how to visualize

[andraderenew]

Dear community: My question goes to how to run the code in eegnb examples with this command "python viz". When I run that I have to change certain things inside the code of course. So I change 'eegnb_examples' for 'local' and 'muse2016' for 'muse2'. Still that doesn't make the trick. What shall I do further on?

File "01r__n170_viz.py", line 63, in data_dir = eegnb_data_path) File "/Users/andraderenew/Downloads/eeg-notebooks-master/eegnb/analysis/utils.py", line 163, in load_data verbose=verbose, File "/Users/andraderenew/Downloads/eeg-notebooks-master/eegnb/analysis/utils.py", line 84, in load_csv_as_raw raws = concatenate_raws(raw, verbose=verbose) File "", line 22, in concatenate_raws File "/Users/andraderenew/opt/anaconda3/envs/eeg-notebooks/lib/python3.7/site-packages/mne/io/base.py", line 2465, in concatenate_raws raws[0].append(raws[1:], preload) IndexError: list index out of range

[JohnGriffiths]

Hi there.

The problem seems to be that the script is not finding any recording files.

Are you wanting to run this on the eegnb example dataset or on your own recordings?

In either case, check that the file path being generated at the start of the script is indeed pointing to a folder with .csv files in on your Machine.

[andraderenew]

I want to run this on a file being recorded with eegnb although I don't know how to check the path is the correct one. Shall I print?

[andraderenew]

the issue for me here is that I can check tht output of these two lines by printing

eegnb_data_path = os.path.join(os.path.expanduser('~/'),'.eegnb', 'data')
n170_data_path = os.path.join(eegnb_data_path, 'visual-N170', 'local')

but not of this line

raw = load_data(subject,session,
                experiment='visual-N170', site='eegnb_examples', device_name='muse2',
                data_dir = eegnb_data_path)

this is something I don't know how it reads inside.

I attach the code I changed

eegnb_data_path = os.path.join(os.path.expanduser('~/'),'.eegnb', 'data')
n170_data_path = os.path.join(eegnb_data_path, 'visual-N170', 'local')

# If dataset hasn't been downloaded yet, download it
if not os.path.isdir(n170_data_path):
    fetch_dataset(data_dir=eegnb_data_path, experiment='visual-N170', site='eegnb_examples');

subject = 1
session = 1
raw = load_data(subject,session,
                experiment='visual-N170', site='eegnb_examples', device_name='muse2',
                data_dir = eegnb_data_path)

I don't know if I have to change 'eegnb_examples' to 'local'

[andraderenew]

I have tried with python console and I used local as well and nothing seems to work. It says it expects 6 arguments and saw 6.

raw = load_data(subject, session, experiment='visual-N170',site='local',device_name='muse2', data_dir='~/.eegnb/data/')

raw = load_csv_as_raw('/Users/andraderenew/.eegnb/data/visual-N170/local/muse2/subject0001/session001/recording_2021-05-21-08.15.41.csv') Traceback (most recent call last): File "", line 1, in NameError: name 'load_csv_as_raw' is not defined raw = load_data(subject, session, experiment='visual-N170', site='local', device_name='muse2', data_dir='~/.eegnb/data/') ['TP9', 'AF7', 'AF8', 'TP10', 'Right AUX', 'stim'] ['TP9', 'AF7', 'AF8', 'TP10', 'Right AUX', 'stim'] Creating RawArray with float64 data, n_channels=6, n_times=12 Range : 0 ... 11 = 0.000 ... 0.043 secs Ready. Traceback (most recent call last): File "", line 1, in File "/Users/andraderenew/Downloads/eeg-notebooks-master/eegnb/analysis/utils.py", line 163, in load_data verbose=verbose, File "/Users/andraderenew/Downloads/eeg-notebooks-master/eegnb/analysis/utils.py", line 62, in load_csv_as_raw data = pd.read_csv(fn) File "/Users/andraderenew/opt/anaconda3/envs/eeg-notebooks/lib/python3.7/site-packages/pandas/io/parsers.py", line 688, in read_csv return _read(filepath_or_buffer, kwds) File "/Users/andraderenew/opt/anaconda3/envs/eeg-notebooks/lib/python3.7/site-packages/pandas/io/parsers.py", line 460, in _read data = parser.read(nrows) File "/Users/andraderenew/opt/anaconda3/envs/eeg-notebooks/lib/python3.7/site-packages/pandas/io/parsers.py", line 1198, in read ret = self._engine.read(nrows) File "/Users/andraderenew/opt/anaconda3/envs/eeg-notebooks/lib/python3.7/site-packages/pandas/io/parsers.py", line 2157, in read data = self._reader.read(nrows) File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader.read File "pandas/_libs/parsers.pyx", line 862, in pandas._libs.parsers.TextReader._read_low_memory File "pandas/_libs/parsers.pyx", line 918, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 905, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 2042, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 6 fields in line 14, saw 7

[oreHGA]

Error tokenizing data. C error: Expected 6 fields in line 14, saw 7

Hi @andraderenew, reading through the parser error, I think this may be from the recorded .csv file... can you check the content of the .csv file on like 14 and see how many entries you have?

