1, tmax=.9, cmap='jet')

timepoints=[-.1,.1,.3,.5,.7,]
fig, axis = plt.subplots(1, len(timepoints), figsize=(20,3))
for i,laten in enumerate(timepoints):
####TOPOPLOT MAP######
    power_minus.plot_topomap(ch_type='grad', tmin=laten, tmax=laten+.1, fmin=20, fmax=25,
                       baseline=(-0.5, 0), mode='zscore', axes=axis[i],
                       vmin=-10, vmax=10, show=False, cmap='jet', title=str(laten))
mne.viz.tight_layout()
plt.show()

Thanks,
Jeff Stout
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20180221/4340f75a/attachment-0001.html
-------------- next part --------------
A non-text attachment was scrubbed...
Name: plot_topo.png
Type: image/png
Size: 584964 bytes
Desc: plot_topo.png
Url : http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20180221/4340f75a/attachment-0002.png
-------------- next part --------------
A non-text attachment was scrubbed...
Name: plot_topomap.png
Type: image/png
Size: 129961 bytes
Desc: plot_topomap.png
Url : http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20180221/4340f75a/attachment-0003.png

2

Hi Jeff,

Could it be that your topos are combined gradiometers (and are thus squared
and positive), whereas the time freqs are all sensors?

(By the way, cmap='jet' is not recommended:
https://jakevdp.github.io/blog/2014/10/16/how-bad-is-your-colormap/)

JR

3

yes by taking the RMS of the gradiometers you loose the sign.

I don't know what could be a better way here.

You could display just the planar1 or planar2 setting eg ch_type='planar1'
in plot_topomap

HTH
Alex