Note
Click here to download the full example code or to run this example in your browser via Binder
09. Storing empty room data in BIDS format¶
This example demonstrates how to store empty room data in BIDS format and how to retrieve them.
# Authors: Mainak Jas <mainakjas@gmail.com>
#
# License: BSD (3-clause)
We are dealing with MEG data, which is often accompanied by so-called “empty room” recordings for noise modeling. Below we show that we can use MNE-BIDS to also save such a recording with the just converted data.
Let us first import mne_bids.
import os.path as op
from datetime import datetime, timezone
import mne
from mne.datasets import sample
from mne_bids import write_raw_bids, read_raw_bids, make_bids_basename
And define the paths and event_id dictionary.
data_path = sample.data_path()
raw_fname = op.join(data_path, 'MEG', 'sample', 'sample_audvis_raw.fif')
bids_path = op.join(data_path, '..', 'MNE-sample-data-bids')
# Specify the raw_file and events_data and run the BIDS conversion.
raw = mne.io.read_raw_fif(raw_fname)
bids_basename = make_bids_basename(subject='01', session='01',
task='audiovisual', run='01')
write_raw_bids(raw, bids_basename, bids_path, overwrite=True)
Out:
Opening raw data file /home/stefanappelhoff/mne_data/MNE-sample-data/MEG/sample/sample_audvis_raw.fif...
Read a total of 3 projection items:
PCA-v1 (1 x 102) idle
PCA-v2 (1 x 102) idle
PCA-v3 (1 x 102) idle
Range : 25800 ... 192599 = 42.956 ... 320.670 secs
Ready.
Current compensation grade : 0
Opening raw data file /home/stefanappelhoff/mne_data/MNE-sample-data/MEG/sample/sample_audvis_raw.fif...
Read a total of 3 projection items:
PCA-v1 (1 x 102) idle
PCA-v2 (1 x 102) idle
PCA-v3 (1 x 102) idle
Range : 25800 ... 192599 = 42.956 ... 320.670 secs
Ready.
Current compensation grade : 0
Creating folder: /home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/participants.tsv'...
participant_id age sex hand
sub-01 n/a n/a n/a
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-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"
}
},
"hand": {
"Description": "Handedness of the participant",
"Levels": {
"R": "right",
"L": "left",
"A": "ambidextrous"
}
}
}
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/sub-01_ses-01_scans.tsv'...
filename acq_time
meg/sub-01_ses-01_task-audiovisual_run-01_meg.fif 2002-12-03T19:01:10
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_coordsystem.json'...
{
"MEGCoordinateSystem": "Elekta",
"MEGCoordinateUnits": "m",
"HeadCoilCoordinates": {
"NAS": [
3.725290298461914e-09,
0.10260561108589172,
4.190951585769653e-09
],
"LPA": [
-0.07137660682201385,
0.0,
5.122274160385132e-09
],
"RPA": [
0.07526767998933792,
0.0,
5.587935447692871e-09
],
"coil1": [
0.032922741025686264,
0.09897983074188232,
0.07984329760074615
],
"coil2": [
-0.06998106092214584,
0.06771647930145264,
0.06888450682163239
],
"coil3": [
-0.07260829955339432,
-0.02086828649044037,
0.0971473976969719
],
"coil4": [
0.04996863007545471,
-0.007233052980154753,
0.1228904277086258
]
},
"HeadCoilCoordinateSystem": "RAS",
"HeadCoilCoordinateUnits": "m"
}
320 events found
Event IDs: [ 1 2 3 4 5 32]
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_events.tsv'...
onset duration value sample
3.6246181587150867 0.0 2 2177
4.237323479067476 0.0 3 2545
4.946596485779753 0.0 1 2971
5.692498614904401 0.0 4 3419
6.41342634238425 0.0 2 3852
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.2.2",
"Authors": [
"MNE-BIDS"
]
}
Effective window size : 0.426 (s)
/home/stefanappelhoff/Desktop/bids/mne-bids/mne_bids/write.py:559: UserWarning: No line frequency found, defaulting to 60 Hz estimated from multi-taper FFT on 10 seconds of data.
