Note
Click here to download the full example code or to run this example in your browser via Binder
BIDS conversion for group studies¶
Here, we show how to do BIDS conversion for group studies. The data from Wakeman et al. 1 is available here: https://openneuro.org/datasets/ds000117
References¶
- 1
Wakeman, Daniel G., and Richard N. Henson. “A multi-subject, multi-modal human neuroimaging dataset.” Scientific data, 2 (2015): 150001.
# Authors: Mainak Jas <mainak.jas@telecom-paristech.fr>
# Teon Brooks <teon.brooks@gmail.com>
# License: BSD (3-clause)
Let us import mne_bids
import os.path as op
import mne
from mne_bids import write_raw_bids, make_bids_basename
from mne_bids.datasets import fetch_faces_data
from mne_bids.utils import print_dir_tree
And fetch the data. .. warning:: This will download 7.9 GB of data for one subject!
subject_ids = [1]
runs = range(1, 7)
home = op.expanduser('~')
data_path = op.join(home, 'mne_data', 'mne_bids_examples')
repo = 'ds000117'
fetch_faces_data(data_path, repo, subject_ids)
output_path = op.join(data_path, 'ds000117-bids')
Define event_ids.
event_id = {
'face/famous/first': 5,
'face/famous/immediate': 6,
'face/famous/long': 7,
'face/unfamiliar/first': 13,
'face/unfamiliar/immediate': 14,
'face/unfamiliar/long': 15,
'scrambled/first': 17,
'scrambled/immediate': 18,
'scrambled/long': 19,
}
Let us loop over the subjects and create BIDS-compatible folder
for subject_id in subject_ids:
subject = 'sub%03d' % subject_id
for run in runs:
raw_fname = op.join(data_path, repo, subject, 'MEG',
'run_%02d_raw.fif' % run)
raw = mne.io.read_raw_fif(raw_fname)
bids_basename = make_bids_basename(subject=str(subject_id),
session='01', task='VisualFaces',
run=str(run))
write_raw_bids(raw, bids_basename, output_path, event_id=event_id,
overwrite=True)
Out:
Opening raw data file /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117/sub001/MEG/run_01_raw.fif...
Read a total of 8 projection items:
mag_ssp_upright.fif : PCA-mags-v1 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v2 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v3 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v4 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v5 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v1 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v2 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v3 (1 x 306) idle
Range : 268400 ... 815099 = 244.000 ... 740.999 secs
Ready.
Current compensation grade : 0
Opening raw data file /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117/sub001/MEG/run_01_raw.fif...
Read a total of 8 projection items:
mag_ssp_upright.fif : PCA-mags-v1 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v2 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v3 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v4 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v5 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v1 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v2 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v3 (1 x 306) idle
Range : 268400 ... 815099 = 244.000 ... 740.999 secs
Ready.
Current compensation grade : 0
Creating folder: /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg
/home/stefanappelhoff/miniconda3/envs/mne_bids3/lib/python3.6/site-packages/numpy/lib/arraysetops.py:569: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
mask |= (ar1 == a)
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/participants.tsv'...
participant_id age sex hand
sub-1 10 M n/a
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-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/mne_bids_examples/ds000117-bids/sub-1/ses-01/sub-1_ses-01_scans.tsv'...
filename acq_time
meg/sub-1_ses-01_task-VisualFaces_run-1_meg.fif 2009-04-07T16:39:35
meg/sub-1_ses-01_task-VisualFaces_run-2_meg.fif 2009-04-07T16:52:59
meg/sub-1_ses-01_task-VisualFaces_run-3_meg.fif 2009-04-07T17:02:25
meg/sub-1_ses-01_task-VisualFaces_run-4_meg.fif 2009-04-07T17:17:45
meg/sub-1_ses-01_task-VisualFaces_run-5_meg.fif 2009-04-07T17:27:38
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_coordsystem.json'...
