Could you help me find events from ".set" file?

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Hello, I am a student learning MNE-python.
I have trouble finding events in my ".set" file. It appears empty.
I've also tried mne.io.read_epochs_eeglab with my another epoched
".set" file, but the list of events is also empty.
To be specific, my raw eeg file was '.vhdr', '.vmrk', and
'.eeg.(BrainProduct)', with no stim_channel. And the data had no
problem when I pre-processed and ran statistics with EEGLAB and
ERPlab. Could you please help me?
I attach my continuous eeg file('001.set' , '001.fdt'), and epoched
one("001_sync.set", '001_sync.fdt")

Thank you.

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Hi!

Your markers are probably in raw.annotations. If you want to convert them to events, use mne.events_from_annotations(raw).

Clemens

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Thank you so much!! It worked!
but I've faced with another problem making custom epochs. Could you give me
some advice?

Thank you!!

I see this error even though I picked 18 channels :

ValueError: All picks must be < n_channels (30), got 30

This is my code :

event_id = {'S 4':4, 'S 6':6, 'S 7':7, 'S 1':1, 'S 5':5, 'S
3':3, 'S 2':2}
events= mne.events_from_annotations(raw)
n_channels = 32
sampling_rate = 500
info = mne.create_info(n_channels, sampling_rate)
channel_names = ['Fp1', 'Fp2', 'F3', 'F4', 'C3', 'C4', 'P3', 'P4',
'O1', 'O2', 'F7', 'F8', 'T7', 'T8', 'P7', 'P8', 'Fz', 'Cz', 'Pz',
'FC1', 'FC2', 'CP1', 'CP2', 'FC5', 'FC6', 'CP5', 'CP6', 'TP9', 'TP10',
'EOG', 'M1', 'M2']
channel_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', 'eog', 'bio', 'bio']
sfreq = 500
info['description'] = 'My custom dataset'
info['bads'] = ['Fp1', 'Fp2', 'F7', 'F8', 'T7', 'T8', 'TP9', 'TP10']
include = ['F3', 'F4', 'C3', 'C4', 'P3', 'P4', 'O1', 'O2', 'P7', 'P8',
'FC1', 'FC2', 'CP1', 'CP2', 'FC5', 'FC6', 'CP5', 'CP6']
picks = mne.pick_channels(channel_names, include=include,
exclude=info['bads'], ordered=False)
tmin= -0.2
tmax = 0.8
custom_epochs = mne.EpochsArray(raw, info, picks, events, event_id)

2019? 5? 22? (?) ?? 10:26, Brunner, Clemens (clemens.brunner at uni-graz.at) <
clemens.brunner at uni-graz.at>?? ??:

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Could you try mne.read_epochs_eeglab again? It looks like your .set file already contains the epochs, so this function should do the job. You certainly shouldn't have to construct your own info object, because this information should already be present in raw.info.

Without the data file it is difficult to tell what the exact problem is, so feel free to send it to me if my suggestion doesn't work.

Clemens

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Thank you for your reply.
It worked perfectly and you saved my day!

but could you take a look at another issue?
I get this error when I try to plot with the option, "spatial colors =
True" on Jupyter notebook. :

TypeError: get_tightbbox() got an unexpected keyword argument
'bbox_extra_artists'

Thank you.

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What matplotlib version are you using? This was a regression introduced in 3.0.1, but it should be fixed in matplotlib 3.0.2 and later (I recommend that you use the latest release if possible, which is 3.1.0).

Clemens

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I think mine is 3.1.0!

Requirement already satisfied: matplotlib in
/anaconda3/lib/python3.7/site-packages (3.1.0)

Requirement already satisfied: python-dateutil>=2.1 in
/anaconda3/lib/python3.7/site-packages (from matplotlib) (2.7.3)

Requirement already satisfied: kiwisolver>=1.0.1 in
/anaconda3/lib/python3.7/site-packages (from matplotlib) (1.0.1)

Requirement already satisfied: numpy>=1.11 in
/anaconda3/lib/python3.7/site-packages (from matplotlib) (1.15.1)

Requirement already satisfied: cycler>=0.10 in
/anaconda3/lib/python3.7/site-packages (from matplotlib) (0.10.0)

Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in
/anaconda3/lib/python3.7/site-packages (from matplotlib) (2.2.0)

Requirement already satisfied: six>=1.5 in
/anaconda3/lib/python3.7/site-packages (from
python-dateutil>=2.1->matplotlib) (1.11.0)

Requirement already satisfied: setuptools in
/anaconda3/lib/python3.7/site-packages (from kiwisolver>=1.0.1->matplotlib)
(40.6.3)

2019? 5? 23? (?) ?? 8:00, Brunner, Clemens (clemens.brunner at uni-graz.at) <
clemens.brunner at uni-graz.at>?? ??:

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You are probably in a venv which still has the old version - at least the error messages point to "/anaconda3/envs/mne/lib/python3.6", which is not the env where you have matplotlib 3.1.0 (which also has Python 3.7 and not 3.6).

Clemens

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Thank you. I've updated matplotlib and I don't see the error anymore.
but the plots still come in black and white.
I've got these warnings. Is there any way to make my plots in colors?
Thank you for your time.

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That's weird. Can you try different matplotlib backends?

Does anyone else have any idea what's going on? I have never used evoked.plot with spatial_colors myself.

Clemens

11

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that's weird

can you share a file? save your data in fif with evoked.save

Alex

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Sure. Thank you for your precious time.
Here is my evoked file.

...and since I'm new to MNE and facing new problems every day, can I ask
one more question?
I used to preprocess multiple files one by one on eeglab, but I'm wondering
if I should concatenate all of my files first and then preprocess on MNE.
Thank you!
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hi,

you have one EOG channel that has no channel location. Do:

evoked.set_channel_types({'EOG': 'eog'})

and it should solve your problem.

HTH
Alex

14

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It worked nicely! Thank you so much so far!!

2019? 5? 25? (?) ?? 4:22, Alexandre Gramfort <alexandre.gramfort at inria.fr>??
??: