Note
Click here to download the full example code or to run this example in your browser via Binder
Convert EEG data to BIDS format¶
In this example, we use MNE-BIDS to create a BIDS-compatible directory of EEG data. Specifically, we will follow these steps:
Download some EEG data from the PhysioBank database.
Load the data, extract information, and save in a new BIDS directory
Check the result and compare it with the standard
# Authors: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
# License: BSD (3-clause)
We are importing everything we need for this example:
import os
import shutil as sh
import mne
from mne.datasets import eegbci
from mne_bids import write_raw_bids, make_bids_basename
from mne_bids.utils import print_dir_tree
Step 1: Download the data¶
First, we need some data to work with. We will use the EEG Motor Movement/Imagery Dataset available on the PhysioBank database.
The data consists of 109 volunteers performing 14 experimental runs each. For each subject, there were two baseline tasks (1. eyes open, 2. eyes closed) as well as four different motor imagery tasks. For the present example, we will show how to format the data for two subjects and selected tasks to comply with the Brain Imaging Data Structure (BIDS).
Conveniently, there is already a data loading function available with MNE-Python:
# Make a directory to save the data to
home = os.path.expanduser('~')
mne_dir = os.path.join(home, 'mne_data')
if not os.path.exists(mne_dir):
os.makedirs(mne_dir)
# Define which tasks we want to download.
tasks = [2, # This is 2 minutes of eyes closed rest
4, # This is run #1 of imagining to close left or right fist
12] # This is run #2 of imagining to close left or right fist
# Download the data for subjects 1 and 2
for subj_idx in [1, 2]:
eegbci.load_data(subject=subj_idx,
runs=tasks,
path=mne_dir,
update_path=True)
Let’s see whether the data has been downloaded using a quick visualization of the directory tree.
data_dir = os.path.join(mne_dir, 'MNE-eegbci-data')
print_dir_tree(data_dir)
Out:
|MNE-eegbci-data/
|--- files/
|------ eegmmidb/
|--------- 1.0.0/
|------------ S001/
|--------------- S001R12.edf
|--------------- S001R04.edf
|--------------- S001R02.edf
|------------ S002/
|--------------- S002R04.edf
|--------------- S002R12.edf
|--------------- S002R02.edf
|--- physiobank/
|------ database/
|--------- eegmmidb/
|------------ S004/
|--------------- S004R01.edf
|------------ S001/
|--------------- S001R12.edf
|--------------- S001R04.edf
|--------------- S001R02.edf
|------------ S002/
|--------------- S002R04.edf
|--------------- S002R12.edf
|--------------- S002R02.edf
The data are in the European Data Format ‘.edf’, which is good for us because next to the BrainVision format, EDF is one of the recommended file formats for EEG BIDS. However, apart from the data format, we need to build a directory structure and supply meta data files to properly bidsify this data.
Step 2: Formatting as BIDS¶
Let’s start by formatting a single subject. We are reading the data using
MNE-Python’s io module and the read_raw_edf() function. Note that we
must use preload=False, the default in MNE-Python. It prevents the data
from being loaded and modified when converting to BIDS.
edf_path = eegbci.load_data(subject=1, runs=2)[0]
raw = mne.io.read_raw_edf(edf_path, preload=False)
Out:
Extracting EDF parameters from /home/stefanappelhoff/mne_data/MNE-eegbci-data/physiobank/database/eegmmidb/S001/S001R02.edf...
EDF file detected
Setting channel info structure...
Creating raw.info structure...
The annotations stored in the file must be read in separately and converted into a 2D numpy array of events that is compatible with MNE.
annot = mne.read_annotations(edf_path)
raw.set_annotations(annot)
events, event_id = mne.events_from_annotations(raw)
print(raw)
Out:
Used Annotations descriptions: ['T0']
<RawEDF | S001R02.edf, n_channels x n_times : 64 x 9760 (61.0 sec), ~128 kB, data not loaded>
With this step, we have everything to start a new BIDS directory using
our data. To do that, we can use write_raw_bids()
Generally, write_raw_bids() tries to extract as much
meta data as possible from the raw data and then formats it in a BIDS
compatible way. write_raw_bids() takes a bunch of inputs, most of
which are however optional. The required inputs are:
rawbids_basenameoutput_path
… as you can see in the docstring:
print(write_raw_bids.__doc__)
Out:
Walk over a folder of files and create BIDS compatible folder.
.. warning:: The original files are simply copied over. This function
cannot convert modify data files from one format to another.
Modification of the original data files is not allowed.
Parameters
----------
raw : instance of mne.io.Raw
The raw data. It must be an instance of mne.Raw. The data should not be
loaded on disk, i.e., raw.preload must be False.
bids_basename : str
The base filename of the BIDS compatible files. Typically, this can be
generated using make_bids_basename.
Example: `sub-01_ses-01_task-testing_acq-01_run-01`.