'on 10 seconds of data.'.format(powerlinefrequency))
Reading 0 ... 166799 = 0.000 ... 277.714 secs...
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_meg.json'...
{
"TaskName": "audiovisual",
"Manufacturer": "Elekta",
"PowerLineFrequency": 60,
"SamplingFrequency": 600.614990234375,
"SoftwareFilters": "n/a",
"RecordingDuration": 277.7136813300495,
"RecordingType": "continuous",
"DewarPosition": "n/a",
"DigitizedLandmarks": false,
"DigitizedHeadPoints": false,
"MEGChannelCount": 306,
"MEGREFChannelCount": 0,
"EEGChannelCount": 60,
"EOGChannelCount": 1,
"ECGChannelCount": 0,
"EMGChannelCount": 0,
"MiscChannelCount": 0,
"TriggerChannelCount": 9
}
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_channels.tsv'...
name type units low_cutoff high_cutoff description sampling_frequency status
MEG 0113 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good
MEG 0112 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good
MEG 0111 MEGMAG T 0.10000000149011612 172.17630004882812 Magnetometer 600.614990234375 good
MEG 0122 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good
MEG 0123 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good
Copying data files to /home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_meg
Overwriting existing file.
Writing /home/stefanappelhoff/mne_data/MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_meg.fif
Closing /home/stefanappelhoff/mne_data/MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_meg.fif [done]
'/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids'
Specify some empty room data and run BIDS conversion on it.
er_raw_fname = op.join(data_path, 'MEG', 'sample', 'ernoise_raw.fif')
er_raw = mne.io.read_raw_fif(er_raw_fname)
# For empty room data we need to specify the recording date in the format
# YYYYMMDD for the session id.
er_date = er_raw.info['meas_date'].strftime('%Y%m%d')
print(er_date)
Out:
Opening raw data file /home/stefanappelhoff/mne_data/MNE-sample-data/MEG/sample/ernoise_raw.fif...
Isotrak not found
Read a total of 3 projection items:
PCA-v1 (1 x 102) idle
PCA-v2 (1 x 102) idle
PCA-v3 (1 x 102) idle
Range : 19800 ... 85867 = 32.966 ... 142.965 secs
Ready.
Current compensation grade : 0
20021206
The measurement date is
Out:
20021203
We also need to specify that the subject ID is ‘emptyroom’, and that the task is ‘noise’ (these are BIDS rules).
er_bids_basename = make_bids_basename(subject='emptyroom', session=er_date,
task='noise')
write_raw_bids(er_raw, er_bids_basename, bids_path, overwrite=True)
Out:
Opening raw data file /home/stefanappelhoff/mne_data/MNE-sample-data/MEG/sample/ernoise_raw.fif...
Isotrak not found
Read a total of 3 projection items:
PCA-v1 (1 x 102) idle
PCA-v2 (1 x 102) idle
PCA-v3 (1 x 102) idle
Range : 19800 ... 85867 = 32.966 ... 142.965 secs
Ready.
Current compensation grade : 0
Creating folder: /home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021206/meg
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/participants.tsv'...
participant_id age sex hand
sub-01 n/a n/a n/a
sub-emptyroom n/a n/a n/a
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-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"
}
},
"hand": {
"Description": "Handedness of the participant",
"Levels": {
"R": "right",
"L": "left",
"A": "ambidextrous"
}
}
}
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021206/sub-emptyroom_ses-20021206_scans.tsv'...
filename acq_time
meg/sub-emptyroom_ses-20021206_task-noise_meg.fif 2002-12-06T15:16:18
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.2.2",
"Authors": [
"MNE-BIDS"
]
}
Effective window size : 0.426 (s)
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021206/meg/sub-emptyroom_ses-20021206_task-noise_meg.json'...