{
"MEGCoordinateSystem": "Elekta",
"MEGCoordinateUnits": "m",
"HeadCoilCoordinates": {
"NAS": [
6.350555636913668e-10,
0.10185277462005615,
-1.2766878665360082e-09
],
"LPA": [
-0.07355359941720963,
-5.226810984026997e-09,
-6.564203847148065e-09
],
"RPA": [
0.07877404987812042,
-2.563174561487358e-08,
-5.883831200037548e-09
],
"coil1": [
0.020418334752321243,
0.09947940707206726,
0.06992102414369583
],
"coil2": [
0.07411128282546997,
0.0064362590201199055,
0.09744320064783096
],
"coil3": [
0.018864190205931664,
-0.020370930433273315,
0.1332322508096695
],
"coil4": [
0.014254843816161156,
-0.0912255346775055,
0.08386014401912689
],
"coil5": [
-0.07725043594837189,
-0.009882151149213314,
0.07862507551908493
]
},
"HeadCoilCoordinateSystem": "RAS",
"HeadCoilCoordinateUnits": "m"
}
296 events found
Event IDs: [ 5 6 7 13 14 15 17 18 19 256 261 262 263 269
270 271 273 274 275 4096 4101 4102 4103 4109 4110 4111 4114]
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-1_events.tsv'...
onset duration trial_type value sample
22.958181818181817 0.0 scrambled/first 17 25254
23.73181818181818 0.0 n/a 273 26105
26.04909090909091 0.0 scrambled/first 17 28654
26.92818181818182 0.0 n/a 273 29621
29.222727272727273 0.0 face/unfamiliar/first 13 32145
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.2.0"
}
Reading 0 ... 546699 = 0.000 ... 496.999 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/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-1_meg.json'...
{
"TaskName": "VisualFaces",
"Manufacturer": "Elekta",
"PowerLineFrequency": 50.0,
"SamplingFrequency": 1100.0,
"SoftwareFilters": "n/a",
"RecordingDuration": 496.9990909090909,
"RecordingType": "continuous",
"DewarPosition": "n/a",
"DigitizedLandmarks": false,
"DigitizedHeadPoints": false,
"MEGChannelCount": 306,
"MEGREFChannelCount": 0,
"EEGChannelCount": 74,
"EOGChannelCount": 0,
"ECGChannelCount": 0,
"EMGChannelCount": 0,
"MiscChannelCount": 12,
"TriggerChannelCount": 3
}
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-1_channels.tsv'...
name type units low_cutoff high_cutoff description sampling_frequency status
MEG0113 MEGGRADPLANAR T/m 0.0 356.3999938964844 Planar Gradiometer 1100.0 good
MEG0112 MEGGRADPLANAR T/m 0.0 356.3999938964844 Planar Gradiometer 1100.0 good
MEG0111 MEGMAG T 0.0 356.3999938964844 Magnetometer 1100.0 good
MEG0122 MEGGRADPLANAR T/m 0.0 356.3999938964844 Planar Gradiometer 1100.0 good
MEG0123 MEGGRADPLANAR T/m 0.0 356.3999938964844 Planar Gradiometer 1100.0 good
Copying data files to /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-1_meg.fif
Overwriting existing file.
Writing /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-1_meg.fif
Closing /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-1_meg.fif [done]
Opening raw data file /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117/sub001/MEG/run_02_raw.fif...
Read a total of 8 projection items:
mag_ssp_upright.fif : PCA-mags-v1 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v2 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v3 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v4 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v5 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v1 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v2 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v3 (1 x 306) idle
Range : 30800 ... 580799 = 28.000 ... 527.999 secs
Ready.
Current compensation grade : 0
Opening raw data file /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117/sub001/MEG/run_02_raw.fif...
Read a total of 8 projection items:
mag_ssp_upright.fif : PCA-mags-v1 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v2 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v3 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v4 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v5 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v1 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v2 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v3 (1 x 306) idle
Range : 30800 ... 580799 = 28.000 ... 527.999 secs
Ready.
Current compensation grade : 0
Creating folder: /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/participants.tsv'...
participant_id age sex hand
sub-1 10 M n/a
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-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/mne_bids_examples/ds000117-bids/sub-1/ses-01/sub-1_ses-01_scans.tsv'...
filename acq_time
meg/sub-1_ses-01_task-VisualFaces_run-1_meg.fif 2009-04-07T16:39:35
meg/sub-1_ses-01_task-VisualFaces_run-2_meg.fif 2009-04-07T16:52:59
meg/sub-1_ses-01_task-VisualFaces_run-3_meg.fif 2009-04-07T17:02:25
meg/sub-1_ses-01_task-VisualFaces_run-4_meg.fif 2009-04-07T17:17:45
meg/sub-1_ses-01_task-VisualFaces_run-5_meg.fif 2009-04-07T17:27:38
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_coordsystem.json'...
