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,
BIDSPath, print_dir_tree)
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_root = 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)
raw.info['line_freq'] = 60 # specify power line frequency as required by BIDS
bids_path = BIDSPath(subject='01', session='01',
task='audiovisual', run='01', root=bids_root)
write_raw_bids(raw, bids_path, overwrite=True)
Out:
Opening raw data file /Users/hoechenberger/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.
Opening raw data file /Users/hoechenberger/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.
Writing '/Users/hoechenberger/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 '/Users/hoechenberger/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 '/Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_coordsystem.json'...
{
"MEGCoordinateSystem": "ElektaNeuromag",
"MEGCoordinateUnits": "m",
"MEGCoordinateSystemDescription": "n/a",
"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": "ElektaNeuromag",
"HeadCoilCoordinateUnits": "m"
}
/Users/hoechenberger/Development/mne-bids/mne_bids/utils.py:246: RuntimeWarning: No events found or provided. Please make sure to set channel type using raw.set_channel_types or provide events_data.
warn('No events found or provided. Please make sure to'
Writing '/Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.4.0",
"DatasetType": "raw",
"Authors": [
"Please cite MNE-BIDS in your publication before removing this (citations in README)"
]
}
Reading 0 ... 166799 = 0.000 ... 277.714 secs...
Writing '/Users/hoechenberger/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 '/Users/hoechenberger/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 status_description
MEG 0113 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good n/a
MEG 0112 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good n/a
MEG 0111 MEGMAG T 0.10000000149011612 172.17630004882812 Magnetometer 600.614990234375 good n/a
MEG 0122 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good n/a
MEG 0123 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good n/a
Copying data files to sub-01_ses-01_task-audiovisual_run-01_meg.fif
Overwriting existing file.
Writing /Users/hoechenberger/mne_data/MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_meg.fif
Closing /Users/hoechenberger/mne_data/MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_meg.fif [done]
Writing '/Users/hoechenberger/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
Wrote /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/sub-01_ses-01_scans.tsv entry with meg/sub-01_ses-01_task-audiovisual_run-01_meg.fif.
BIDSPath(
root: /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids
datatype: meg
basename: sub-01_ses-01_task-audiovisual_run-01_meg.fif)
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)
er_raw.info['line_freq'] = 60 # specify power line frequency as req. by BIDS
# 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 /Users/hoechenberger/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.
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_path = BIDSPath(subject='emptyroom', session=er_date,
task='noise', root=bids_root)
write_raw_bids(er_raw, er_bids_path, overwrite=True)
Out:
Opening raw data file /Users/hoechenberger/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.
Writing '/Users/hoechenberger/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 '/Users/hoechenberger/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 of electrodes.tsv is not supported for data type "meg". Skipping ...
/Users/hoechenberger/Development/mne-bids/mne_bids/utils.py:246: RuntimeWarning: No events found or provided. Please make sure to set channel type using raw.set_channel_types or provide events_data.
warn('No events found or provided. Please make sure to'
Writing '/Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.4.0",
"DatasetType": "raw",
"Authors": [
"Please cite MNE-BIDS in your publication before removing this (citations in README)"
]
}
Writing '/Users/hoechenberger/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 '/Users/hoechenberger/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 status_description
MEG 0113 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good n/a
MEG 0112 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good n/a
MEG 0111 MEGMAG T 0.10000000149011612 172.17630004882812 Magnetometer 600.614990234375 good n/a
MEG 0122 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good n/a
MEG 0123 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good n/a
Copying data files to sub-emptyroom_ses-20021206_task-noise_meg.fif
Writing /Users/hoechenberger/mne_data/MNE-sample-data-bids/sub-emptyroom/ses-20021206/meg/sub-emptyroom_ses-20021206_task-noise_meg.fif
Closing /Users/hoechenberger/mne_data/MNE-sample-data-bids/sub-emptyroom/ses-20021206/meg/sub-emptyroom_ses-20021206_task-noise_meg.fif [done]
Writing '/Users/hoechenberger/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
Wrote /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021206/sub-emptyroom_ses-20021206_scans.tsv entry with meg/sub-emptyroom_ses-20021206_task-noise_meg.fif.
BIDSPath(
root: /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids
datatype: meg
basename: sub-emptyroom_ses-20021206_task-noise_meg.fif)
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_path.update(session=date)
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_path, overwrite=True)
Out:
Opening raw data file /Users/hoechenberger/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.
