The following electrodes have overlapping positions, which causes problems during visualization: VPVA, VNVB, HPHL, HNHR, Erbs, OrbOcc, Mass

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1

The following electrodes have overlapping positions, which causes problems during visualization:
VPVA, VNVB, HPHL, HNHR, Erbs, OrbOcc, Mass

  • MNE version: e.g. 0.24.0
  • operating system: e.g. macOS 12 / Windows 10 / Ubuntu 18.04

:page_facing_up:

Screenshot (181)
Screenshot (181)1920×1080 251 KB

Please also provide relevant code snippets – ideally a minimal working example (MWE).

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2

Hello @rajesh9121, and welcome to the forum!

Unfortunately, you don’t provide enough information for us to fully grasp the issue, so we can only guess. I assume that all mentioned sensors have been assigned location (0, 0, 0).

You can check this by looking at the montage:

montage = raw.get_montage()
print(montage.dig)

Do you actually need these channels in your analysis? They bear quite uncommon names.

Best wishes,
Richard

3

Screenshot (182)
Screenshot (182)1920×1080 321 KB

here is the result of the above query
montage = raw.get_montage()
print(montage.dig)
image
image1920×1080 291 KB

4

can you help me… actually iam watching your videos on youtube channel. in my data projection data not found. and position of electrodes also not there

5

Hello, can you please paste the output as text and not as screenshots, they’re extremely difficult to work with for me as I’m using the forum mostly from my phone. Copy & paste the text, select it, and click on the Preformatted text button in the toolbar to ensure it gets displayed correctly. Thank you.

6 
Fitting ICA to data using 33 channels (please be patient, this may take a while)
Selecting by number: 20 components
C:\Users\alaja\AppData\Local\Temp\ipykernel_22168\1702439165.py:2: RuntimeWarning: The data has not been high-pass filtered. For good ICA performance, it should be high-pass filtered (e.g., with a 1.0 Hz lower bound) before fitting ICA.
  ica.fit(raw)
Fitting ICA took 7.8s.
    Using multitaper spectrum estimation with 7 DPSS windows
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
~\AppData\Local\Temp\ipykernel_22168\1702439165.py in <cell line: 4>()
      2 ica.fit(raw)
      3 ica.exclude = [1, 2]  # details on how we picked these are omitted here
----> 4 ica.plot_properties(raw, picks=ica.exclude)

~\anaconda3\envs\mne\lib\site-packages\mne\preprocessing\ica.py in plot_properties(self, inst, picks, axes, dB, plot_std, topomap_args, image_args, psd_args, figsize, show, reject, reject_by_annotation, verbose)
   1950                         psd_args=None, figsize=None, show=True, reject='auto',
   1951                         reject_by_annotation=True, *, verbose=None):
-> 1952         return plot_ica_properties(self, inst, picks=picks, axes=axes,
   1953                                    dB=dB, plot_std=plot_std,
   1954                                    topomap_args=topomap_args,

<decorator-gen-186> in plot_ica_properties(ica, inst, picks, axes, dB, plot_std, topomap_args, image_args, psd_args, figsize, show, reject, reject_by_annotation, verbose)

~\anaconda3\envs\mne\lib\site-packages\mne\viz\ica.py in plot_ica_properties(ica, inst, picks, axes, dB, plot_std, topomap_args, image_args, psd_args, figsize, show, reject, reject_by_annotation, verbose)
    334     .. versionadded:: 0.13
    335     """
--> 336     return _fast_plot_ica_properties(ica, inst, picks=picks, axes=axes, dB=dB,
    337                                      plot_std=plot_std,
    338                                      topomap_args=topomap_args,

~\anaconda3\envs\mne\lib\site-packages\mne\viz\ica.py in _fast_plot_ica_properties(ica, inst, picks, axes, dB, plot_std, topomap_args, image_args, psd_args, figsize, show, reject, precomputed_data, reject_by_annotation, verbose)
    446 
    447         # the actual plot
--> 448         fig = _plot_ica_properties(
    449             pick, ica, inst, psds_mean, freqs, ica_data.shape[1],
    450             epoch_var, plot_lowpass_edge,

~\anaconda3\envs\mne\lib\site-packages\mne\viz\ica.py in _plot_ica_properties(pick, ica, inst, psds_mean, freqs, n_trials, epoch_var, plot_lowpass_edge, epochs_src, set_title_and_labels, plot_std, psd_ylabel, spectrum_std, topomap_args, image_args, fig, axes, kind, dropped_indices)
    147     # --------
    148     # component topomap
--> 149     _plot_ica_topomap(ica, pick, show=False, axes=topo_ax, **topomap_args)
    150 
    151     # image and erp