{
"MEGCoordinateSystem": "Elekta",
"MEGCoordinateUnits": "m",
"HeadCoilCoordinates": {
"NAS": [
6.350555636913668e-10,
0.10185277462005615,
-1.2766878665360082e-09
],
"LPA": [
-0.07355359941720963,
-5.226810984026997e-09,
-6.564203847148065e-09
],
"RPA": [
0.07877404987812042,
-2.563174561487358e-08,
-5.883831200037548e-09
],
"coil1": [
0.020418334752321243,
0.09947940707206726,
0.06992102414369583
],
"coil2": [
0.07411128282546997,
0.0064362590201199055,
0.09744320064783096
],
"coil3": [
0.018864190205931664,
-0.020370930433273315,
0.1332322508096695
],
"coil4": [
0.014254843816161156,
-0.0912255346775055,
0.08386014401912689
],
"coil5": [
-0.07725043594837189,
-0.009882151149213314,
0.07862507551908493
]
},
"HeadCoilCoordinateSystem": "RAS",
"HeadCoilCoordinateUnits": "m"
}
296 events found
Event IDs: [ 5 6 7 13 14 15 17 18 19 256 261 262 263 269
270 271 273 274 275 4096 4109 4110 4111]
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-2_events.tsv'...
onset duration trial_type value sample
28.03272727272727 0.0 scrambled/first 17 30836
28.837272727272726 0.0 n/a 273 31721
31.156363636363636 0.0 face/unfamiliar/first 13 34272
32.13181818181818 0.0 n/a 256 35345
34.21363636363636 0.0 face/famous/first 5 37635
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.2.0"
}
Reading 0 ... 549999 = 0.000 ... 499.999 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/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-2_meg.json'...
{
"TaskName": "VisualFaces",
"Manufacturer": "Elekta",
"PowerLineFrequency": 50.0,
"SamplingFrequency": 1100.0,
"SoftwareFilters": "n/a",
"RecordingDuration": 499.9990909090909,
"RecordingType": "continuous",
"DewarPosition": "n/a",
"DigitizedLandmarks": false,
"DigitizedHeadPoints": false,
"MEGChannelCount": 306,
"MEGREFChannelCount": 0,
"EEGChannelCount": 74,
"EOGChannelCount": 0,
"ECGChannelCount": 0,
"EMGChannelCount": 0,
"MiscChannelCount": 12,
"TriggerChannelCount": 3
}
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-2_channels.tsv'...
name type units low_cutoff high_cutoff description sampling_frequency status
MEG0113 MEGGRADPLANAR T/m 0.0 356.3999938964844 Planar Gradiometer 1100.0 good
MEG0112 MEGGRADPLANAR T/m 0.0 356.3999938964844 Planar Gradiometer 1100.0 good
MEG0111 MEGMAG T 0.0 356.3999938964844 Magnetometer 1100.0 good
MEG0122 MEGGRADPLANAR T/m 0.0 356.3999938964844 Planar Gradiometer 1100.0 good
MEG0123 MEGGRADPLANAR T/m 0.0 356.3999938964844 Planar Gradiometer 1100.0 good
Copying data files to /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-2_meg.fif
Overwriting existing file.
Writing /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-2_meg.fif
Closing /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-2_meg.fif [done]
Opening raw data file /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117/sub001/MEG/run_03_raw.fif...
Read a total of 8 projection items:
mag_ssp_upright.fif : PCA-mags-v1 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v2 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v3 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v4 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v5 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v1 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v2 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v3 (1 x 306) idle
Range : 187000 ... 417999 = 170.000 ... 379.999 secs
Ready.
Current compensation grade : 0
Opening raw data file /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117/sub001/MEG/run_03_raw.fif...
Read a total of 8 projection items:
mag_ssp_upright.fif : PCA-mags-v1 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v2 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v3 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v4 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v5 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v1 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v2 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v3 (1 x 306) idle
Range : 187000 ... 417999 = 170.000 ... 379.999 secs
Ready.
