.. note:: :class: sphx-glr-download-link-note Click :ref:`here ` to download the full example code .. rst-class:: sphx-glr-example-title .. _sphx_glr_auto_examples_convert_group_studies.py: ================================= BIDS conversion for group studies ================================= Here, we show how to do BIDS conversion for group studies. The data is available here: https://openfmri.org/dataset/ds000117/ References ---------- [1] Wakeman, Daniel G., and Richard N. Henson. "A multi-subject, multi-modal human neuroimaging dataset." Scientific data, 2 (2015): 150001. .. code-block:: default # Authors: Mainak Jas # Teon Brooks # License: BSD (3-clause) Let us import ``mne_bids`` .. code-block:: default import os.path as op import mne from mne_bids import write_raw_bids from mne_bids.datasets import fetch_faces_data from mne_bids.utils import print_dir_tree And fetch the data. .. code-block:: default subject_ids = [1] runs = range(1, 7) data_path = op.join(op.expanduser('~'), 'mne_data') repo = 'ds000117' fetch_faces_data(data_path, repo, subject_ids) output_path = op.join(data_path, 'ds000117-bids') .. warning:: This will download 7.9 GB of data for one subject! Define event_ids. .. code-block:: default 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 .. code-block:: default 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 = ('sub-%02d_ses-01_task-VisualFaces_run-%d' % (subject_id, run)) write_raw_bids(raw, bids_basename, output_path, event_id=event_id, overwrite=True) .. rst-class:: sphx-glr-script-out Out: .. code-block:: none Opening raw data file /home/stefanappelhoff/mne_data/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/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 Writing '/home/stefanappelhoff/mne_data/ds000117-bids/participants.tsv'... participant_id age sex group 0 sub-01 10 M n/a 1 sub-1 10 M n/a Writing '/home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/sub-01_ses-01_scans.tsv'... filename acq_time 0 meg/sub-01_ses-01_task-VisualFaces_run-1_meg.fif 2009-04-07T16:39:35 1 meg/sub-01_ses-01_task-VisualFaces_run-2_meg.fif 2009-04-07T16:52:59 2 meg/sub-01_ses-01_task-VisualFaces_run-3_meg.fif 2009-04-07T17:02:25 3 meg/sub-01_ses-01_task-VisualFaces_run-4_meg.fif 2009-04-07T17:17:45 4 meg/sub-01_ses-01_task-VisualFaces_run-5_meg.fif 2009-04-07T17:27:38 296 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/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-1_events.tsv'... onset duration trial_type event_value event_sample 0 22.958182 0.0 scrambled/first 17 25254 1 23.731818 0.0 NaN 273 26105 2 26.049091 0.0 scrambled/first 17 28654 3 26.928182 0.0 NaN 273 29621 4 29.222727 0.0 face/unfamiliar/first 13 32145 Writing '/home/stefanappelhoff/mne_data/ds000117-bids/dataset_description.json'... { "Name": " ", "BIDSVersion": "1.1.1 (draft)" } Reading 0 ... 546699 = 0.000 ... 496.999 secs... Writing '/home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_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/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-1_channels.tsv'... name type units description sampling_frequency \ 0 MEG0113 MEGGRADPLANAR T/m Planar Gradiometer 1100.0 1 MEG0112 MEGGRADPLANAR T/m Planar Gradiometer 1100.0 2 MEG0111 MEGMAG T Magnetometer 1100.0 3 MEG0122 MEGGRADPLANAR T/m Planar Gradiometer 1100.0 4 MEG0123 MEGGRADPLANAR T/m Planar Gradiometer 1100.0 low_cutoff high_cutoff status 0 0.0 356.399994 good 1 0.0 356.399994 good 2 0.0 356.399994 good 3 0.0 356.399994 good 4 0.0 356.399994 good Copying data files to /home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-1_meg.fif /home/stefanappelhoff/Desktop/bids/mne-bids/examples/convert_group_studies.py:76: RuntimeWarning: This filename (/home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-1_meg.fif) does not conform to MNE naming conventions. All raw files should end with raw.fif, raw_sss.fif, raw_tsss.fif, raw.fif.gz, raw_sss.fif.gz or raw_tsss.fif.gz overwrite=True) Overwriting existing file. Writing /home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-1_meg.fif Closing /home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-1_meg.fif [done] Opening raw data file /home/stefanappelhoff/mne_data/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/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 Writing '/home/stefanappelhoff/mne_data/ds000117-bids/participants.tsv'... participant_id age sex group 0 sub-01 10 M n/a 1 sub-1 10 M n/a Writing '/home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/sub-01_ses-01_scans.tsv'... filename