~\anaconda3\envs\mne\lib\site-packages\mne\viz\topomap.py in _plot_ica_topomap(ica, idx, ch_type, res, vmin, vmax, cmap, colorbar, title, show, outlines, contours, image_interp, axes, sensors, allow_ref_meg, extrapolate, sphere, border)
   1046     data = ica.get_components()[:, idx]
   1047     data_picks, pos, merge_channels, names, _, sphere, clip_origin = \
-> 1048         _prepare_topomap_plot(ica, ch_type, sphere=sphere)
   1049     data = data[data_picks]
   1050     outlines = _make_head_outlines(sphere, pos, outlines, clip_origin)

~\anaconda3\envs\mne\lib\site-packages\mne\viz\topomap.py in _prepare_topomap_plot(inst, ch_type, sphere)
     82 
     83     # special case for merging grad channels
---> 84     layout = find_layout(info)
     85     if (ch_type == 'grad' and layout is not None and
     86             (layout.kind.startswith('Vectorview') or

~\anaconda3\envs\mne\lib\site-packages\mne\channels\layout.py in find_layout(info, ch_type, exclude)
    424             raise RuntimeError('Cannot make EEG layout, no measurement info '
    425                                'was passed to `find_layout`')
--> 426         return make_eeg_layout(info, exclude=exclude)
    427     elif has_csd_coils and ch_type in [None, 'csd']:
    428         return make_eeg_layout(info, exclude=exclude, csd=True)

~\anaconda3\envs\mne\lib\site-packages\mne\channels\layout.py in make_eeg_layout(info, radius, width, height, exclude, csd)
    260         pick_kwargs.update(csd=True, eeg=False)
    261     picks = pick_types(info, **pick_kwargs)
--> 262     loc2d = _find_topomap_coords(info, picks)
    263     names = [info['chs'][i]['ch_name'] for i in picks]
    264 

~\anaconda3\envs\mne\lib\site-packages\mne\channels\layout.py in _find_topomap_coords(info, picks, layout, ignore_overlap, to_sphere, sphere)
    623         pos = np.asarray(pos)
    624     else:
--> 625         pos = _auto_topomap_coords(
    626             info, picks, ignore_overlap=ignore_overlap, to_sphere=to_sphere,
    627             sphere=sphere)

~\anaconda3\envs\mne\lib\site-packages\mne\channels\layout.py in _auto_topomap_coords(info, picks, ignore_overlap, to_sphere, sphere)
    722         ]
    723 
--> 724         raise ValueError('The following electrodes have overlapping positions,'
    725                          ' which causes problems during visualization:\n' +
    726                          ', '.join(problematic_electrodes))

ValueError: The following electrodes have overlapping positions, which causes problems during visualization:
VPVA, VNVB, HPHL, HNHR, Erbs, OrbOcc, Mass
7 
[quote="rajesh9121, post:3, topic:5216"]
montage = raw.get_montage()
print(montage.dig)
[/quote]

#CHOOSE WHICH RAW FILE TO RUN IN NEXT TWO LINES BELOW!!!
#raw = mne.io.read_raw_edf(raw_data_file, preload=True)
# THE EMOTIV FLEX EDF FILE IS CALLED: raw_qtest_file
raw = mne.io.read_raw_brainvision('numinous_test_data/ses-1/eeg/sub-19681349_ses-1_task-restEC_eeg.vhdr',preload=True)

#raw = mne.io.read_raw_edf('numinous_test_data/ses-1/eeg/sub-19681349_ses-1_task-restEC_eeg.vhdr', preload=True)
#raw = mne.io.read_raw_edf(raw_5meo2, preload=True)

print(raw.info)

print(raw.info['dig'])

ch_names = raw.info['ch_names'] 
ch_types = ['eeg','eeg','eeg','eeg','eeg','eeg','eeg','eeg','eeg','eeg','eeg','eeg','eeg','eeg','eeg','eeg','eeg','eeg','eeg',
           'eeg','eeg','eeg','eeg','eeg','eeg','eeg','eeg','eeg','eeg','eeg','eeg','eeg','eeg']
info = mne.create_info(ch_names=ch_names, sfreq=256, ch_types=ch_types)
raw.info = info
print(raw.info)

montage_kind = "standard_1020"
montage =  mne.channels.make_standard_montage(montage_kind)
raw.set_montage(montage, match_case=False,on_missing='ignore')

