Note
Go to the end to download the full example code.
Line noise filtering script¶
Filters the 60Hz line noise from the data, as well as the harmonics. Includes environment checks for SLURM jobs for convenience
import mne
import os
from ieeg.io import save_derivative, raw_from_layout
from ieeg.mt_filter import line_filter
from ieeg.viz.ensemble import figure_compare
from bids import BIDSLayout
Set up paths¶
HOME = os.path.expanduser("~")
# check if currently running a slurm job
# if so, set the root directory to the workspace
if 'SLURM_ARRAY_TASK_ID' in os.environ.keys():
LAB_root = os.path.join(HOME, "workspace", "CoganLab")
subject = int(os.environ['SLURM_ARRAY_TASK_ID'])
else: # if not then set box directory
LAB_root = os.path.join(HOME, "Box", "CoganLab")
subject = 5
Load Data¶
misc_path = mne.datasets.misc.data_path()
raw = mne.io.read_raw(misc_path / 'seeg' / 'sample_seeg_ieeg.fif', preload=True)
Opening raw data file /home/docs/mne_data/MNE-misc-data/seeg/sample_seeg_ieeg.fif...
Range : 1310640 ... 1370605 = 1311.411 ... 1371.411 secs
Ready.
Reading 0 ... 59965 = 0.000 ... 60.000 secs...
Filter Data¶
A filter length of 700 ms does a good job of removing 60Hz line noise, while a Filter length of 20000 ms does a good job of removing the harmonics (120Hz, 180Hz, 240Hz)
filt = line_filter(raw,
mt_bandwidth=10.,
n_jobs=1,
filter_length='700ms',
verbose=10,
freqs=[60],
notch_widths=20)
Using multitaper spectrum estimation with 13 DPSS windows
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plot the data before and after filtering
figure_compare([raw, filt],
labels=["Un", ""],
avg=True,
n_jobs=1,
verbose=10,
proj=True,
fmax=250)
No projector specified for this dataset. Please consider the method self.add_proj.
Effective window size : 1.000 (s)
Spectogram using 999-point FFT on 999 samples with 0 overlap and hamming window
Plotting power spectral density (dB=True).
/home/docs/checkouts/readthedocs.org/user_builds/ieeg-pipelines/checkouts/latest/ieeg/viz/ensemble.py:48: UserWarning: This figure was using a layout engine that is incompatible with subplots_adjust and/or tight_layout; not calling subplots_adjust.
fig.subplots_adjust(top=0.85)
No projector specified for this dataset. Please consider the method self.add_proj.
Effective window size : 1.000 (s)
Spectogram using 999-point FFT on 999 samples with 0 overlap and hamming window
Plotting power spectral density (dB=True).
/home/docs/checkouts/readthedocs.org/user_builds/ieeg-pipelines/checkouts/latest/ieeg/viz/ensemble.py:48: UserWarning: This figure was using a layout engine that is incompatible with subplots_adjust and/or tight_layout; not calling subplots_adjust.
fig.subplots_adjust(top=0.85)
Save the Data¶
Save your line noise cleaned data to bids_root/derivatives/test folder
bids_root = mne.datasets.epilepsy_ecog.data_path()
layout = BIDSLayout(bids_root)
raw = raw_from_layout(layout,
subject="pt1",
preload=True,
extension=".vhdr")
# Check if derivatives folder exists and create if not
if not os.path.exists(os.path.join(bids_root, "derivatives")):
os.mkdir(os.path.join(bids_root, "derivatives"))
os.mkdir(os.path.join(bids_root, "derivatives", "test"))
elif not os.path.exists(os.path.join(bids_root, "derivatives", "test")):
os.mkdir(os.path.join(bids_root, "derivatives", "test"))
# save the data
save_derivative(raw, layout, "test", True)
Extracting parameters from /home/docs/mne_data/MNE-epilepsy-ecog-data/sub-pt1/ses-presurgery/ieeg/sub-pt1_ses-presurgery_task-ictal_ieeg.vhdr...
Setting channel info structure...
Reading events from /home/docs/mne_data/MNE-epilepsy-ecog-data/sub-pt1/ses-presurgery/ieeg/sub-pt1_ses-presurgery_task-ictal_events.tsv.
Reading channel info from /home/docs/mne_data/MNE-epilepsy-ecog-data/sub-pt1/ses-presurgery/ieeg/sub-pt1_ses-presurgery_task-ictal_channels.tsv.
Reading electrode coords from /home/docs/mne_data/MNE-epilepsy-ecog-data/sub-pt1/ses-presurgery/ieeg/sub-pt1_ses-presurgery_space-fsaverage_electrodes.tsv.
