# Plotting of mne.combine\_evoked output based on AverageTFR input (mutiple channels) only shows TFR output of the first channel

**URL:** <https://mne.discourse.group/t/plotting-of-mne-combine-evoked-output-based-on-averagetfr-input-mutiple-channels-only-shows-tfr-output-of-the-first-channel/3008>\
**Category:** Support & Discussions\
**Tags:** time-frequency\
**Created:** [April 19, 2021, 3:53am UTC](https://mne.discourse.group/t/plotting-of-mne-combine-evoked-output-based-on-averagetfr-input-mutiple-channels-only-shows-tfr-output-of-the-first-channel/3008 "2021-04-19T03:53:24Z")\
**Posts on this page:** 9\
**Page:** 1

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**Author:** ![AaronAng](https://avatars.discourse-cdn.com/v4/letter/a/ac8455/32.png) [@AaronAng](https://mne.discourse.group/u/AaronAng)\
**Post date:** [April 19, 2021, 3:53am UTC](https://mne.discourse.group/t/plotting-of-mne-combine-evoked-output-based-on-averagetfr-input-mutiple-channels-only-shows-tfr-output-of-the-first-channel/3008/1 "2021-04-19T03:53:24Z")

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- MNE-Python version: 0.22.0
- operating system: Windows 10

Hi everyone,

Please refer to the following figures:

 ![2013_Combine1](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/e6de6e2767fafb603a121a150c37dd1988520966.png)

 ![2013_Single](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/6d2fa2d1fd9d52fd0200204a08fbd8f78a3a7fa6.png)

I’d like to draw attention to the middle plots (red-blue freq plot) in each of these two figures, which were created using the following codes extract:

```python
ch_name = ['MEG2013','MEG2022','MEG2023'] #For top plot
ch_name = ['MEG2013'] #For bottom plot

epochsFIF_condtion1.pick_channels(ch_name)
epochsFIF_condtion2.pick_channels(ch_name)

tfr_epochs_1 = tfr_morlet(epochsFIF_condtion1, freqs,
                                          n_cycles=n_cycles, decim=decim, use_fft=False,
                                          return_itc=False, average=False)
                
tfr_epochs_2 = tfr_morlet(epochsFIF_condtion2, freqs,
                                          n_cycles=n_cycles, decim=decim, use_fft=False,
                                          return_itc=False, average=False)

this_tfr1 = tfr_epochs_1.average()
this_tfr2 = tfr_epochs_2.average()

## Appended as this is a loop function that creates tfr_morlet data out of multiple participants.
## all_power_sets are a collection of data of all participants
all_power_set.append(this_tfr1)
all_power_set2.append(this_tfr2)   

## Loop ends here after all participants' data have been extracted. Codes below this are only reached
## after the all_power_sets have been filled with all participants' data.
##---------------------------------

## Create averaged data across all participants
tfr_condition_1 = mne.grand_average(all_power_set, interpolate_bads=True, drop_bads=True)
tfr_condition_2 = mne.grand_average(all_power_set2, interpolate_bads=True, drop_bads=True)

tfr_contrast = mne.combine_evoked([tfr_condition_1, tfr_condition_2],
                                      weights=[1, -1])
tfr_contrast.plot(axes=ax2, vmin=vmin, vmax=vmax)

```

The top middle plot was created based on information from 3 sensors whereas the bottom middle plot was created based on information from 1 sensor. However, both plots look exactly the same. Changing the position of sensors in `ch_name` makes no difference as it always plot the sensor with the smallest number (ie. 2013). I was expecting the top plot to show the averaged time-freq activity across the three sensors but this is not happening.

Am I missing a step somewhere to get the plotting done right? Or is this some kind of bug?

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<div class="post-metadata">

**Author:** ![agramfort](https://avatars.discourse-cdn.com/v4/letter/a/7c8e57/32.png) [@agramfort](https://mne.discourse.group/u/agramfort)\
**Post date:** [April 19, 2021, 6:26am UTC](https://mne.discourse.group/t/plotting-of-mne-combine-evoked-output-based-on-averagetfr-input-mutiple-channels-only-shows-tfr-output-of-the-first-channel/3008/2 "2021-04-19T06:26:44Z")

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you can compare numerical values with numpy and do the numerics looking at tfr\_condition\_1.data etc.  
Basically the data attributes of the TFR objects.

but looking at the plots they look similar but not exactly the same.