This will write the following files in the correct subfolder of the
output_path::
sub-01_ses-01_task-testing_acq-01_run-01_meg.fif
sub-01_ses-01_task-testing_acq-01_run-01_meg.json
sub-01_ses-01_task-testing_acq-01_run-01_channels.tsv
sub-01_ses-01_task-testing_acq-01_run-01_coordsystem.json
and the following one if events_data is not None::
sub-01_ses-01_task-testing_acq-01_run-01_events.tsv
and add a line to the following files::
participants.tsv
scans.tsv
Note that the modality 'meg' is automatically inferred from the raw
object and extension '.fif' is copied from raw.filenames.
output_path : str
The path of the root of the BIDS compatible folder. The session and
subject specific folders will be populated automatically by parsing
bids_basename.
events_data : str | array | None
The events file. If a string, a path to the events file. If an array,
the MNE events array (shape n_events, 3). If None, events will be
inferred from the stim channel using `mne.find_events`.
event_id : dict | None
The event id dict used to create a 'trial_type' column in events.tsv
overwrite : bool
Whether to overwrite existing files or data in files.
Defaults to False.
If overwrite is True, any existing files with the same BIDS parameters
will be overwritten with the exception of the `participants.tsv` and
`scans.tsv` files. For these files, parts of pre-existing data that
match the current data will be replaced.
If overwrite is False, no existing data will be overwritten or
replaced.
verbose : bool
If verbose is True, this will print a snippet of the sidecar files. If
False, no content will be printed.
Returns
-------
output_path : str
The path of the root of the BIDS compatible folder.
Notes
-----
For the participants.tsv file, the raw.info['subjects_info'] should be
updated and raw.info['meas_date'] should not be None to compute the age
of the participant correctly.
We loaded ‘S001R02.edf’, which corresponds to subject 1 in the second task. The second task was to rest with closed eyes.
subject_id = '001' # zero padding to account for >100 subjects in this dataset
task = 'resteyesclosed'
raw_file = raw
output_path = os.path.join(home, 'mne_data', 'eegmmidb_bids')
Now we just need to specify a few more EEG details to get something sensible:
# Brief description of the event markers present in the data. This will become
# the `trial_type` column in our BIDS `events.tsv`. We know about the event
# meaning from the documentation on PhysioBank
trial_type = {'rest': 0, 'imagine left fist': 1, 'imagine right fist': 2}
# Now convert our data to be in a new BIDS dataset.
bids_basename = make_bids_basename(subject=subject_id, task=task)
write_raw_bids(raw_file, bids_basename, output_path, event_id=trial_type,
events_data=events, overwrite=True)
Out:
Extracting EDF parameters from /home/stefanappelhoff/mne_data/MNE-eegbci-data/physiobank/database/eegmmidb/S001/S001R02.edf...
EDF file detected
Setting channel info structure...
Creating raw.info structure...
Creating folder: /home/stefanappelhoff/mne_data/eegmmidb_bids/sub-001/eeg
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/participants.tsv'...
participant_id age sex
sub-001 n/a n/a
sub-002 n/a n/a
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/participants.json'...
{
"participant_id": {
"Description": "Unique participant identifier"
},
"age": {
"Description": "Age of the participant at time of testing",
"Units": "years"
},
"sex": {
"Description": "Biological sex of the participant",
"Levels": {
"F": "female",
"M": "male"
}
}
}
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-001/sub-001_scans.tsv'...
filename acq_time
eeg/sub-001_task-imaginefists_run-1_eeg.edf 2009-08-12T18:15:00
eeg/sub-001_task-imaginefists_run-2_eeg.edf 2009-08-12T18:15:00
eeg/sub-001_task-resteyesclosed_eeg.edf 2009-08-12T18:15:00
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-001/eeg/sub-001_task-resteyesclosed_events.tsv'...
onset duration trial_type value sample
0.0 0.0 imagine left fist 1 0
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.2.0"
}
/home/stefanappelhoff/Desktop/bids/mne-bids/mne_bids/write.py:407: UserWarning: No line frequency found, defaulting to 50 Hz
warn('No line frequency found, defaulting to 50 Hz')
Reading 0 ... 9759 = 0.000 ... 60.994 secs...
/home/stefanappelhoff/miniconda3/envs/mne_bids3/lib/python3.6/site-packages/mne/utils/docs.py:830: DeprecationWarning: Function read_montage is deprecated; ``read_montage`` is deprecated and will be removed in v0.20. Please use ``read_dig_fif``, ``read_dig_egi``, ``read_custom_montage``, or ``read_dig_captrack`` to read a digitization based on your needs instead; or ``make_standard_montage`` to create ``DigMontage`` based on template; or ``make_dig_montage`` to create a ``DigMontage`` out of np.arrays
warnings.warn(msg, category=DeprecationWarning)
/home/stefanappelhoff/miniconda3/envs/mne_bids3/lib/python3.6/site-packages/mne/utils/docs.py:813: DeprecationWarning: Class Montage is deprecated; Montage class is deprecated and will be removed in v0.20. Please use DigMontage instead.
warnings.warn(msg, category=DeprecationWarning)
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-001/eeg/sub-001_task-resteyesclosed_eeg.json'...