{
"TaskName": "noise",
"Manufacturer": "Elekta",
"PowerLineFrequency": 60,
"SamplingFrequency": 600.614990234375,
"SoftwareFilters": "n/a",
"RecordingDuration": 109.9989195644601,
"RecordingType": "continuous",
"DewarPosition": "n/a",
"DigitizedLandmarks": false,
"DigitizedHeadPoints": false,
"MEGChannelCount": 306,
"MEGREFChannelCount": 0,
"EEGChannelCount": 0,
"EOGChannelCount": 0,
"ECGChannelCount": 0,
"EMGChannelCount": 0,
"MiscChannelCount": 0,
"TriggerChannelCount": 9
}
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021206/meg/sub-emptyroom_ses-20021206_task-noise_channels.tsv'...
name type units low_cutoff high_cutoff description sampling_frequency status
MEG 0113 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good
MEG 0112 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good
MEG 0111 MEGMAG T 0.10000000149011612 172.17630004882812 Magnetometer 600.614990234375 good
MEG 0122 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good
MEG 0123 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good
Copying data files to /home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021206/meg/sub-emptyroom_ses-20021206_task-noise_meg
Writing /home/stefanappelhoff/mne_data/MNE-sample-data-bids/sub-emptyroom/ses-20021206/meg/sub-emptyroom_ses-20021206_task-noise_meg.fif
Closing /home/stefanappelhoff/mne_data/MNE-sample-data-bids/sub-emptyroom/ses-20021206/meg/sub-emptyroom_ses-20021206_task-noise_meg.fif [done]
'/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids'
Just to illustrate, we can save more than one empty room file for different dates. Here, they will all contain the same data but in your study, they will be different on different days.
dates = ['20021204', '20021201', '20021001']
for date in dates:
er_bids_basename = make_bids_basename(subject='emptyroom', session=date,
task='noise')
er_meas_date = datetime.strptime(date, '%Y%m%d')
er_raw.set_meas_date(er_meas_date.replace(tzinfo=timezone.utc))
write_raw_bids(er_raw, er_bids_basename, bids_path, overwrite=True)
Out:
Opening raw data file /home/stefanappelhoff/mne_data/MNE-sample-data/MEG/sample/ernoise_raw.fif...
Isotrak not found
Read a total of 3 projection items:
PCA-v1 (1 x 102) idle
PCA-v2 (1 x 102) idle
PCA-v3 (1 x 102) idle
Range : 19800 ... 85867 = 32.966 ... 142.965 secs
Ready.
Current compensation grade : 0
Creating folder: /home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021204/meg
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/participants.tsv'...
participant_id age sex hand
sub-01 n/a n/a n/a
sub-emptyroom n/a n/a n/a
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-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"
}
},
"hand": {
"Description": "Handedness of the participant",
"Levels": {
"R": "right",
"L": "left",
"A": "ambidextrous"
}
}
}
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021204/sub-emptyroom_ses-20021204_scans.tsv'...
filename acq_time
meg/sub-emptyroom_ses-20021204_task-noise_meg.fif 2002-12-04T00:00:00
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.2.2",
"Authors": [
"MNE-BIDS"
]
}
Effective window size : 0.426 (s)
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021204/meg/sub-emptyroom_ses-20021204_task-noise_meg.json'...
{
"TaskName": "noise",
"Manufacturer": "Elekta",
"PowerLineFrequency": 60,
"SamplingFrequency": 600.614990234375,
"SoftwareFilters": "n/a",
"RecordingDuration": 109.9989195644601,
"RecordingType": "continuous",
"DewarPosition": "n/a",
"DigitizedLandmarks": false,
"DigitizedHeadPoints": false,
"MEGChannelCount": 306,
"MEGREFChannelCount": 0,
"EEGChannelCount": 0,
"EOGChannelCount": 0,
"ECGChannelCount": 0,
"EMGChannelCount": 0,
"MiscChannelCount": 0,
"TriggerChannelCount": 9
}
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021204/meg/sub-emptyroom_ses-20021204_task-noise_channels.tsv'...