/home/docs/checkouts/readthedocs.org/user_builds/ieeg-pipelines/checkouts/latest/ieeg/io.py:283: RuntimeWarning: DigMontage is only a subset of info. There are 3 channel positions not present in the DigMontage. The channels missing from the montage are:
['RQ1', 'RQ2', 'N/A'].
Consider using inst.rename_channels to match the montage nomenclature, or inst.set_channel_types if these are not EEG channels, or use the on_missing parameter if the channel positions are allowed to be unknown in your analyses.
whole_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)
/home/docs/checkouts/readthedocs.org/user_builds/ieeg-pipelines/checkouts/latest/ieeg/io.py:283: RuntimeWarning: Unable to map the following column(s) to to MNE:
outcome: S
engel_score: 1.0
ilae_score: 2.0
date_follow_up: n/a
ethnicity: 0.0
years_follow_up: 3.0
site: NIH
clinical_complexity: 1.0
whole_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)
Reading 0 ... 269079 = 0.000 ... 269.079 secs...
Writing '/home/docs/mne_data/MNE-epilepsy-ecog-data/derivatives/test/README'...
Writing '/home/docs/mne_data/MNE-epilepsy-ecog-data/derivatives/test/participants.tsv'...
Writing '/home/docs/mne_data/MNE-epilepsy-ecog-data/derivatives/test/participants.json'...
Writing '/home/docs/mne_data/MNE-epilepsy-ecog-data/derivatives/test/sub-pt1/ses-presurgery/ieeg/sub-pt1_ses-presurgery_space-fsaverage_electrodes.tsv'...
Writing '/home/docs/mne_data/MNE-epilepsy-ecog-data/derivatives/test/sub-pt1/ses-presurgery/ieeg/sub-pt1_ses-presurgery_space-fsaverage_coordsystem.json'...
The provided raw data contains annotations, but you did not pass an "event_id" mapping from annotation descriptions to event codes. We will generate arbitrary event codes. To specify custom event codes, please pass "event_id".
Used Annotations descriptions: [np.str_('AD1-4, ATT1,2'), np.str_('AST1,3'), np.str_('G16'), np.str_('PD'), np.str_('SLT1-3'), np.str_('offset'), np.str_('onset')]
Writing '/home/docs/mne_data/MNE-epilepsy-ecog-data/derivatives/test/sub-pt1/ses-presurgery/ieeg/sub-pt1_ses-presurgery_task-ictal_desc-test_events.tsv'...
Writing '/home/docs/mne_data/MNE-epilepsy-ecog-data/derivatives/test/sub-pt1/ses-presurgery/ieeg/sub-pt1_ses-presurgery_task-ictal_desc-test_events.json'...
Writing '/home/docs/mne_data/MNE-epilepsy-ecog-data/derivatives/test/dataset_description.json'...
Writing '/home/docs/mne_data/MNE-epilepsy-ecog-data/derivatives/test/sub-pt1/ses-presurgery/ieeg/sub-pt1_ses-presurgery_task-ictal_desc-test_ieeg.json'...
Writing '/home/docs/mne_data/MNE-epilepsy-ecog-data/derivatives/test/sub-pt1/ses-presurgery/ieeg/sub-pt1_ses-presurgery_task-ictal_desc-test_channels.tsv'...
Copying data files to sub-pt1_ses-presurgery_task-ictal_desc-test_ieeg.edf
/home/docs/checkouts/readthedocs.org/user_builds/ieeg-pipelines/checkouts/latest/ieeg/io.py:438: RuntimeWarning: Converting data files to EDF format
write_raw_bids(run, bids_path, allow_preload=True, format=format,
/home/docs/checkouts/readthedocs.org/user_builds/ieeg-pipelines/checkouts/latest/ieeg/io.py:438: RuntimeWarning: EDF format requires equal-length data blocks, so 0.92 seconds of edge values were appended to all channels when writing the final block.
write_raw_bids(run, bids_path, allow_preload=True, format=format,
Writing '/home/docs/mne_data/MNE-epilepsy-ecog-data/derivatives/test/sub-pt1/ses-presurgery/sub-pt1_ses-presurgery_scans.tsv'...
Wrote /home/docs/mne_data/MNE-epilepsy-ecog-data/derivatives/test/sub-pt1/ses-presurgery/sub-pt1_ses-presurgery_scans.tsv entry with ieeg/sub-pt1_ses-presurgery_task-ictal_desc-test_ieeg.edf.
Total running time of the script: (0 minutes 26.979 seconds)
Estimated memory usage: 3200 MB
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