#THIS confirms that we have now added the digitization points
print(raw.info['dig'])

#The plots below rely on digitzation points being added: 
#raw.plot_projs_topomap()
raw.plot_psd_topo()
raw.plot_sensors()
montage.plot()
#print(raw.info["sfreq"])
#raw.plot_projs_topomap()    #### OF COURSE THIS LEADS TO A ZERO DIVISION ERROR SINCE THERE ARE NO PROJECTIONS IN ANY OF OUR FILES AS INDICATED IN: print(raw.info)
#ICA.plot_components(raw)





<Info | 7 non-empty values
 bads: []
 ch_names: Fp1, Fp2, F7, F3, Fz, F4, F8, FC3, FCz, FC4, T7, C3, Cz, C4, T8, ...
 chs: 33 EEG
 custom_ref_applied: False
 highpass: 0.0 Hz
 lowpass: 250.0 Hz
 meas_date: unspecified
 nchan: 33
 projs: []
 sfreq: 500.0 Hz
>
None
<Info | 7 non-empty values
 bads: []
 ch_names: Fp1, Fp2, F7, F3, Fz, F4, F8, FC3, FCz, FC4, T7, C3, Cz, C4, T8, ...
 chs: 33 EEG
 custom_ref_applied: False
 highpass: 0.0 Hz
 lowpass: 128.0 Hz
 meas_date: unspecified
 nchan: 33
 projs: []
 sfreq: 256.0 Hz
>
[<DigPoint |        LPA : (-82.5, 0.0, 0.0) mm      : head frame>, <DigPoint |     Nasion : (-0.0, 114.0, 0.0) mm     : head frame>, <DigPoint |        RPA : (82.5, -0.0, -0.0) mm     : head frame>, <DigPoint |     EEG #1 : (-30.9, 114.6, 27.9) mm   : head frame>, <DigPoint |     EEG #3 : (28.4, 115.3, 27.7) mm    : head frame>, <DigPoint |    EEG #16 : (-71.9, 73.1, 25.8) mm    : head frame>, <DigPoint |    EEG #18 : (-51.8, 86.7, 78.7) mm    : head frame>, <DigPoint |    EEG #20 : (-1.2, 93.3, 102.6) mm    : head frame>, <DigPoint |    EEG #22 : (50.3, 87.4, 77.3) mm     : head frame>, <DigPoint |    EEG #24 : (71.4, 74.5, 25.1) mm     : head frame>, <DigPoint |    EEG #29 : (-61.9, 57.1, 93.8) mm    : head frame>, <DigPoint |    EEG #31 : (-1.3, 63.5, 126.6) mm    : head frame>, <DigPoint |    EEG #33 : (60.6, 57.7, 93.8) mm     : head frame>, <DigPoint |    EEG #38 : (-86.0, 14.9, 31.2) mm    : head frame>, <DigPoint |    EEG #40 : (-67.1, 23.4, 104.5) mm   : head frame>, <DigPoint |    EEG #42 : (-1.4, 27.6, 140.2) mm    : head frame>, <DigPoint |    EEG #44 : (65.3, 23.6, 103.7) mm    : head frame>, <DigPoint |    EEG #46 : (83.3, 15.3, 31.0) mm     : head frame>, <DigPoint |    EEG #51 : (-65.5, -11.9, 107.8) mm  : head frame>, <DigPoint |    EEG #53 : (-1.5, -10.5, 141.5) mm   : head frame>, <DigPoint |    EEG #55 : (64.7, -12.0, 107.7) mm   : head frame>, <DigPoint |    EEG #60 : (-74.5, -42.1, 41.3) mm   : head frame>, <DigPoint |    EEG #62 : (-55.0, -44.2, 99.9) mm   : head frame>, <DigPoint |    EEG #64 : (-1.7, -45.2, 126.7) mm   : head frame>, <DigPoint |    EEG #66 : (53.6, -44.3, 100.5) mm   : head frame>, <DigPoint |    EEG #68 : (71.0, -42.3, 41.2) mm    : head frame>, <DigPoint |    EEG #81 : (-31.6, -80.6, 54.8) mm   : head frame>, <DigPoint |    EEG #82 : (-2.1, -82.8, 60.7) mm    : head frame>, <DigPoint |    EEG #83 : (27.7, -80.5, 54.7) mm    : head frame>]
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
~\AppData\Local\Temp\ipykernel_5452\2638937880.py in <cell line: 29>()
     27 #The plots below rely on digitzation points being added:
     28 #raw.plot_projs_topomap()
---> 29 raw.plot_psd_topo()
     30 raw.plot_sensors()
     31 montage.plot()