name type units low_cutoff high_cutoff description sampling_frequency status
MEG 0113 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good
MEG 0112 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good
MEG 0111 MEGMAG T 0.10000000149011612 172.17630004882812 Magnetometer 600.614990234375 good
MEG 0122 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good
MEG 0123 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good
Copying data files to /home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021204/meg/sub-emptyroom_ses-20021204_task-noise_meg
Writing /home/stefanappelhoff/mne_data/MNE-sample-data-bids/sub-emptyroom/ses-20021204/meg/sub-emptyroom_ses-20021204_task-noise_meg.fif
Closing /home/stefanappelhoff/mne_data/MNE-sample-data-bids/sub-emptyroom/ses-20021204/meg/sub-emptyroom_ses-20021204_task-noise_meg.fif [done]
Opening raw data file /home/stefanappelhoff/mne_data/MNE-sample-data/MEG/sample/ernoise_raw.fif...
Isotrak not found
Read a total of 3 projection items:
PCA-v1 (1 x 102) idle
PCA-v2 (1 x 102) idle
PCA-v3 (1 x 102) idle
Range : 19800 ... 85867 = 32.966 ... 142.965 secs
Ready.
Current compensation grade : 0
Creating folder: /home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021201/meg
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/participants.tsv'...
participant_id age sex hand
sub-01 n/a n/a n/a
sub-emptyroom n/a n/a n/a
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-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"
}
},
"hand": {
"Description": "Handedness of the participant",
"Levels": {
"R": "right",
"L": "left",
"A": "ambidextrous"
}
}
}
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021201/sub-emptyroom_ses-20021201_scans.tsv'...
filename acq_time
meg/sub-emptyroom_ses-20021201_task-noise_meg.fif 2002-12-01T00:00:00
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.2.2",
"Authors": [
"MNE-BIDS"
]
}
Effective window size : 0.426 (s)
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021201/meg/sub-emptyroom_ses-20021201_task-noise_meg.json'...
{
"TaskName": "noise",
"Manufacturer": "Elekta",
"PowerLineFrequency": 60,
"SamplingFrequency": 600.614990234375,
"SoftwareFilters": "n/a",
"RecordingDuration": 109.9989195644601,
"RecordingType": "continuous",
"DewarPosition": "n/a",
"DigitizedLandmarks": false,
"DigitizedHeadPoints": false,
"MEGChannelCount": 306,
"MEGREFChannelCount": 0,
"EEGChannelCount": 0,
"EOGChannelCount": 0,
"ECGChannelCount": 0,
"EMGChannelCount": 0,
"MiscChannelCount": 0,
"TriggerChannelCount": 9
}
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021201/meg/sub-emptyroom_ses-20021201_task-noise_channels.tsv'...
name type units low_cutoff high_cutoff description sampling_frequency status
MEG 0113 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good
MEG 0112 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good
MEG 0111 MEGMAG T 0.10000000149011612 172.17630004882812 Magnetometer 600.614990234375 good
MEG 0122 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good
MEG 0123 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good
Copying data files to /home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021201/meg/sub-emptyroom_ses-20021201_task-noise_meg
Writing /home/stefanappelhoff/mne_data/MNE-sample-data-bids/sub-emptyroom/ses-20021201/meg/sub-emptyroom_ses-20021201_task-noise_meg.fif
Closing /home/stefanappelhoff/mne_data/MNE-sample-data-bids/sub-emptyroom/ses-20021201/meg/sub-emptyroom_ses-20021201_task-noise_meg.fif [done]
Opening raw data file /home/stefanappelhoff/mne_data/MNE-sample-data/MEG/sample/ernoise_raw.fif...
Isotrak not found
Read a total of 3 projection items:
PCA-v1 (1 x 102) idle
PCA-v2 (1 x 102) idle
PCA-v3 (1 x 102) idle
Range : 19800 ... 85867 = 32.966 ... 142.965 secs
Ready.
