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
import shutil
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.
To ensure the output path doesn’t contain any leftover files from previous tests and example runs, we simply delete it.
Warning
Do not delete directories that may contain important data!
Specify the raw_file and events_data and run the BIDS conversion, and write the BIDS data.
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 /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.
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.
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/README'...
References
----------
Appelhoff, S., Sanderson, M., Brooks, T., Vliet, M., Quentin, R., Holdgraf, C., Chaumon, M., Mikulan, E., Tavabi, K., Höchenberger, R., Welke, D., Brunner, C., Rockhill, A., Larson, E., Gramfort, A. and Jas, M. (2019). MNE-BIDS: Organizing electrophysiological data into the BIDS format and facilitating their analysis. Journal of Open Source Software 4: (1896). https://doi.org/10.21105/joss.01896
Niso, G., Gorgolewski, K. J., Bock, E., Brooks, T. L., Flandin, G., Gramfort, A., Henson, R. N., Jas, M., Litvak, V., Moreau, J., Oostenveld, R., Schoffelen, J., Tadel, F., Wexler, J., Baillet, S. (2018). MEG-BIDS, the brain imaging data structure extended to magnetoencephalography. Scientific Data, 5, 180110. https://doi.org/10.1038/sdata.2018.110
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/meg/sub-01_ses-01_coordsystem.json'...
{
"MEGCoordinateSystem": "ElektaNeuromag",
"MEGCoordinateUnits": "m",
"MEGCoordinateSystemDescription": "RAS orientation and the origin between the ears",
"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",
"AnatomicalLandmarkCoordinates": {
"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
]
},
"AnatomicalLandmarkCoordinateSystem": "ElektaNeuromag",
"AnatomicalLandmarkCoordinateUnits": "m"
}
/home/stefanappelhoff/Desktop/bids/mne-bids/mne_bids/read.py:164: RuntimeWarning: No events found or provided. Please add annotations to the raw data, or provide the events_data and event_id parameters. For resting state data, BIDS recommends naming the task using labels beginning with "rest".
warn('No events found or provided. Please add annotations to the raw '
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.6.0",
"DatasetType": "raw",
"Authors": [
"[Unspecified]"
]
}
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": true,
"DigitizedHeadPoints": true,
"MEGChannelCount": 306,
"MEGREFChannelCount": 0,
"ContinuousHeadLocalization": false,
"HeadCoilFrequency": [],
"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 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
Reserving possible split file sub-01_ses-01_task-audiovisual_run-01_split-01_meg.fif
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]
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 2002-12-03T19:01:10.720100Z
Wrote /home/stefanappelhoff/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: /home/stefanappelhoff/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 /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.
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 /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.
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 of electrodes.tsv is not supported for data type "meg". Skipping ...
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.6.0",
"DatasetType": "raw",
"Authors": [
"[Unspecified]"
]
}
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,
"ContinuousHeadLocalization": false,
"HeadCoilFrequency": [],
"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 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
Reserving possible split file sub-emptyroom_ses-20021206_task-noise_split-01_meg.fif
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]
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 2002-12-06T15:16:18.982786Z
Wrote /home/stefanappelhoff/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: /home/stefanappelhoff/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 /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.
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 of electrodes.tsv is not supported for data type "meg". Skipping ...
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.6.0",
"DatasetType": "raw",
"Authors": [
"[Unspecified]"
]
}
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,
"ContinuousHeadLocalization": false,
"HeadCoilFrequency": [],
"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 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
Reserving possible split file sub-emptyroom_ses-20021204_task-noise_split-01_meg.fif
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]
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 2002-12-04T00:00:00.000000Z
Wrote /home/stefanappelhoff/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 /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.
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 of electrodes.tsv is not supported for data type "meg". Skipping ...
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.6.0",
"DatasetType": "raw",
"Authors": [
"[Unspecified]"
]
}
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,
"ContinuousHeadLocalization": false,
"HeadCoilFrequency": [],
"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 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
Reserving possible split file sub-emptyroom_ses-20021201_task-noise_split-01_meg.fif
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]
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 2002-12-01T00:00:00.000000Z
Wrote /home/stefanappelhoff/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 /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.
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 of electrodes.tsv is not supported for data type "meg". Skipping ...
Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.6.0",
"DatasetType": "raw",
"Authors": [
"[Unspecified]"
]
}
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,
"ContinuousHeadLocalization": false,
"HeadCoilFrequency": [],
"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 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
Reserving possible split file sub-emptyroom_ses-20021001_task-noise_split-01_meg.fif
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]
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 2002-10-01T00:00:00.000000Z
Wrote /home/stefanappelhoff/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
|--------- 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_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:
The MEG sidecar file does not contain an "AssociatedEmptyRoom" entry. Will try to find a matching empty-room recording based on the measurement date …
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.
/home/stefanappelhoff/Desktop/bids/mne-bids/mne_bids/path.py:1290: RuntimeWarning: Did not find any events.tsv associated with sub-01_ses-01_task-audiovisual_run-01.
The search_str was "/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/**/sub-01_ses-01*events.tsv"
warn(msg)
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:529: 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(ch_type_map_avail)
/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(bids_path=er_bids_path)
print(raw)
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.
/home/stefanappelhoff/Desktop/bids/mne-bids/mne_bids/path.py:1290: RuntimeWarning: Did not find any events.tsv associated with sub-emptyroom_ses-20021204_task-noise.
The search_str was "/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-emptyroom/**/sub-emptyroom_ses-20021204*events.tsv"
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:529: 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(ch_type_map_avail)
<Raw | sub-emptyroom_ses-20021204_task-noise_meg.fif, 315 x 66068 (110.0 s), ~366 kB, data not loaded>
Total running time of the script: ( 0 minutes 2.305 seconds)