~\anaconda3\envs\mne\lib\site-packages\mne\io\base.py in plot_psd_topo(self, tmin, tmax, fmin, fmax, proj, n_fft, n_overlap, layout, color, fig_facecolor, axis_facecolor, dB, show, block, n_jobs, axes, verbose)
   1589                       show=True, block=False, n_jobs=1, axes=None,
   1590                       verbose=None):
-> 1591         return plot_raw_psd_topo(self, tmin=tmin, tmax=tmax, fmin=fmin,
   1592                                  fmax=fmax, proj=proj, n_fft=n_fft,
   1593                                  n_overlap=n_overlap, layout=layout,

<decorator-gen-184> in plot_raw_psd_topo(raw, tmin, tmax, fmin, fmax, proj, n_fft, n_overlap, layout, color, fig_facecolor, axis_facecolor, dB, show, block, n_jobs, axes, verbose)

~\anaconda3\envs\mne\lib\site-packages\mne\viz\raw.py in plot_raw_psd_topo(raw, tmin, tmax, fmin, fmax, proj, n_fft, n_overlap, layout, color, fig_facecolor, axis_facecolor, dB, show, block, n_jobs, axes, verbose)
    500     if layout is None:
    501         from ..channels.layout import find_layout
--> 502         layout = find_layout(raw.info)
    503 
    504     psds, freqs = psd_welch(raw, tmin=tmin, tmax=tmax, fmin=fmin,

~\anaconda3\envs\mne\lib\site-packages\mne\channels\layout.py in find_layout(info, ch_type, exclude)
    424             raise RuntimeError('Cannot make EEG layout, no measurement info '
    425                                'was passed to `find_layout`')
--> 426         return make_eeg_layout(info, exclude=exclude)
    427     elif has_csd_coils and ch_type in [None, 'csd']:
    428         return make_eeg_layout(info, exclude=exclude, csd=True)

~\anaconda3\envs\mne\lib\site-packages\mne\channels\layout.py in make_eeg_layout(info, radius, width, height, exclude, csd)
    260         pick_kwargs.update(csd=True, eeg=False)
    261     picks = pick_types(info, **pick_kwargs)
--> 262     loc2d = _find_topomap_coords(info, picks)
    263     names = [info['chs'][i]['ch_name'] for i in picks]
    264 

~\anaconda3\envs\mne\lib\site-packages\mne\channels\layout.py in _find_topomap_coords(info, picks, layout, ignore_overlap, to_sphere, sphere)
    623         pos = np.asarray(pos)
    624     else:
--> 625         pos = _auto_topomap_coords(
    626             info, picks, ignore_overlap=ignore_overlap, to_sphere=to_sphere,
    627             sphere=sphere)

~\anaconda3\envs\mne\lib\site-packages\mne\channels\layout.py in _auto_topomap_coords(info, picks, ignore_overlap, to_sphere, sphere)
    722         ]
    723 
--> 724         raise ValueError('The following electrodes have overlapping positions,'
    725                          ' which causes problems during visualization:\n' +
    726                          ', '.join(problematic_electrodes))

ValueError: The following electrodes have overlapping positions, which causes problems during visualization:
VPVA, VNVB, HPHL, HNHR, Erbs, OrbOcc, Mass
8

The electrodes VPVA, VNVB, HPHL, HNHR, Erbs, OrbOcc, Mass don’t have digitization points associated with them, hence you cannot plot a topographic map that includes these channels. Are these proper EEG channels or what are those anyway? Maybe you should just set their channel type to misc if they don’t include any EEG data anyway…

9 
[20]:

events = mne.find_events(raw_EC, stim_channel='Fp1')

events

[20]:

array([], shape=(0, 3), dtype=int32)

richard event array is showing empty… what should i do in this case

10

This seems like an unrelated question to me. Please open a new topic for new questions. Thank you!

11

I have marked these 7 channels as misc but I am still getting the same error - ValueError: The following electrodes have overlapping positions, which causes problems during visualization:
VPVA, VNVB, HPHL, HNHR, Erbs, OrbOcc, Mass