{
"TaskName": "resteyesclosed",
"Manufacturer": "n/a",
"PowerLineFrequency": 50,
"SamplingFrequency": 160.0,
"SoftwareFilters": "n/a",
"RecordingDuration": 60.99375,
"RecordingType": "continuous",
"EEGReference": "n/a",
"EEGGround": "n/a",
"EEGPlacementScheme": "n/a",
"EEGChannelCount": 64,
"EOGChannelCount": 0,
"ECGChannelCount": 0,
"EMGChannelCount": 0,
"MiscChannelCount": 0,
"TriggerChannelCount": 0
}
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-001/eeg/sub-001_task-resteyesclosed_channels.tsv'...
name type units low_cutoff high_cutoff description sampling_frequency status
Fc5. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fc3. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fc1. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fcz. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fc2. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Copying data files to /home/stefanappelhoff/mne_data/eegmmidb_bids/sub-001/eeg/sub-001_task-resteyesclosed_eeg.edf
'/home/stefanappelhoff/mne_data/eegmmidb_bids'
What does our fresh BIDS directory look like?
print_dir_tree(output_path)
Out:
|eegmmidb_bids/
|--- participants.tsv
|--- dataset_description.json
|--- participants.json
|--- sub-002/
|------ sub-002_scans.tsv
|------ eeg/
|--------- sub-002_task-resteyesclosed_eeg.edf
|--------- sub-002_task-resteyesclosed_events.tsv
|--------- sub-002_task-imaginefists_run-1_eeg.json
|--------- sub-002_task-imaginefists_run-2_eeg.json
|--------- sub-002_task-resteyesclosed_channels.tsv
|--------- sub-002_task-imaginefists_run-2_channels.tsv
|--------- sub-002_task-imaginefists_run-1_eeg.edf
|--------- sub-002_task-imaginefists_run-1_events.tsv
|--------- sub-002_task-imaginefists_run-1_channels.tsv
|--------- sub-002_task-imaginefists_run-2_eeg.edf
|--------- sub-002_task-imaginefists_run-2_events.tsv
|--------- sub-002_task-resteyesclosed_eeg.json
|--- sub-001/
|------ sub-001_scans.tsv
|------ eeg/
|--------- sub-001_task-resteyesclosed_eeg.edf
|--------- sub-001_task-imaginefists_run-1_events.tsv
|--------- sub-001_task-resteyesclosed_events.tsv
|--------- sub-001_task-imaginefists_run-2_channels.tsv
|--------- sub-001_task-imaginefists_run-1_eeg.json
|--------- sub-001_task-imaginefists_run-1_channels.tsv
|--------- sub-001_task-imaginefists_run-2_eeg.json
|--------- sub-001_task-resteyesclosed_channels.tsv
|--------- sub-001_task-imaginefists_run-2_eeg.edf
|--------- sub-001_task-imaginefists_run-2_events.tsv
|--------- sub-001_task-imaginefists_run-1_eeg.edf
|--------- sub-001_task-resteyesclosed_eeg.json
Looks good so far, let’s convert the data for all tasks and subjects.
# Start with a clean directory
sh.rmtree(output_path)
# Some initial information that we found in the PhysioBank documentation
task_names = {2: 'resteyesclosed',
4: 'imaginefists', # run 1
12: 'imaginefists' # run 2
}
run_mapping = {2: None, # for resting eyes closed task, there was only one run
4: '1',
12: '2'
}
# Now go over subjects and *bidsify*
for subj_idx in [1, 2]:
for task_idx in [2, 4, 12]:
# Load the data
edf_path = eegbci.load_data(subject=subj_idx, runs=task_idx)[0]
raw = mne.io.read_raw_edf(edf_path, preload=False, stim_channel=None)
annot = mne.read_annotations(edf_path)
raw.set_annotations(annot)
events, event_id = mne.events_from_annotations(raw)
bids_basename = make_bids_basename(subject='{:03}'.format(subj_idx),
task=task_names[task_idx],
run=run_mapping[task_idx])
write_raw_bids(raw, bids_basename, output_path, event_id=trial_type,
events_data=events, overwrite=True)
Out:
Extracting EDF parameters from /home/stefanappelhoff/mne_data/MNE-eegbci-data/physiobank/database/eegmmidb/S001/S001R02.edf...
EDF file detected
Setting channel info structure...
Creating raw.info structure...
Used Annotations descriptions: ['T0']
Extracting EDF parameters from /home/stefanappelhoff/mne_data/MNE-eegbci-data/physiobank/database/eegmmidb/S001/S001R02.edf...