Current compensation grade : 0
Creating folder: /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/participants.tsv'...
participant_id age sex hand
sub-1 10 M n/a
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-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/mne_bids_examples/ds000117-bids/sub-1/ses-01/sub-1_ses-01_scans.tsv'...
filename acq_time
meg/sub-1_ses-01_task-VisualFaces_run-1_meg.fif 2009-04-07T16:39:35
meg/sub-1_ses-01_task-VisualFaces_run-2_meg.fif 2009-04-07T16:52:59
meg/sub-1_ses-01_task-VisualFaces_run-3_meg.fif 2009-04-07T17:02:25
meg/sub-1_ses-01_task-VisualFaces_run-4_meg.fif 2009-04-07T17:17:45
meg/sub-1_ses-01_task-VisualFaces_run-5_meg.fif 2009-04-07T17:27:38
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_coordsystem.json'...
{
"MEGCoordinateSystem": "Elekta",
"MEGCoordinateUnits": "m",
"HeadCoilCoordinates": {
"NAS": [
6.350555636913668e-10,
0.10185277462005615,
-1.2766878665360082e-09
],
"LPA": [
-0.07355359941720963,
-5.226810984026997e-09,
-6.564203847148065e-09
],
"RPA": [
0.07877404987812042,
-2.563174561487358e-08,
-5.883831200037548e-09
],
"coil1": [
0.020418334752321243,
0.09947940707206726,
0.06992102414369583
],
"coil2": [
0.07411128282546997,
0.0064362590201199055,
0.09744320064783096
],
"coil3": [
0.018864190205931664,
-0.020370930433273315,
0.1332322508096695
],
"coil4": [
0.014254843816161156,
-0.0912255346775055,
0.08386014401912689
],
"coil5": [
-0.07725043594837189,
-0.009882151149213314,
0.07862507551908493
]
},
"HeadCoilCoordinateSystem": "RAS",
"HeadCoilCoordinateUnits": "m"
}
119 events found
Event IDs: [ 5 6 7 13 14 15 17 18 19 256 261 262 263 269
270 271 273 274 275 4096 4103 4110 4352]
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-3_events.tsv'...
onset duration trial_type value sample
24.56 0.0 scrambled/first 17 27016
25.27090909090909 0.0 n/a 273 27798
27.7 0.0 scrambled/immediate 18 30470
28.55 0.0 n/a 256 31405
30.740909090909092 0.0 scrambled/first 17 33815
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.2.0"
}
Reading 0 ... 230999 = 0.000 ... 209.999 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/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-3_meg.json'...
{
"TaskName": "VisualFaces",
"Manufacturer": "Elekta",
"PowerLineFrequency": 50.0,
"SamplingFrequency": 1100.0,
"SoftwareFilters": "n/a",
"RecordingDuration": 209.9990909090909,
"RecordingType": "continuous",
"DewarPosition": "n/a",
"DigitizedLandmarks": false,
"DigitizedHeadPoints": false,
"MEGChannelCount": 306,
"MEGREFChannelCount": 0,
"EEGChannelCount": 74,
"EOGChannelCount": 0,
"ECGChannelCount": 0,
"EMGChannelCount": 0,
"MiscChannelCount": 12,
"TriggerChannelCount": 3
}
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-3_channels.tsv'...
name type units low_cutoff high_cutoff description sampling_frequency status
MEG0113 MEGGRADPLANAR T/m 0.0 356.3999938964844 Planar Gradiometer 1100.0 good
MEG0112 MEGGRADPLANAR T/m 0.0 356.3999938964844 Planar Gradiometer 1100.0 good
MEG0111 MEGMAG T 0.0 356.3999938964844 Magnetometer 1100.0 good
MEG0122 MEGGRADPLANAR T/m 0.0 356.3999938964844 Planar Gradiometer 1100.0 good
MEG0123 MEGGRADPLANAR T/m 0.0 356.3999938964844 Planar Gradiometer 1100.0 good
Copying data files to /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-3_meg.fif
Overwriting existing file.
Writing /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-3_meg.fif
Closing /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-3_meg.fif [done]
Opening raw data file /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117/sub001/MEG/run_04_raw.fif...
Read a total of 8 projection items:
mag_ssp_upright.fif : PCA-mags-v1 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v2 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v3 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v4 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v5 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v1 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v2 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v3 (1 x 306) idle
Range : 47300 ... 590699 = 43.000 ... 536.999 secs
Ready.