Alex

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<div class="post-metadata">

**Author:** ![AaronAng](https://avatars.discourse-cdn.com/v4/letter/a/ac8455/32.png) [@AaronAng](https://mne.discourse.group/u/AaronAng)\
**Post date:** [April 19, 2021, 8:45am UTC](https://mne.discourse.group/t/plotting-of-mne-combine-evoked-output-based-on-averagetfr-input-mutiple-channels-only-shows-tfr-output-of-the-first-channel/3008/3 "2021-04-19T08:45:18Z")

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Hi @agramfort,

Thanks for the reply! Still a little puzzled. I have now tried a different comparison using 1 vs. 20 gradiometers but the TFR output is looking the same. I believe that is unlikely that the TFR plot for 20 grads would be anywhere near the single grad.

 ![compare](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/88945d6ab3a9bd25bb746d9019cf106806f04f53.png)

Here above I have the TFR output from 1 grad and 20 grad, which looks too similar to me. The two tfr\_contrast objects look correct in terms of the length of data corresponding to the number of sensors, as reflected in the console output. The data is right, but `tfr_contrast.plot()` for the 20 grads seem to be plotting the TFR of only the first array in the list of tfr\_contrast object. Shouldn’t it be attempting to plot the average TFR of all 20 grads instead?

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<div class="post-metadata">

**Author:** ![agramfort](https://avatars.discourse-cdn.com/v4/letter/a/7c8e57/32.png) [@agramfort](https://mne.discourse.group/u/agramfort)\
**Post date:** [April 19, 2021, 9:50am UTC](https://mne.discourse.group/t/plotting-of-mne-combine-evoked-output-based-on-averagetfr-input-mutiple-channels-only-shows-tfr-output-of-the-first-channel/3008/4 "2021-04-19T09:50:29Z")

</div>

can you replicate using one dataset from mne? maybe the mne somato dataset?

so we can investigate.

Alex

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<div class="post-metadata">

**Author:** ![cbrnr](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/cbrnr/32/1409_2.png) [@cbrnr](https://mne.discourse.group/u/cbrnr)\
**Post date:** [April 19, 2021, 10:01am UTC](https://mne.discourse.group/t/plotting-of-mne-combine-evoked-output-based-on-averagetfr-input-mutiple-channels-only-shows-tfr-output-of-the-first-channel/3008/5 "2021-04-19T10:01:05Z")

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There are several things that don’t work as expected; could the behavior you’re seeing be the issue described here?

> <https://github.com/mne-tools/mne-python/issues/9125>
>
> Although AverageTFR.plot() has a picks argument, only the first channel is plotted. I don't think this is by design - or...

(Or the related issues [BUG: TFR.plot misc issues · Issue #8013 · mne-tools/mne-python · GitHub](https://github.com/mne-tools/mne-python/issues/8013) and [https://github.com/mne-tools/mne-python/pull/9150](https://github.com/mne-tools/mne-python/pull/9150))

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<div class="post-metadata">

**Author:** ![AaronAng](https://avatars.discourse-cdn.com/v4/letter/a/ac8455/32.png) [@AaronAng](https://mne.discourse.group/u/AaronAng)\
**Post date:** [April 19, 2021, 10:10am UTC](https://mne.discourse.group/t/plotting-of-mne-combine-evoked-output-based-on-averagetfr-input-mutiple-channels-only-shows-tfr-output-of-the-first-channel/3008/6 "2021-04-19T10:10:13Z")

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Hey @cbrnr,

Yes, it seems like the same exact issue.

My tfr\_contrast is an `AverageTFR` as well. So I guess the fix is still underway?

@agramfort I can try to replicate using the somato data but on a brief glance of the somato data file, it seems like there is only one event in the entire data file. Gonna go grab dinner for now. I can try to play around later in the evening by adding an additional baseline event to maybe make a simple working example closest to my `combine_evoked` setup, if required?

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<div class="post-metadata">

**Author:** ![cbrnr](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/cbrnr/32/1409_2.png) [@cbrnr](https://mne.discourse.group/u/cbrnr)\
**Post date:** [April 19, 2021, 10:49am UTC](https://mne.discourse.group/t/plotting-of-mne-combine-evoked-output-based-on-averagetfr-input-mutiple-channels-only-shows-tfr-output-of-the-first-channel/3008/7 "2021-04-19T10:49:30Z")

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@AaronAng can you check out PR #9150 and see if this fixes the problem for you?