EDF file detected
Setting channel info structure...
Creating raw.info structure...
Creating folder: /home/stefanappelhoff/mne_data/eegmmidb_bids/sub-001/eeg
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/participants.tsv'...
participant_id age sex
sub-001 n/a n/a
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/participants.json'...
{
"participant_id": {
"Description": "Unique participant identifier"
},
"age": {
"Description": "Age of the participant at time of testing",
"Units": "years"
},
"sex": {
"Description": "Biological sex of the participant",
"Levels": {
"F": "female",
"M": "male"
}
}
}
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-001/sub-001_scans.tsv'...
filename acq_time
eeg/sub-001_task-resteyesclosed_eeg.edf 2009-08-12T18:15:00
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-001/eeg/sub-001_task-resteyesclosed_events.tsv'...
onset duration trial_type value sample
0.0 0.0 imagine left fist 1 0
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.2.0"
}
Reading 0 ... 9759 = 0.000 ... 60.994 secs...
/home/stefanappelhoff/miniconda3/envs/mne_bids3/lib/python3.6/site-packages/mne/utils/docs.py:830: DeprecationWarning: Function read_montage is deprecated; ``read_montage`` is deprecated and will be removed in v0.20. Please use ``read_dig_fif``, ``read_dig_egi``, ``read_custom_montage``, or ``read_dig_captrack`` to read a digitization based on your needs instead; or ``make_standard_montage`` to create ``DigMontage`` based on template; or ``make_dig_montage`` to create a ``DigMontage`` out of np.arrays
warnings.warn(msg, category=DeprecationWarning)
/home/stefanappelhoff/miniconda3/envs/mne_bids3/lib/python3.6/site-packages/mne/utils/docs.py:813: DeprecationWarning: Class Montage is deprecated; Montage class is deprecated and will be removed in v0.20. Please use DigMontage instead.
warnings.warn(msg, category=DeprecationWarning)
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-001/eeg/sub-001_task-resteyesclosed_eeg.json'...
{
"TaskName": "resteyesclosed",
"Manufacturer": "n/a",
"PowerLineFrequency": 50,
"SamplingFrequency": 160.0,
"SoftwareFilters": "n/a",
"RecordingDuration": 60.99375,
"RecordingType": "continuous",
"EEGReference": "n/a",
"EEGGround": "n/a",
"EEGPlacementScheme": "n/a",
"EEGChannelCount": 64,
"EOGChannelCount": 0,
"ECGChannelCount": 0,
"EMGChannelCount": 0,
"MiscChannelCount": 0,
"TriggerChannelCount": 0
}
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-001/eeg/sub-001_task-resteyesclosed_channels.tsv'...
name type units low_cutoff high_cutoff description sampling_frequency status
Fc5. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fc3. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fc1. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fcz. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fc2. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Copying data files to /home/stefanappelhoff/mne_data/eegmmidb_bids/sub-001/eeg/sub-001_task-resteyesclosed_eeg.edf
Extracting EDF parameters from /home/stefanappelhoff/mne_data/MNE-eegbci-data/physiobank/database/eegmmidb/S001/S001R04.edf...
EDF file detected
Setting channel info structure...
Creating raw.info structure...
Used Annotations descriptions: ['T0', 'T1', 'T2']
Extracting EDF parameters from /home/stefanappelhoff/mne_data/MNE-eegbci-data/physiobank/database/eegmmidb/S001/S001R04.edf...
EDF file detected
Setting channel info structure...
Creating raw.info structure...
Creating folder: /home/stefanappelhoff/mne_data/eegmmidb_bids/sub-001/eeg
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/participants.tsv'...
participant_id age sex
sub-001 n/a n/a
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/participants.json'...
{
"participant_id": {
"Description": "Unique participant identifier"
},
"age": {
"Description": "Age of the participant at time of testing",
"Units": "years"
},
"sex": {
"Description": "Biological sex of the participant",
"Levels": {
"F": "female",
"M": "male"
}
}
}
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-001/sub-001_scans.tsv'...
filename acq_time
eeg/sub-001_task-imaginefists_run-1_eeg.edf 2009-08-12T18:15:00
eeg/sub-001_task-resteyesclosed_eeg.edf 2009-08-12T18:15:00
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-001/eeg/sub-001_task-imaginefists_run-1_events.tsv'...
onset duration trial_type value sample
0.0 0.0 imagine left fist 1 0
4.2 0.0 n/a 3 672
8.3 0.0 imagine left fist 1 1328
12.5 0.0 imagine right fist 2 2000
16.6 0.0 imagine left fist 1 2656
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.2.0"
}
Reading 0 ... 19999 = 0.000 ... 124.994 secs...