Current compensation grade : 0
Opening raw data file /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117/sub001/MEG/run_04_raw.fif...
Read a total of 8 projection items:
mag_ssp_upright.fif : PCA-mags-v1 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v2 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v3 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v4 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v5 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v1 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v2 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v3 (1 x 306) idle
Range : 47300 ... 590699 = 43.000 ... 536.999 secs
Ready.
Current compensation grade : 0
Creating folder: /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/participants.tsv'...
participant_id age sex hand
sub-1 10 M n/a
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-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/mne_bids_examples/ds000117-bids/sub-1/ses-01/sub-1_ses-01_scans.tsv'...
filename acq_time
meg/sub-1_ses-01_task-VisualFaces_run-1_meg.fif 2009-04-07T16:39:35
meg/sub-1_ses-01_task-VisualFaces_run-2_meg.fif 2009-04-07T16:52:59
meg/sub-1_ses-01_task-VisualFaces_run-3_meg.fif 2009-04-07T17:02:25
meg/sub-1_ses-01_task-VisualFaces_run-4_meg.fif 2009-04-07T17:17:45
meg/sub-1_ses-01_task-VisualFaces_run-5_meg.fif 2009-04-07T17:27:38
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_coordsystem.json'...
{
"MEGCoordinateSystem": "Elekta",
"MEGCoordinateUnits": "m",
"HeadCoilCoordinates": {
"NAS": [
6.350555636913668e-10,
0.10185277462005615,
-1.2766878665360082e-09
],
"LPA": [
-0.07355359941720963,
-5.226810984026997e-09,
-6.564203847148065e-09
],
"RPA": [
0.07877404987812042,
-2.563174561487358e-08,
-5.883831200037548e-09
],
"coil1": [
0.020418334752321243,
0.09947940707206726,
0.06992102414369583
],
"coil2": [
0.07411128282546997,
0.0064362590201199055,
0.09744320064783096
],
"coil3": [
0.018864190205931664,
-0.020370930433273315,
0.1332322508096695
],
"coil4": [
0.014254843816161156,
-0.0912255346775055,
0.08386014401912689
],
"coil5": [
-0.07725043594837189,
-0.009882151149213314,
0.07862507551908493
]
},
"HeadCoilCoordinateSystem": "RAS",
"HeadCoilCoordinateUnits": "m"
}
294 events found
Event IDs: [ 5 6 7 13 14 15 17 18 19 256 261 262 263 269
270 271 273 274 275 4096 4109 4110]
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-4_events.tsv'...
onset duration trial_type value sample
25.407272727272726 0.0 face/unfamiliar/first 13 27948
26.21909090909091 0.0 n/a 269 28841
28.49818181818182 0.0 face/unfamiliar/immediate 14 31348
29.337272727272726 0.0 n/a 270 32271
31.78909090909091 0.0 face/unfamiliar/first 13 34968
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.2.0"
}
Reading 0 ... 543399 = 0.000 ... 493.999 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/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-4_meg.json'...
{
"TaskName": "VisualFaces",
"Manufacturer": "Elekta",
"PowerLineFrequency": 50.0,
"SamplingFrequency": 1100.0,
"SoftwareFilters": "n/a",
"RecordingDuration": 493.9990909090909,
"RecordingType": "continuous",
"DewarPosition": "n/a",
"DigitizedLandmarks": false,
"DigitizedHeadPoints": false,
"MEGChannelCount": 306,
"MEGREFChannelCount": 0,
"EEGChannelCount": 74,
"EOGChannelCount": 0,
"ECGChannelCount": 0,
"EMGChannelCount": 0,
"MiscChannelCount": 12,
"TriggerChannelCount": 3
}
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-4_channels.tsv'...
name type units low_cutoff high_cutoff description sampling_frequency status
MEG0113 MEGGRADPLANAR T/m 0.0 356.3999938964844 Planar Gradiometer 1100.0 good
MEG0112 MEGGRADPLANAR T/m 0.0 356.3999938964844 Planar Gradiometer 1100.0 good
MEG0111 MEGMAG T 0.0 356.3999938964844 Magnetometer 1100.0 good
MEG0122 MEGGRADPLANAR T/m 0.0 356.3999938964844 Planar Gradiometer 1100.0 good
MEG0123 MEGGRADPLANAR T/m 0.0 356.3999938964844 Planar Gradiometer 1100.0 good
Copying data files to /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-4_meg.fif
Overwriting existing file.