Writing '/Users/hoechenberger/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 '/Users/hoechenberger/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 of electrodes.tsv is not supported for data type "meg". Skipping ...
/Users/hoechenberger/Development/mne-bids/mne_bids/utils.py:246: RuntimeWarning: No events found or provided. Please make sure to set channel type using raw.set_channel_types or provide events_data.
warn('No events found or provided. Please make sure to'
Writing '/Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.4.0",
"DatasetType": "raw",
"Authors": [
"Please cite MNE-BIDS in your publication before removing this (citations in README)"
]
}
Writing '/Users/hoechenberger/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 '/Users/hoechenberger/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 status_description
MEG 0113 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good n/a
MEG 0112 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good n/a
MEG 0111 MEGMAG T 0.10000000149011612 172.17630004882812 Magnetometer 600.614990234375 good n/a
MEG 0122 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good n/a
MEG 0123 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good n/a
Copying data files to sub-emptyroom_ses-20021204_task-noise_meg.fif
Writing /Users/hoechenberger/mne_data/MNE-sample-data-bids/sub-emptyroom/ses-20021204/meg/sub-emptyroom_ses-20021204_task-noise_meg.fif
Closing /Users/hoechenberger/mne_data/MNE-sample-data-bids/sub-emptyroom/ses-20021204/meg/sub-emptyroom_ses-20021204_task-noise_meg.fif [done]
Writing '/Users/hoechenberger/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
Wrote /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021204/sub-emptyroom_ses-20021204_scans.tsv entry with meg/sub-emptyroom_ses-20021204_task-noise_meg.fif.
Opening raw data file /Users/hoechenberger/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.
Writing '/Users/hoechenberger/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 '/Users/hoechenberger/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 of electrodes.tsv is not supported for data type "meg". Skipping ...
/Users/hoechenberger/Development/mne-bids/mne_bids/utils.py:246: RuntimeWarning: No events found or provided. Please make sure to set channel type using raw.set_channel_types or provide events_data.
warn('No events found or provided. Please make sure to'
Writing '/Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.4.0",
"DatasetType": "raw",
"Authors": [
"Please cite MNE-BIDS in your publication before removing this (citations in README)"
]
}
Writing '/Users/hoechenberger/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 '/Users/hoechenberger/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 status_description
MEG 0113 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good n/a
MEG 0112 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good n/a
MEG 0111 MEGMAG T 0.10000000149011612 172.17630004882812 Magnetometer 600.614990234375 good n/a
MEG 0122 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good n/a
MEG 0123 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good n/a
Copying data files to sub-emptyroom_ses-20021201_task-noise_meg.fif
Writing /Users/hoechenberger/mne_data/MNE-sample-data-bids/sub-emptyroom/ses-20021201/meg/sub-emptyroom_ses-20021201_task-noise_meg.fif
Closing /Users/hoechenberger/mne_data/MNE-sample-data-bids/sub-emptyroom/ses-20021201/meg/sub-emptyroom_ses-20021201_task-noise_meg.fif [done]
Writing '/Users/hoechenberger/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
Wrote /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021201/sub-emptyroom_ses-20021201_scans.tsv entry with meg/sub-emptyroom_ses-20021201_task-noise_meg.fif.
Opening raw data file /Users/hoechenberger/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.
Writing '/Users/hoechenberger/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 '/Users/hoechenberger/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 of electrodes.tsv is not supported for data type "meg". Skipping ...
/Users/hoechenberger/Development/mne-bids/mne_bids/utils.py:246: RuntimeWarning: No events found or provided. Please make sure to set channel type using raw.set_channel_types or provide events_data.
warn('No events found or provided. Please make sure to'
Writing '/Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.4.0",
"DatasetType": "raw",
"Authors": [
"Please cite MNE-BIDS in your publication before removing this (citations in README)"
]
}
Writing '/Users/hoechenberger/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 '/Users/hoechenberger/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 status_description
MEG 0113 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good n/a
MEG 0112 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good n/a
MEG 0111 MEGMAG T 0.10000000149011612 172.17630004882812 Magnetometer 600.614990234375 good n/a
MEG 0122 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good n/a
MEG 0123 MEGGRADPLANAR T/m 0.10000000149011612 172.17630004882812 Planar Gradiometer 600.614990234375 good n/a
Copying data files to sub-emptyroom_ses-20021001_task-noise_meg.fif
Writing /Users/hoechenberger/mne_data/MNE-sample-data-bids/sub-emptyroom/ses-20021001/meg/sub-emptyroom_ses-20021001_task-noise_meg.fif
Closing /Users/hoechenberger/mne_data/MNE-sample-data-bids/sub-emptyroom/ses-20021001/meg/sub-emptyroom_ses-20021001_task-noise_meg.fif [done]
Writing '/Users/hoechenberger/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
Wrote /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021001/sub-emptyroom_ses-20021001_scans.tsv entry with meg/sub-emptyroom_ses-20021001_task-noise_meg.fif.