[ErikBjare]

@oreHGA The reason is probably due to an unmarked Markers column which starts outputting data at the 15th sample, see: https://github.com/NeuroTechX/eeg-notebooks/issues/108

[andraderenew]

I added 14 zeros(which I figured is what could fix this correct me if I'm wrong) and now I have this error

Traceback (most recent call last): File "01r__n170_viz.py", line 61, in raw = load_data(subject,session, File "/Users/andraderenew/eeg-notebooks/eegnb/analysis/utils.py", line 157, in load_data return load_csv_as_raw( File "/Users/andraderenew/eeg-notebooks/eegnb/analysis/utils.py", line 84, in load_csv_as_raw raws = concatenate_raws(raw, verbose=verbose) File "", line 22, in concatenate_raws File "/Users/andraderenew/opt/anaconda3/lib/python3.8/site-packages/mne/io/base.py", line 2213, in concatenate_raws raws[0].append(raws[1:], preload) IndexError: list index out of range

[ErikBjare]

Did you also add a header "Marker1" or such?

On Sun, Jun 20, 2021, 12:24 andraderenew @.***> wrote:

I added 14 zeros(which I figured is what could fix this correct me if I'm wrong) and now I have this error

Traceback (most recent call last): File "01r__n170_viz.py", line 61, in raw = load_data(subject,session, File "/Users/andraderenew/eeg-notebooks/eegnb/analysis/utils.py", line 157, in load_data return load_csv_as_raw( File "/Users/andraderenew/eeg-notebooks/eegnb/analysis/utils.py", line 84, in load_csv_as_raw raws = concatenate_raws(raw, verbose=verbose) File "", line 22, in concatenate_raws File "/Users/andraderenew/opt/anaconda3/lib/python3.8/site-packages/mne/io/base.py", line 2213, in concatenate_raws raws[0].append(raws[1:], preload) IndexError: list index out of range

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[andraderenew]

sorry I didn't know, so now I did add it but I still have this error.

(eeg-notebooks) andraderenew@Renes-MacBook-Air visual_n170 % python viz Traceback (most recent call last): File "01r__n170_viz.py", line 63, in data_dir = eegnb_data_path) File "/Users/andraderenew/eeg-notebooks/eegnb/analysis/utils.py", line 163, in load_data verbose=verbose, File "/Users/andraderenew/eeg-notebooks/eegnb/analysis/utils.py", line 84, in load_csv_as_raw raws = concatenate_raws(raw, verbose=verbose) File "", line 22, in concatenate_raws File "/Users/andraderenew/opt/anaconda3/envs/eeg-notebooks/lib/python3.7/site-packages/mne/io/base.py", line 2465, in concatenate_raws raws[0].append(raws[1:], preload) IndexError: list index out of range

[oreHGA]

Hi @andraderenew:

This error is pointing toward the file path not being specified correctly when load_data() is called.

Couple questions here:

• What OS are you using?
• Where does your recorded file live, by default it should be in the ~/.eegnb/ directory. Can you confirm you have recording files present in this directory?

Be sure that you have folders "subject0001" and "session001" in the data directory... this is what the subject and session value point to in the code below

• Can you share a screenshot what your recording file looks like? (it helps if we're able to see the first 30 columns at least)

Finally in your code snippet for loading the data, can you ensure it looks like this & give it another run:

eegnb_data_path = os.path.join(os.path.expanduser('~/'),'.eegnb', 'data')
n170_data_path = os.path.join(eegnb_data_path, 'visual-N170', 'local')

# If dataset hasn't been downloaded yet, download it
if not os.path.isdir(n170_data_path):
    fetch_dataset(data_dir=eegnb_data_path, experiment='visual-N170', site='eegnb_examples');

subject = 1
session = 1
raw = load_data(subject,session,
                experiment='visual-N170', site='local', device_name='muse2',
                data_dir = eegnb_data_path)

[andraderenew]

On 2 Jul 2021, at 08:14, Ore Ogundipe @.***> wrote:

Hi @andraderenew https://github.com/andraderenew:

This error is pointing toward the file path not being specified correctly in the

What OS are you using? Mac OS big sur 11.4

Where does your recorded file live, by default it should be in the ~/.eegnb/ directory. Can you confirm you have recording files present in this directory https://user-images.githubusercontent.com/13490968/124229045-dd395f00-dac1-11eb-8b00-152189d270c6.pngHere you have the screenshot Be sure that you have folders "subject0001" and "session001" in the data directory... this is what the subject and session value point to in the code below

Can you share a screenshot what your recording file looks like? (it helps if we're able to see the first 30 columns at least)

Finally in your code snippet for loading the data, can you ensure it looks like this & give it another run:

eegnb_data_path = os.path.join(os.path.expanduser('~/'),'.eegnb', 'data') n170_data_path = os.path.join(eegnb_data_path, 'visual-N170', 'local')

If dataset hasn't been downloaded yet, download it

if not os.path.isdir(n170_data_path): fetch_dataset(data_dir=eegnb_data_path, experiment='visual-N170', site='eegnb_examples');

subject = 1 session = 1 raw = load_data(subject,session, experiment='visual-N170', site='local', device_name='muse2', data_dir = eegnb_data_path)

This is what I get using the code provided!!!

(eeg-notebooks) andraderenew@Renes-MacBook-Air visual_n170 % python viz Traceback (most recent call last): File "01r__n170_viz.py", line 63, in data_dir = eegnb_data_path) File "/Users/andraderenew/eeg-notebooks/eegnb/analysis/utils.py", line 163, in load_data verbose=verbose, File "/Users/andraderenew/eeg-notebooks/eegnb/analysis/utils.py", line 65, in load_csv_as_raw ch_names = [list(data.columns)[i] for i in ch_ind] + ["stim"] File "/Users/andraderenew/eeg-notebooks/eegnb/analysis/utils.py", line 65, in ch_names = [list(data.columns)[i] for i in ch_ind] + ["stim"] IndexError: list index out of range

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