Writing /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-4_meg.fif
Closing /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-4_meg.fif [done]
Opening raw data file /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117/sub001/MEG/run_05_raw.fif...
Read a total of 8 projection items:
mag_ssp_upright.fif : PCA-mags-v1 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v2 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v3 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v4 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v5 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v1 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v2 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v3 (1 x 306) idle
Range : 283800 ... 820599 = 258.000 ... 745.999 secs
Ready.
Current compensation grade : 0
Opening raw data file /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117/sub001/MEG/run_05_raw.fif...
Read a total of 8 projection items:
mag_ssp_upright.fif : PCA-mags-v1 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v2 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v3 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v4 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v5 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v1 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v2 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v3 (1 x 306) idle
Range : 283800 ... 820599 = 258.000 ... 745.999 secs
Ready.
Current compensation grade : 0
Creating folder: /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/participants.tsv'...
participant_id age sex hand
sub-1 10 M n/a
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-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/mne_bids_examples/ds000117-bids/sub-1/ses-01/sub-1_ses-01_scans.tsv'...
filename acq_time
meg/sub-1_ses-01_task-VisualFaces_run-1_meg.fif 2009-04-07T16:39:35
meg/sub-1_ses-01_task-VisualFaces_run-2_meg.fif 2009-04-07T16:52:59
meg/sub-1_ses-01_task-VisualFaces_run-3_meg.fif 2009-04-07T17:02:25
meg/sub-1_ses-01_task-VisualFaces_run-4_meg.fif 2009-04-07T17:17:45
meg/sub-1_ses-01_task-VisualFaces_run-5_meg.fif 2009-04-07T17:27:38
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_coordsystem.json'...
{
"MEGCoordinateSystem": "Elekta",
"MEGCoordinateUnits": "m",
"HeadCoilCoordinates": {
"NAS": [
6.350555636913668e-10,
0.10185277462005615,
-1.2766878665360082e-09
],
"LPA": [
-0.07355359941720963,
-5.226810984026997e-09,
-6.564203847148065e-09
],
"RPA": [
0.07877404987812042,
-2.563174561487358e-08,
-5.883831200037548e-09
],
"coil1": [
0.020418334752321243,
0.09947940707206726,
0.06992102414369583
],
"coil2": [
0.07411128282546997,
0.0064362590201199055,
0.09744320064783096
],
"coil3": [
0.018864190205931664,
-0.020370930433273315,
0.1332322508096695
],
"coil4": [
0.014254843816161156,
-0.0912255346775055,
0.08386014401912689
],
"coil5": [
-0.07725043594837189,
-0.009882151149213314,
0.07862507551908493
]
},
"HeadCoilCoordinateSystem": "RAS",
"HeadCoilCoordinateUnits": "m"
}
292 events found
Event IDs: [ 5 6 7 13 14 15 17 18 19 256 261 262 263 269
270 271 273 274 275 4096 4103 4110 4111]
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-5_events.tsv'...
onset duration trial_type value sample
25.71727272727273 0.0 face/famous/first 5 28289
26.46909090909091 0.0 n/a 261 29116
29.023636363636363 0.0 scrambled/first 17 31926
29.599090909090908 0.0 n/a 273 32559
32.13090909090909 0.0 scrambled/immediate 18 35344
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.2.0"
}
Reading 0 ... 536799 = 0.000 ... 487.999 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/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-5_meg.json'...