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<div class="post-metadata">

**Author:** ![AaronAng](https://avatars.discourse-cdn.com/v4/letter/a/ac8455/32.png) [@AaronAng](https://mne.discourse.group/u/AaronAng)\
**Post date:** [April 19, 2021, 2:50pm UTC](https://mne.discourse.group/t/plotting-of-mne-combine-evoked-output-based-on-averagetfr-input-mutiple-channels-only-shows-tfr-output-of-the-first-channel/3008/8 "2021-04-19T14:50:04Z")

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@cbrnr Tried replacing the tfr.py file with the following commit [mne-python/tfr.py at tfr\_misc\_issues · eort/mne-python · GitHub](https://github.com/eort/mne-python/blob/tfr_misc_issues/mne/time_frequency/tfr.py) but I’m getting an error. This was generated using the codes with the somato data example at the bottom of this reply.

 ![error](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/65c7528c9a31c7a9383e6f889fad12d04485ddf4.png)

@agramfort the issue can be replicated using the somato example. Note that plotting `picks='all'`, is no different from plotting the first channel in `picks=[0]`.

```python
import os.path as op

import numpy as np
import matplotlib.pyplot as plt

import mne
from mne.time_frequency import tfr_morlet, psd_multitaper, psd_welch
from mne.datasets import somato

from IPython import get_ipython
get_ipython().run_line_magic('matplotlib', 'qt')

data_path = somato.data_path()
subject = '01'
task = 'somato'
raw_fname = op.join(data_path, 'sub-{}'.format(subject), 'meg',
                    'sub-{}_task-{}_meg.fif'.format(subject, task))

# Setup for reading the raw data
raw = mne.io.read_raw_fif(raw_fname)
events = mne.find_events(raw, stim_channel='STI 014')

# picks MEG gradiometers
picks = mne.pick_types(raw.info, meg='grad', eeg=False, eog=True, stim=False)

# Construct Epochs
event_id, tmin, tmax = 1, -1., 3.
baseline = (None, 0)
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, picks=picks,
                    baseline=baseline, reject=dict(grad=4000e-13, eog=350e-6),
                    preload=True)

epochs.resample(200., npad='auto') # resample to reduce computation time

# define frequencies of interest (log-spaced)
freqs = np.logspace(*np.log10([6, 35]), num=8)
n_cycles = freqs / 2. # different number of cycle per frequency
power, itc = tfr_morlet(epochs, freqs=freqs, n_cycles=n_cycles, use_fft=True,
                        return_itc=True, decim=3, n_jobs=1)

## Able to plot specific sensor data
power.plot(picks=[82], baseline=(-0.5, 0), vmin=-0.6, vmax=0.6, mode='logratio', title=power.ch_names[82])
## But once you set picks='all', .plot() only plots the first channel in the list of channels.
power.plot(picks='all', baseline=(-0.5, 0), vmin=-0.6, vmax=0.6, mode='logratio', title='all')
## Notice that the first channel's activity is a replica of the 'all' plot.
power.plot(picks=[0], baseline=(-0.5, 0), vmin=-0.6, vmax=0.6, mode='logratio', title=power.ch_names[0])
## Even selecting a reduced list of sensors lead to the same error of plotting only the first sensor
power.plot(picks=['MEG 0113', 'MEG 0112', 'MEG 0122', 'MEG 0123', 'MEG 0132'], baseline=(-0.5, 0), vmin=-0.6, vmax=0.6, mode='logratio', title='sub-selected sensors')

mne.viz.tight_layout()
plt.show()

```

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<div class="post-metadata">

**Author:** ![agramfort](https://avatars.discourse-cdn.com/v4/letter/a/7c8e57/32.png) [@agramfort](https://mne.discourse.group/u/agramfort)\
**Post date:** [April 20, 2021, 7:18am UTC](https://mne.discourse.group/t/plotting-of-mne-combine-evoked-output-based-on-averagetfr-input-mutiple-channels-only-shows-tfr-output-of-the-first-channel/3008/9 "2021-04-20T07:18:21Z")

</div>

you’re answer is in

[https://github.com/mne-tools/mne-python/blob/main/mne/time\_frequency/tfr.py#L1383](https://github.com/mne-tools/mne-python/blob/main/mne/time_frequency/tfr.py#L1383)

@larsoner wrote this apparently.

can you open an issue on github maybe?

Alex