/home/stefanappelhoff/miniconda3/envs/mne_bids3/lib/python3.6/site-packages/mne/utils/docs.py:830: DeprecationWarning: Function read_montage is deprecated; ``read_montage`` is deprecated and will be removed in v0.20. Please use ``read_dig_fif``, ``read_dig_egi``, ``read_custom_montage``, or ``read_dig_captrack`` to read a digitization based on your needs instead; or ``make_standard_montage`` to create ``DigMontage`` based on template; or ``make_dig_montage`` to create a ``DigMontage`` out of np.arrays
warnings.warn(msg, category=DeprecationWarning)
/home/stefanappelhoff/miniconda3/envs/mne_bids3/lib/python3.6/site-packages/mne/utils/docs.py:813: DeprecationWarning: Class Montage is deprecated; Montage class is deprecated and will be removed in v0.20. Please use DigMontage instead.
warnings.warn(msg, category=DeprecationWarning)
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-001/eeg/sub-001_task-imaginefists_run-1_eeg.json'...
{
"TaskName": "imaginefists",
"Manufacturer": "n/a",
"PowerLineFrequency": 50,
"SamplingFrequency": 160.0,
"SoftwareFilters": "n/a",
"RecordingDuration": 124.99375,
"RecordingType": "continuous",
"EEGReference": "n/a",
"EEGGround": "n/a",
"EEGPlacementScheme": "n/a",
"EEGChannelCount": 64,
"EOGChannelCount": 0,
"ECGChannelCount": 0,
"EMGChannelCount": 0,
"MiscChannelCount": 0,
"TriggerChannelCount": 0
}
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-001/eeg/sub-001_task-imaginefists_run-1_channels.tsv'...
name type units low_cutoff high_cutoff description sampling_frequency status
Fc5. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fc3. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fc1. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fcz. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fc2. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Copying data files to /home/stefanappelhoff/mne_data/eegmmidb_bids/sub-001/eeg/sub-001_task-imaginefists_run-1_eeg.edf
Extracting EDF parameters from /home/stefanappelhoff/mne_data/MNE-eegbci-data/physiobank/database/eegmmidb/S001/S001R12.edf...
EDF file detected
Setting channel info structure...
Creating raw.info structure...
Used Annotations descriptions: ['T0', 'T1', 'T2']
Extracting EDF parameters from /home/stefanappelhoff/mne_data/MNE-eegbci-data/physiobank/database/eegmmidb/S001/S001R12.edf...
EDF file detected
Setting channel info structure...
Creating raw.info structure...
Creating folder: /home/stefanappelhoff/mne_data/eegmmidb_bids/sub-001/eeg
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/participants.tsv'...
participant_id age sex
sub-001 n/a n/a
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/participants.json'...
{
"participant_id": {
"Description": "Unique participant identifier"
},
"age": {
"Description": "Age of the participant at time of testing",
"Units": "years"
},
"sex": {
"Description": "Biological sex of the participant",
"Levels": {
"F": "female",
"M": "male"
}
}
}
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-001/sub-001_scans.tsv'...
filename acq_time
eeg/sub-001_task-imaginefists_run-1_eeg.edf 2009-08-12T18:15:00
eeg/sub-001_task-imaginefists_run-2_eeg.edf 2009-08-12T18:15:00
eeg/sub-001_task-resteyesclosed_eeg.edf 2009-08-12T18:15:00
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-001/eeg/sub-001_task-imaginefists_run-2_events.tsv'...
onset duration trial_type value sample
0.0 0.0 imagine left fist 1 0
4.2 0.0 n/a 3 672
8.3 0.0 imagine left fist 1 1328
12.5 0.0 imagine right fist 2 2000
16.6 0.0 imagine left fist 1 2656
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.2.0"
}
Reading 0 ... 19999 = 0.000 ... 124.994 secs...
/home/stefanappelhoff/miniconda3/envs/mne_bids3/lib/python3.6/site-packages/mne/utils/docs.py:830: DeprecationWarning: Function read_montage is deprecated; ``read_montage`` is deprecated and will be removed in v0.20. Please use ``read_dig_fif``, ``read_dig_egi``, ``read_custom_montage``, or ``read_dig_captrack`` to read a digitization based on your needs instead; or ``make_standard_montage`` to create ``DigMontage`` based on template; or ``make_dig_montage`` to create a ``DigMontage`` out of np.arrays
warnings.warn(msg, category=DeprecationWarning)
/home/stefanappelhoff/miniconda3/envs/mne_bids3/lib/python3.6/site-packages/mne/utils/docs.py:813: DeprecationWarning: Class Montage is deprecated; Montage class is deprecated and will be removed in v0.20. Please use DigMontage instead.
warnings.warn(msg, category=DeprecationWarning)
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-001/eeg/sub-001_task-imaginefists_run-2_eeg.json'...