{
"TaskName": "VisualFaces",
"Manufacturer": "Elekta",
"PowerLineFrequency": 50.0,
"SamplingFrequency": 1100.0,
"SoftwareFilters": "n/a",
"RecordingDuration": 487.9990909090909,
"RecordingType": "continuous",
"DewarPosition": "n/a",
"DigitizedLandmarks": false,
"DigitizedHeadPoints": false,
"MEGChannelCount": 306,
"MEGREFChannelCount": 0,
"EEGChannelCount": 74,
"EOGChannelCount": 0,
"ECGChannelCount": 0,
"EMGChannelCount": 0,
"MiscChannelCount": 12,
"TriggerChannelCount": 3
}
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-5_channels.tsv'...
name type units low_cutoff high_cutoff description sampling_frequency status
MEG0113 MEGGRADPLANAR T/m 0.0 356.3999938964844 Planar Gradiometer 1100.0 good
MEG0112 MEGGRADPLANAR T/m 0.0 356.3999938964844 Planar Gradiometer 1100.0 good
MEG0111 MEGMAG T 0.0 356.3999938964844 Magnetometer 1100.0 good
MEG0122 MEGGRADPLANAR T/m 0.0 356.3999938964844 Planar Gradiometer 1100.0 good
MEG0123 MEGGRADPLANAR T/m 0.0 356.3999938964844 Planar Gradiometer 1100.0 good
Copying data files to /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-5_meg.fif
Overwriting existing file.
Writing /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-5_meg.fif
Closing /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-5_meg.fif [done]
Opening raw data file /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117/sub001/MEG/run_06_raw.fif...
Read a total of 8 projection items:
mag_ssp_upright.fif : PCA-mags-v1 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v2 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v3 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v4 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v5 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v1 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v2 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v3 (1 x 306) idle
Range : 28600 ... 573099 = 26.000 ... 520.999 secs
Ready.
Current compensation grade : 0
Opening raw data file /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117/sub001/MEG/run_06_raw.fif...
Read a total of 8 projection items:
mag_ssp_upright.fif : PCA-mags-v1 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v2 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v3 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v4 (1 x 306) idle
mag_ssp_upright.fif : PCA-mags-v5 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v1 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v2 (1 x 306) idle
grad_ssp_upright.fif : PCA-grad-v3 (1 x 306) idle
Range : 28600 ... 573099 = 26.000 ... 520.999 secs
Ready.
Current compensation grade : 0
Creating folder: /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/participants.tsv'...
participant_id age sex hand
sub-1 10 M n/a
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-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/mne_bids_examples/ds000117-bids/sub-1/ses-01/sub-1_ses-01_scans.tsv'...
filename acq_time
meg/sub-1_ses-01_task-VisualFaces_run-1_meg.fif 2009-04-07T16:39:35
meg/sub-1_ses-01_task-VisualFaces_run-2_meg.fif 2009-04-07T16:52:59
meg/sub-1_ses-01_task-VisualFaces_run-3_meg.fif 2009-04-07T17:02:25
meg/sub-1_ses-01_task-VisualFaces_run-4_meg.fif 2009-04-07T17:17:45
meg/sub-1_ses-01_task-VisualFaces_run-5_meg.fif 2009-04-07T17:27:38
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_coordsystem.json'...
{
"MEGCoordinateSystem": "Elekta",
"MEGCoordinateUnits": "m",
"HeadCoilCoordinates": {
"NAS": [
6.350555636913668e-10,
0.10185277462005615,
-1.2766878665360082e-09
],
"LPA": [
-0.07355359941720963,
-5.226810984026997e-09,
-6.564203847148065e-09
],
"RPA": [
0.07877404987812042,
-2.563174561487358e-08,
-5.883831200037548e-09
],
"coil1": [
0.020418334752321243,
0.09947940707206726,
0.06992102414369583
],
"coil2": [
0.07411128282546997,
0.0064362590201199055,
0.09744320064783096
],
"coil3": [
0.018864190205931664,
-0.020370930433273315,
0.1332322508096695
],
"coil4": [
0.014254843816161156,
-0.0912255346775055,
0.08386014401912689
],
"coil5": [
-0.07725043594837189,
-0.009882151149213314,
0.07862507551908493
]
},
"HeadCoilCoordinateSystem": "RAS",
"HeadCoilCoordinateUnits": "m"
}
296 events found
Event IDs: [ 5 6 7 13 14 15 17 18 19 256 261 262 263 269
270 271 273 274 275 4096 4110]
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-6_events.tsv'...
onset duration trial_type value sample
25.204545454545453 0.0 face/famous/first 5 27725
25.85 0.0 n/a 261 28435
28.345454545454544 0.0 scrambled/first 17 31180
29.024545454545454 0.0 n/a 273 31927
31.47 0.0 face/famous/first 5 34617
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/dataset_description.json'...