Current compensation grade : 0
Creating folder: /home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021001/meg
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/participants.tsv'...
participant_id age sex hand
sub-01 n/a n/a n/a
sub-emptyroom n/a n/a n/a
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-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"
}
},
"hand": {
"Description": "Handedness of the participant",
"Levels": {
"R": "right",
"L": "left",
"A": "ambidextrous"
}
}
}
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021001/sub-emptyroom_ses-20021001_scans.tsv'...
filename acq_time
meg/sub-emptyroom_ses-20021001_task-noise_meg.fif 2002-10-01T00:00:00
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.2.2",
"Authors": [
"MNE-BIDS"
]
}
Effective window size : 0.426 (s)
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021001/meg/sub-emptyroom_ses-20021001_task-noise_meg.json'...
{
"TaskName": "noise",
"Manufacturer": "Elekta",
"PowerLineFrequency": 60,
"SamplingFrequency": 600.614990234375,
"SoftwareFilters": "n/a",
"RecordingDuration": 109.9989195644601,
"RecordingType": "continuous",
"DewarPosition": "n/a",
"DigitizedLandmarks": false,
"DigitizedHeadPoints": false,
"MEGChannelCount": 306,
"MEGREFChannelCount": 0,
"EEGChannelCount": 0,
"EOGChannelCount": 0,
"ECGChannelCount": 0,
"EMGChannelCount": 0,
"MiscChannelCount": 0,
"TriggerChannelCount": 9
}
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021001/meg/sub-emptyroom_ses-20021001_task-noise_channels.tsv'...
name type units low_cutoff high_cutoff description sampling_frequency status
MEG 0113 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good
MEG 0112 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good
MEG 0111 MEGMAG T 0.10000000149011612 172.17630004882812 Magnetometer 600.614990234375 good
MEG 0122 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good
MEG 0123 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good
Copying data files to /home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021001/meg/sub-emptyroom_ses-20021001_task-noise_meg
Writing /home/stefanappelhoff/mne_data/MNE-sample-data-bids/sub-emptyroom/ses-20021001/meg/sub-emptyroom_ses-20021001_task-noise_meg.fif
Closing /home/stefanappelhoff/mne_data/MNE-sample-data-bids/sub-emptyroom/ses-20021001/meg/sub-emptyroom_ses-20021001_task-noise_meg.fif [done]
Let us look at the directory structure
from mne_bids.utils import print_dir_tree # noqa
print_dir_tree(bids_path)
Out:
|MNE-sample-data-bids/
|--- participants.tsv
|--- dataset_description.json
|--- participants.json
|--- sub-emptyroom/
|------ ses-20021201/
|--------- sub-emptyroom_ses-20021201_scans.tsv
|--------- meg/
|------------ sub-emptyroom_ses-20021201_task-noise_meg.json
|------------ sub-emptyroom_ses-20021201_task-noise_channels.tsv
|------------ sub-emptyroom_ses-20021201_task-noise_meg.fif
|------ ses-20021001/
|--------- sub-emptyroom_ses-20021001_scans.tsv
|--------- meg/
|------------ sub-emptyroom_ses-20021001_task-noise_meg.json
|------------ sub-emptyroom_ses-20021001_task-noise_meg.fif
|------------ sub-emptyroom_ses-20021001_task-noise_channels.tsv
|------ ses-20021206/
|--------- sub-emptyroom_ses-20021206_scans.tsv
|--------- meg/
|------------ sub-emptyroom_ses-20021206_task-noise_meg.json
|------------ sub-emptyroom_ses-20021206_task-noise_channels.tsv
|------------ sub-emptyroom_ses-20021206_task-noise_meg.fif
|------ ses-20021204/
|--------- sub-emptyroom_ses-20021204_scans.tsv
|--------- meg/
|------------ sub-emptyroom_ses-20021204_task-noise_meg.json
|------------ sub-emptyroom_ses-20021204_task-noise_meg.fif
|------------ sub-emptyroom_ses-20021204_task-noise_channels.tsv
|--- sub-01/
|------ ses-01/
|--------- sub-01_ses-01_scans.tsv
|--------- meg/
|------------ sub-01_ses-01_coordsystem.json
|------------ sub-01_ses-01_task-audiovisual_run-01_meg.json
|------------ sub-01_ses-01_task-audiovisual_run-01_channels.tsv
|------------ sub-01_ses-01_task-audiovisual_run-01_meg.fif
|------------ sub-01_ses-01_task-audiovisual_run-01_events.tsv
|--------- anat/
|------------ sub-01_ses-01_T1w.nii.gz
|------------ sub-01_ses-01_T1w.json
To get an accurate estimate of the noise, it is important that the empty room recording be as close in date as the raw data. We can retrieve the filename corresponding to the empty room file that is closest in time to the measurement file using MNE-BIDS.