{
"TaskName": "imaginefists",
"Manufacturer": "n/a",
"PowerLineFrequency": 50,
"SamplingFrequency": 160.0,
"SoftwareFilters": "n/a",
"RecordingDuration": 124.99375,
"RecordingType": "continuous",
"EEGReference": "n/a",
"EEGGround": "n/a",
"EEGPlacementScheme": "n/a",
"EEGChannelCount": 64,
"EOGChannelCount": 0,
"ECGChannelCount": 0,
"EMGChannelCount": 0,
"MiscChannelCount": 0,
"TriggerChannelCount": 0
}
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-001/eeg/sub-001_task-imaginefists_run-2_channels.tsv'...
name type units low_cutoff high_cutoff description sampling_frequency status
Fc5. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fc3. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fc1. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fcz. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fc2. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Copying data files to /home/stefanappelhoff/mne_data/eegmmidb_bids/sub-001/eeg/sub-001_task-imaginefists_run-2_eeg.edf
Extracting EDF parameters from /home/stefanappelhoff/mne_data/MNE-eegbci-data/physiobank/database/eegmmidb/S002/S002R02.edf...
EDF file detected
Setting channel info structure...
Creating raw.info structure...
Used Annotations descriptions: ['T0']
Extracting EDF parameters from /home/stefanappelhoff/mne_data/MNE-eegbci-data/physiobank/database/eegmmidb/S002/S002R02.edf...
EDF file detected
Setting channel info structure...
Creating raw.info structure...
Creating folder: /home/stefanappelhoff/mne_data/eegmmidb_bids/sub-002/eeg
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/participants.tsv'...
participant_id age sex
sub-001 n/a n/a
sub-002 n/a n/a
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/participants.json'...
{
"participant_id": {
"Description": "Unique participant identifier"
},
"age": {
"Description": "Age of the participant at time of testing",
"Units": "years"
},
"sex": {
"Description": "Biological sex of the participant",
"Levels": {
"F": "female",
"M": "male"
}
}
}
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-002/sub-002_scans.tsv'...
filename acq_time
eeg/sub-002_task-resteyesclosed_eeg.edf 2009-08-12T18:15:00
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-002/eeg/sub-002_task-resteyesclosed_events.tsv'...
onset duration trial_type value sample
0.0 0.0 imagine left fist 1 0
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.2.0"
}
Reading 0 ... 9759 = 0.000 ... 60.994 secs...
/home/stefanappelhoff/miniconda3/envs/mne_bids3/lib/python3.6/site-packages/mne/utils/docs.py:830: DeprecationWarning: Function read_montage is deprecated; ``read_montage`` is deprecated and will be removed in v0.20. Please use ``read_dig_fif``, ``read_dig_egi``, ``read_custom_montage``, or ``read_dig_captrack`` to read a digitization based on your needs instead; or ``make_standard_montage`` to create ``DigMontage`` based on template; or ``make_dig_montage`` to create a ``DigMontage`` out of np.arrays
warnings.warn(msg, category=DeprecationWarning)
/home/stefanappelhoff/miniconda3/envs/mne_bids3/lib/python3.6/site-packages/mne/utils/docs.py:813: DeprecationWarning: Class Montage is deprecated; Montage class is deprecated and will be removed in v0.20. Please use DigMontage instead.
warnings.warn(msg, category=DeprecationWarning)
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-002/eeg/sub-002_task-resteyesclosed_eeg.json'...
{
"TaskName": "resteyesclosed",
"Manufacturer": "n/a",
"PowerLineFrequency": 50,
"SamplingFrequency": 160.0,
"SoftwareFilters": "n/a",
"RecordingDuration": 60.99375,
"RecordingType": "continuous",
"EEGReference": "n/a",
"EEGGround": "n/a",
"EEGPlacementScheme": "n/a",
"EEGChannelCount": 64,
"EOGChannelCount": 0,
"ECGChannelCount": 0,
"EMGChannelCount": 0,
"MiscChannelCount": 0,
"TriggerChannelCount": 0
}
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-002/eeg/sub-002_task-resteyesclosed_channels.tsv'...
name type units low_cutoff high_cutoff description sampling_frequency status
Fc5. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fc3. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fc1. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fcz. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fc2. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Copying data files to /home/stefanappelhoff/mne_data/eegmmidb_bids/sub-002/eeg/sub-002_task-resteyesclosed_eeg.edf
Extracting EDF parameters from /home/stefanappelhoff/mne_data/MNE-eegbci-data/physiobank/database/eegmmidb/S002/S002R04.edf...
EDF file detected
Setting channel info structure...
Creating raw.info structure...
Used Annotations descriptions: ['T0', 'T1', 'T2']
Extracting EDF parameters from /home/stefanappelhoff/mne_data/MNE-eegbci-data/physiobank/database/eegmmidb/S002/S002R04.edf...
EDF file detected
Setting channel info structure...
Creating raw.info structure...
Creating folder: /home/stefanappelhoff/mne_data/eegmmidb_bids/sub-002/eeg
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/participants.tsv'...
participant_id age sex
sub-001 n/a n/a
sub-002 n/a n/a
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/participants.json'...