Let us look at the directory structure
Out:
|MNE-sample-data-bids/
|--- README
|--- dataset_description.json
|--- participants.json
|--- participants.tsv
|--- sub-01/
|------ ses-01/
|--------- sub-01_ses-01_scans.tsv
|--------- anat/
|------------ sub-01_ses-01_T1w.json
|------------ sub-01_ses-01_T1w.nii.gz
|------------ sub-01_ses-01_task-audiovisual_run-01_T1w.json
|------------ sub-01_ses-01_task-audiovisual_run-01_T1w.nii.gz
|--------- meg/
|------------ sub-01_ses-01_coordsystem.json
|------------ sub-01_ses-01_task-audiovisual_run-01_channels.tsv
|------------ sub-01_ses-01_task-audiovisual_run-01_events.tsv
|------------ sub-01_ses-01_task-audiovisual_run-01_meg.fif
|------------ sub-01_ses-01_task-audiovisual_run-01_meg.json
|--- sub-emptyroom/
|------ ses-20021001/
|--------- sub-emptyroom_ses-20021001_scans.tsv
|--------- meg/
|------------ sub-emptyroom_ses-20021001_task-noise_channels.tsv
|------------ sub-emptyroom_ses-20021001_task-noise_meg.fif
|------------ sub-emptyroom_ses-20021001_task-noise_meg.json
|------ ses-20021201/
|--------- sub-emptyroom_ses-20021201_scans.tsv
|--------- meg/
|------------ sub-emptyroom_ses-20021201_task-noise_channels.tsv
|------------ sub-emptyroom_ses-20021201_task-noise_meg.fif
|------------ sub-emptyroom_ses-20021201_task-noise_meg.json
|------ ses-20021204/
|--------- sub-emptyroom_ses-20021204_scans.tsv
|--------- meg/
|------------ sub-emptyroom_ses-20021204_task-noise_channels.tsv
|------------ sub-emptyroom_ses-20021204_task-noise_meg.fif
|------------ sub-emptyroom_ses-20021204_task-noise_meg.json
|------ ses-20021206/
|--------- sub-emptyroom_ses-20021206_scans.tsv
|--------- meg/
|------------ sub-emptyroom_ses-20021206_task-noise_channels.tsv
|------------ sub-emptyroom_ses-20021206_task-noise_meg.fif
|------------ sub-emptyroom_ses-20021206_task-noise_meg.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 basename corresponding to the empty room recording that is closest in time to the experimental measurement.
er_bids_path = bids_path.find_empty_room()
print(er_bids_path)
Out:
Opening raw data file /Users/hoechenberger/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.
Reading events from /Users/hoechenberger/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 /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_channels.tsv.
/Users/hoechenberger/Development/mne-bids/mne_bids/read.py:246: 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)
/Users/hoechenberger/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(bids_path=er_bids_path)
print(raw)
Out:
Opening raw data file /Users/hoechenberger/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.
/Users/hoechenberger/Development/mne-bids/mne_bids/path.py:1024: RuntimeWarning: Did not find any events.tsv associated with sub-emptyroom_ses-20021204_task-noise.
The search_str was "/Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/**/sub-emptyroom_ses-20021204*events.tsv"
warn(msg)
Reading channel info from /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/ses-20021204/meg/sub-emptyroom_ses-20021204_task-noise_channels.tsv.
/Users/hoechenberger/Development/mne-bids/mne_bids/read.py:246: 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)
/Users/hoechenberger/Development/mne-bids/mne_bids/path.py:1024: RuntimeWarning: Did not find any coordsystem.json associated with sub-emptyroom_ses-20021204_task-noise.
The search_str was "/Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/**/sub-emptyroom_ses-20021204*coordsystem.json"
warn(msg)
<Raw | sub-emptyroom_ses-20021204_task-noise_meg.fif, 315 x 66068 (110.0 s), ~637 kB, data not loaded>
Total running time of the script: ( 0 minutes 3.416 seconds)