from mne_bids import get_matched_empty_room # noqa
bids_fname = bids_basename + '_meg.fif'
best_er_fname = get_matched_empty_room(bids_fname, bids_path)
print(best_er_fname)
Out:
Opening raw data file /home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_meg.fif...
Read a total of 3 projection items:
PCA-v1 (1 x 102) idle
PCA-v2 (1 x 102) idle
PCA-v3 (1 x 102) idle
Range : 25800 ... 192599 = 42.956 ... 320.670 secs
Ready.
Current compensation grade : 0
Reading events from /home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_events.tsv.
Reading channel info from /home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_channels.tsv.
/home/stefanappelhoff/Desktop/bids/mne-bids/mne_bids/read.py:275: RuntimeWarning: The unit for channel(s) STI 001, STI 002, STI 003, STI 004, STI 005, STI 006, STI 014, STI 015, STI 016 has changed from V to NA.
raw.set_channel_types(channel_type_dict)
/home/stefanappelhoff/Desktop/bids/mne-bids/mne_bids/utils.py:635: UserWarning: Did not find any electrodes.tsv file associated with sub-01_ses-01_task-audiovisual_run-01_meg.fif.
The search_str was "/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/**/sub-01_ses-01*electrodes.tsv"
warnings.warn(msg)
/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021204/meg/sub-emptyroom_ses-20021204_task-noise_meg.fif
Finally, we can read the empty room file using
raw = read_raw_bids(best_er_fname, bids_path)
Out:
Opening raw data file /home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021204/meg/sub-emptyroom_ses-20021204_task-noise_meg.fif...
Isotrak not found
Read a total of 3 projection items:
PCA-v1 (1 x 102) idle
PCA-v2 (1 x 102) idle
PCA-v3 (1 x 102) idle
Range : 19800 ... 85867 = 32.966 ... 142.965 secs
Ready.
Current compensation grade : 0
/home/stefanappelhoff/Desktop/bids/mne-bids/mne_bids/utils.py:635: UserWarning: Did not find any events.tsv file associated with sub-emptyroom_ses-20021204_task-noise_meg.fif.
The search_str was "/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/**/sub-emptyroom_ses-20021204*events.tsv"
warnings.warn(msg)
Reading channel info from /home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021204/meg/sub-emptyroom_ses-20021204_task-noise_channels.tsv.
/home/stefanappelhoff/Desktop/bids/mne-bids/mne_bids/read.py:275: RuntimeWarning: The unit for channel(s) STI 001, STI 002, STI 003, STI 004, STI 005, STI 006, STI 014, STI 015, STI 016 has changed from V to NA.
raw.set_channel_types(channel_type_dict)
/home/stefanappelhoff/Desktop/bids/mne-bids/mne_bids/utils.py:635: UserWarning: Did not find any electrodes.tsv file associated with sub-emptyroom_ses-20021204_task-noise_meg.fif.
The search_str was "/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/**/sub-emptyroom_ses-20021204*electrodes.tsv"
warnings.warn(msg)
/home/stefanappelhoff/Desktop/bids/mne-bids/mne_bids/utils.py:635: UserWarning: Did not find any coordsystem.json file associated with sub-emptyroom_ses-20021204_task-noise_meg.fif.
The search_str was "/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/**/sub-emptyroom_ses-20021204*coordsystem.json"
warnings.warn(msg)
Total running time of the script: ( 0 minutes 3.918 seconds)