{
"Name": " ",
"BIDSVersion": "1.2.0"
}
Reading 0 ... 544499 = 0.000 ... 494.999 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/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-6_meg.json'...
{
"TaskName": "VisualFaces",
"Manufacturer": "Elekta",
"PowerLineFrequency": 50.0,
"SamplingFrequency": 1100.0,
"SoftwareFilters": "n/a",
"RecordingDuration": 494.9990909090909,
"RecordingType": "continuous",
"DewarPosition": "n/a",
"DigitizedLandmarks": false,
"DigitizedHeadPoints": false,
"MEGChannelCount": 306,
"MEGREFChannelCount": 0,
"EEGChannelCount": 74,
"EOGChannelCount": 0,
"ECGChannelCount": 0,
"EMGChannelCount": 0,
"MiscChannelCount": 12,
"TriggerChannelCount": 3
}
Writing '/home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-6_channels.tsv'...
name type units low_cutoff high_cutoff description sampling_frequency status
MEG0113 MEGGRADPLANAR T/m 0.0 356.3999938964844 Planar Gradiometer 1100.0 good
MEG0112 MEGGRADPLANAR T/m 0.0 356.3999938964844 Planar Gradiometer 1100.0 good
MEG0111 MEGMAG T 0.0 356.3999938964844 Magnetometer 1100.0 good
MEG0122 MEGGRADPLANAR T/m 0.0 356.3999938964844 Planar Gradiometer 1100.0 good
MEG0123 MEGGRADPLANAR T/m 0.0 356.3999938964844 Planar Gradiometer 1100.0 good
Copying data files to /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-6_meg.fif
Overwriting existing file.
Writing /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-6_meg.fif
Closing /home/stefanappelhoff/mne_data/mne_bids_examples/ds000117-bids/sub-1/ses-01/meg/sub-1_ses-01_task-VisualFaces_run-6_meg.fif [done]
Now let’s see the structure of the BIDS folder we created.
print_dir_tree(output_path)
Out:
|ds000117-bids/
|--- participants.tsv
|--- dataset_description.json
|--- participants.json
|--- sub-1/
|------ ses-01/
|--------- sub-1_ses-01_scans.tsv
|--------- meg/
|------------ sub-1_ses-01_task-VisualFaces_run-4_meg.fif
|------------ sub-1_ses-01_task-VisualFaces_run-4_channels.tsv
|------------ sub-1_ses-01_task-VisualFaces_run-2_meg.fif
|------------ sub-1_ses-01_task-VisualFaces_run-5_events.tsv
|------------ sub-1_ses-01_task-VisualFaces_run-5_meg.json
|------------ sub-1_ses-01_task-VisualFaces_run-3_events.tsv
|------------ sub-1_ses-01_task-VisualFaces_run-5_channels.tsv
|------------ sub-1_ses-01_task-VisualFaces_run-1_channels.tsv
|------------ sub-1_ses-01_task-VisualFaces_run-4_meg.json
|------------ sub-1_ses-01_task-VisualFaces_run-6_meg.fif
|------------ sub-1_ses-01_task-VisualFaces_run-3_channels.tsv
|------------ sub-1_ses-01_task-VisualFaces_run-6_events.tsv
|------------ sub-1_ses-01_task-VisualFaces_run-1_meg.fif
|------------ sub-1_ses-01_task-VisualFaces_run-6_meg.json
|------------ sub-1_ses-01_task-VisualFaces_run-6_channels.tsv
|------------ sub-1_ses-01_task-VisualFaces_run-1_meg.json
|------------ sub-1_ses-01_task-VisualFaces_run-3_meg.json
|------------ sub-1_ses-01_task-VisualFaces_run-3_meg.fif
|------------ sub-1_ses-01_task-VisualFaces_run-2_events.tsv
|------------ sub-1_ses-01_coordsystem.json
|------------ sub-1_ses-01_task-VisualFaces_run-5_meg.fif
|------------ sub-1_ses-01_task-VisualFaces_run-4_events.tsv
|------------ sub-1_ses-01_task-VisualFaces_run-2_meg.json
|------------ sub-1_ses-01_task-VisualFaces_run-2_channels.tsv
|------------ sub-1_ses-01_task-VisualFaces_run-1_events.tsv
Total running time of the script: ( 0 minutes 38.505 seconds)
