mne使用教程（二）

02 working_with_BIDS _data

envs:

• matplotlib 3.4.3
• pathlib 1.0.1
• mne 0.23.0
• mne-bids 0.8

Working with BIDS data

import matplotlib
import pathlib

import mne
import mne_bids

import warnings
warnings.filterwarnings("ignore")

matplotlib.use("Qt5Agg")

Read the input data we wish to convert to BIDS

sample_data_dir = mne.datasets.sample.data_path()
sample_data_dir = pathlib.Path(sample_data_dir)

raw_path = sample_data_dir / 'MEG' / 'sample' / 'sample_audvis_raw.fif'
raw = mne.io.read_raw(raw_path)

events = mne.find_events(raw)
event_id = {
    'Auditory/Left': 1,
    'Auditory/Right': 2,
    'Visual/Left': 3,
    'Visual/Right': 4,
    'Smiley': 5,
    'Button': 32
}

Write the raw data to BIDS

We need to specify the power line frequency

raw.info['line_freq'] = 60

subject_info = {
    'birthday': (1988, 10, 1),
    'sex': 2,
    'hand': 3
}

raw.info['subject_info'] = subject_info
raw.info

Measurement date December 03, 2002 19:01:10 GMT
Experimenter MEG
Participant
Digitized points 146 points
Good channels 102 magnetometer, 203 gradiometer, and 59 EEG channels
Bad channels MEG 2443, EEG 053
EOG channels EOG 061
ECG channels Not available
Sampling frequency 600.61 Hz
Highpass 0.10 Hz
Lowpass 172.18 Hz

Now,actually write the data

out_path = pathlib.Path('out_data/sample_BIDS')

bids_path = mne_bids.BIDSPath(subject='01',
                             session='01',
                             task='audiovisual',
                             run='01',
                             root=out_path)

mne_bids.write_raw_bids(raw, bids_path=bids_path, events_data=events,
                       event_id=event_id,overwrite=True)

BIDSPath(
root: out_data/sample_BIDS
datatype: meg
basename: sub-01_ses-01_task-audiovisual_run-01_meg.fif)

Write MEGIN/Elekta/NeuroMag fine-calibration and crosstalk files

cal_path = sample_data_dir / 'SSS' / 'sss_cal_mgh.dat'
ct_path = sample_data_dir / 'SSS' / 'ct_sparse_mgh.fif'

mne_bids.write_meg_calibration(cal_path, bids_path=bids_path)
mne_bids.write_meg_crosstalk(ct_path, bids_path=bids_path)

Print the created file & dirctory structure

mne_bids.print_dir_tree(out_path)

Generate a data summary

print(mne_bids.make_report(out_path))

Reading BIDS data

Let’s try to read back the data we just stored according to the BIDS specification.

bids_root = pathlib.Path('out_data/sample_BIDS')

bids_path = mne_bids.BIDSPath(subject='01',
                             session='01',
                             task='audiovisual',
                             run='01',
                             datatype='meg',
                             root=bids_root)

raw = mne_bids.read_raw_bids(bids_path)

raw.plot();

Events are sorted as annotations-but we convert between the two.

raw.annotations[0]

OrderedDict([(‘onset’, 46.58058882905339),
(‘duration’, 0.0),
(‘description’, ‘Auditory/Right’),
(‘orig_time’,
datetime.datetime(2002, 12, 3, 19, 1, 10, 720100, tzinfo=datetime.timezone.utc))])

events, event_id = mne.events_from_annotations(raw)

mne.viz.plot_events(events, event_id=event_id, sfreq=raw.info['sfreq']);

Fine the MEG fine-calibration and crosstalk files

bids_path.meg_calibration_fpath

WindowsPath(‘out_data/sample_BIDS/sub-01/ses-01/meg/sub-01_ses-01_acq-calibration_meg.dat’)

bids_path.meg_crosstalk_fpath

WindowsPath(‘out_data/sample_BIDS/sub-01/ses-01/meg/sub-01_ses-01_acq-crosstalk_meg.fif’)

摘自B站：https://www.bilibili.com/video/BV1dt4y1k7LJ/?spm_id_from=333.788.recommend_more_video.0

2021/8/22