{
"participant_id": {
"Description": "Unique participant identifier"
},
"age": {
"Description": "Age of the participant at time of testing",
"Units": "years"
},
"sex": {
"Description": "Biological sex of the participant",
"Levels": {
"F": "female",
"M": "male"
}
}
}
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-002/sub-002_scans.tsv'...
filename acq_time
eeg/sub-002_task-imaginefists_run-1_eeg.edf 2009-08-12T18:15:00
eeg/sub-002_task-resteyesclosed_eeg.edf 2009-08-12T18:15:00
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-002/eeg/sub-002_task-imaginefists_run-1_events.tsv'...
onset duration trial_type value sample
0.0 0.0 imagine left fist 1 0
4.1 0.0 imagine right fist 2 656
8.2 0.0 imagine left fist 1 1312
12.3 0.0 n/a 3 1968
16.4 0.0 imagine left fist 1 2624
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.2.0"
}
Reading 0 ... 19679 = 0.000 ... 122.994 secs...
/home/stefanappelhoff/miniconda3/envs/mne_bids3/lib/python3.6/site-packages/mne/utils/docs.py:830: DeprecationWarning: Function read_montage is deprecated; ``read_montage`` is deprecated and will be removed in v0.20. Please use ``read_dig_fif``, ``read_dig_egi``, ``read_custom_montage``, or ``read_dig_captrack`` to read a digitization based on your needs instead; or ``make_standard_montage`` to create ``DigMontage`` based on template; or ``make_dig_montage`` to create a ``DigMontage`` out of np.arrays
warnings.warn(msg, category=DeprecationWarning)
/home/stefanappelhoff/miniconda3/envs/mne_bids3/lib/python3.6/site-packages/mne/utils/docs.py:813: DeprecationWarning: Class Montage is deprecated; Montage class is deprecated and will be removed in v0.20. Please use DigMontage instead.
warnings.warn(msg, category=DeprecationWarning)
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-002/eeg/sub-002_task-imaginefists_run-1_eeg.json'...
{
"TaskName": "imaginefists",
"Manufacturer": "n/a",
"PowerLineFrequency": 50,
"SamplingFrequency": 160.0,
"SoftwareFilters": "n/a",
"RecordingDuration": 122.99375,
"RecordingType": "continuous",
"EEGReference": "n/a",
"EEGGround": "n/a",
"EEGPlacementScheme": "n/a",
"EEGChannelCount": 64,
"EOGChannelCount": 0,
"ECGChannelCount": 0,
"EMGChannelCount": 0,
"MiscChannelCount": 0,
"TriggerChannelCount": 0
}
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-002/eeg/sub-002_task-imaginefists_run-1_channels.tsv'...
name type units low_cutoff high_cutoff description sampling_frequency status
Fc5. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fc3. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fc1. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fcz. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fc2. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Copying data files to /home/stefanappelhoff/mne_data/eegmmidb_bids/sub-002/eeg/sub-002_task-imaginefists_run-1_eeg.edf
Extracting EDF parameters from /home/stefanappelhoff/mne_data/MNE-eegbci-data/physiobank/database/eegmmidb/S002/S002R12.edf...
EDF file detected
Setting channel info structure...
Creating raw.info structure...
Used Annotations descriptions: ['T0', 'T1', 'T2']
Extracting EDF parameters from /home/stefanappelhoff/mne_data/MNE-eegbci-data/physiobank/database/eegmmidb/S002/S002R12.edf...
EDF file detected
Setting channel info structure...
Creating raw.info structure...
Creating folder: /home/stefanappelhoff/mne_data/eegmmidb_bids/sub-002/eeg
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/participants.tsv'...
participant_id age sex
sub-001 n/a n/a
sub-002 n/a n/a
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/participants.json'...
{
"participant_id": {
"Description": "Unique participant identifier"
},
"age": {
"Description": "Age of the participant at time of testing",
"Units": "years"
},
"sex": {
"Description": "Biological sex of the participant",
"Levels": {
"F": "female",
"M": "male"
}
}
}
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-002/sub-002_scans.tsv'...
filename acq_time
eeg/sub-002_task-imaginefists_run-1_eeg.edf 2009-08-12T18:15:00
eeg/sub-002_task-imaginefists_run-2_eeg.edf 2009-08-12T18:15:00
eeg/sub-002_task-resteyesclosed_eeg.edf 2009-08-12T18:15:00
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-002/eeg/sub-002_task-imaginefists_run-2_events.tsv'...
onset duration trial_type value sample
0.0 0.0 imagine left fist 1 0
4.1 0.0 imagine right fist 2 656
8.2 0.0 imagine left fist 1 1312
12.3 0.0 n/a 3 1968
16.4 0.0 imagine left fist 1 2624
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.2.0"
}
Reading 0 ... 19679 = 0.000 ... 122.994 secs...
/home/stefanappelhoff/miniconda3/envs/mne_bids3/lib/python3.6/site-packages/mne/utils/docs.py:830: DeprecationWarning: Function read_montage is deprecated; ``read_montage`` is deprecated and will be removed in v0.20. Please use ``read_dig_fif``, ``read_dig_egi``, ``read_custom_montage``, or ``read_dig_captrack`` to read a digitization based on your needs instead; or ``make_standard_montage`` to create ``DigMontage`` based on template; or ``make_dig_montage`` to create a ``DigMontage`` out of np.arrays
warnings.warn(msg, category=DeprecationWarning)
/home/stefanappelhoff/miniconda3/envs/mne_bids3/lib/python3.6/site-packages/mne/utils/docs.py:813: DeprecationWarning: Class Montage is deprecated; Montage class is deprecated and will be removed in v0.20. Please use DigMontage instead.
warnings.warn(msg, category=DeprecationWarning)
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-002/eeg/sub-002_task-imaginefists_run-2_eeg.json'...
{
"TaskName": "imaginefists",
"Manufacturer": "n/a",
"PowerLineFrequency": 50,
"SamplingFrequency": 160.0,
"SoftwareFilters": "n/a",
"RecordingDuration": 122.99375,
"RecordingType": "continuous",
"EEGReference": "n/a",
"EEGGround": "n/a",
"EEGPlacementScheme": "n/a",
"EEGChannelCount": 64,
"EOGChannelCount": 0,
"ECGChannelCount": 0,
"EMGChannelCount": 0,
"MiscChannelCount": 0,
"TriggerChannelCount": 0
}
Writing '/home/stefanappelhoff/mne_data/eegmmidb_bids/sub-002/eeg/sub-002_task-imaginefists_run-2_channels.tsv'...
name type units low_cutoff high_cutoff description sampling_frequency status
Fc5. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fc3. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fc1. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fcz. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Fc2. EEG µV 0.0 80.0 ElectroEncephaloGram 160.0 good
Copying data files to /home/stefanappelhoff/mne_data/eegmmidb_bids/sub-002/eeg/sub-002_task-imaginefists_run-2_eeg.edf
Step 3: Check and compare with standard¶
Now we have written our BIDS directory.
print_dir_tree(output_path)
Out:
|eegmmidb_bids/
|--- participants.tsv
|--- dataset_description.json
|--- participants.json
|--- sub-002/
|------ sub-002_scans.tsv
|------ eeg/
|--------- sub-002_task-resteyesclosed_eeg.edf
|--------- sub-002_task-resteyesclosed_events.tsv
|--------- sub-002_task-imaginefists_run-1_eeg.json
|--------- sub-002_task-imaginefists_run-2_eeg.json
|--------- sub-002_task-resteyesclosed_channels.tsv
|--------- sub-002_task-imaginefists_run-2_channels.tsv
|--------- sub-002_task-imaginefists_run-1_eeg.edf
|--------- sub-002_task-imaginefists_run-1_events.tsv
|--------- sub-002_task-imaginefists_run-1_channels.tsv
|--------- sub-002_task-imaginefists_run-2_eeg.edf
|--------- sub-002_task-imaginefists_run-2_events.tsv
|--------- sub-002_task-resteyesclosed_eeg.json
|--- sub-001/
|------ sub-001_scans.tsv
|------ eeg/
|--------- sub-001_task-resteyesclosed_eeg.edf
|--------- sub-001_task-imaginefists_run-1_events.tsv
|--------- sub-001_task-resteyesclosed_events.tsv
|--------- sub-001_task-imaginefists_run-2_channels.tsv
|--------- sub-001_task-imaginefists_run-1_eeg.json
|--------- sub-001_task-imaginefists_run-1_channels.tsv
|--------- sub-001_task-imaginefists_run-2_eeg.json
|--------- sub-001_task-resteyesclosed_channels.tsv
|--------- sub-001_task-imaginefists_run-2_eeg.edf
|--------- sub-001_task-imaginefists_run-2_events.tsv
|--------- sub-001_task-imaginefists_run-1_eeg.edf
|--------- sub-001_task-resteyesclosed_eeg.json
MNE-BIDS has created a suitable directory structure for us, and among other meta data files, it started an events.tsv and channels.tsv and made an initial dataset_description on top!
Now it’s time to manually check the BIDS directory and the meta files to add all the information that MNE-BIDS could not infer. For instance, you must describe EEGReference and EEGGround yourself. It’s easy to find these by searching for “n/a” in the sidecar files.
Remember that there is a convenient javascript tool to validate all your BIDS directories called the “BIDS-validator”, available as a web version and a command line tool:
Web version: https://bids-standard.github.io/bids-validator/
Command line tool: https://www.npmjs.com/package/bids-validator
Total running time of the script: ( 0 minutes 0.584 seconds)