acq_time 0 meg/sub-01_ses-01_task-VisualFaces_run-1_meg.fif 2009-04-07T16:39:35 0 meg/sub-01_ses-01_task-VisualFaces_run-2_meg.fif 2009-04-07T16:52:59 2 meg/sub-01_ses-01_task-VisualFaces_run-3_meg.fif 2009-04-07T17:02:25 3 meg/sub-01_ses-01_task-VisualFaces_run-4_meg.fif 2009-04-07T17:17:45 4 meg/sub-01_ses-01_task-VisualFaces_run-5_meg.fif 2009-04-07T17:27:38 296 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/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-2_events.tsv'... onset duration trial_type event_value event_sample 0 28.032727 0.0 scrambled/first 17 30836 1 28.837273 0.0 NaN 273 31721 2 31.156364 0.0 face/unfamiliar/first 13 34272 3 32.131818 0.0 NaN 256 35345 4 34.213636 0.0 face/famous/first 5 37635 Writing '/home/stefanappelhoff/mne_data/ds000117-bids/dataset_description.json'... { "Name": " ", "BIDSVersion": "1.1.1 (draft)" } Reading 0 ... 549999 = 0.000 ... 499.999 secs... Writing '/home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_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/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-2_channels.tsv'... name type units description sampling_frequency \ 0 MEG0113 MEGGRADPLANAR T/m Planar Gradiometer 1100.0 1 MEG0112 MEGGRADPLANAR T/m Planar Gradiometer 1100.0 2 MEG0111 MEGMAG T Magnetometer 1100.0 3 MEG0122 MEGGRADPLANAR T/m Planar Gradiometer 1100.0 4 MEG0123 MEGGRADPLANAR T/m Planar Gradiometer 1100.0 low_cutoff high_cutoff status 0 0.0 356.399994 good 1 0.0 356.399994 good 2 0.0 356.399994 good 3 0.0 356.399994 good 4 0.0 356.399994 good Copying data files to /home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-2_meg.fif /home/stefanappelhoff/Desktop/bids/mne-bids/examples/convert_group_studies.py:76: RuntimeWarning: This filename (/home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-2_meg.fif) does not conform to MNE naming conventions. All raw files should end with raw.fif, raw_sss.fif, raw_tsss.fif, raw.fif.gz, raw_sss.fif.gz or raw_tsss.fif.gz overwrite=True) Overwriting existing file. Writing /home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-2_meg.fif Closing /home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-2_meg.fif [done] Opening raw data file /home/stefanappelhoff/mne_data/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/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 Writing '/home/stefanappelhoff/mne_data/ds000117-bids/participants.tsv'... participant_id age sex group 0 sub-01 10 M n/a 1 sub-1 10 M n/a Writing '/home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/sub-01_ses-01_scans.tsv'... filename acq_time 0 meg/sub-01_ses-01_task-VisualFaces_run-1_meg.fif 2009-04-07T16:39:35 1 meg/sub-01_ses-01_task-VisualFaces_run-2_meg.fif 2009-04-07T16:52:59 0 meg/sub-01_ses-01_task-VisualFaces_run-3_meg.fif 2009-04-07T17:02:25 3 meg/sub-01_ses-01_task-VisualFaces_run-4_meg.fif 2009-04-07T17:17:45 4 meg/sub-01_ses-01_task-VisualFaces_run-5_meg.fif 2009-04-07T17:27:38 119 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/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-3_events.tsv'... onset duration trial_type event_value event_sample 0 24.560000 0.0 scrambled/first 17 27016 1 25.270909 0.0 NaN 273 27798 2 27.700000 0.0 scrambled/immediate 18 30470 3 28.550000 0.0 NaN 256 31405 4 30.740909 0.0 scrambled/first 17 33815 Writing '/home/stefanappelhoff/mne_data/ds000117-bids/dataset_description.json'... { "Name": " ", "BIDSVersion": "1.1.1 (draft)" } Reading 0 ... 230999 = 0.000 ... 209.999 secs... Writing '/home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_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/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-3_channels.tsv'... name type units description sampling_frequency \ 0 MEG0113 MEGGRADPLANAR T/m Planar Gradiometer 1100.0 1 MEG0112 MEGGRADPLANAR T/m Planar Gradiometer 1100.0 2 MEG0111 MEGMAG T Magnetometer 1100.0 3 MEG0122 MEGGRADPLANAR T/m Planar Gradiometer 1100.0 4 MEG0123 MEGGRADPLANAR T/m Planar Gradiometer 1100.0 low_cutoff high_cutoff status 0 0.0 356.399994 good 1 0.0 356.399994 good 2 0.0 356.399994 good 3 0.0 356.399994 good 4 0.0 356.399994 good Copying data files to /home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-3_meg.fif /home/stefanappelhoff/Desktop/bids/mne-bids/examples/convert_group_studies.py:76: RuntimeWarning: This filename (/home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-3_meg.fif) does not conform to MNE naming conventions. All raw files should end with raw.fif, raw_sss.fif, raw_tsss.fif, raw.fif.gz, raw_sss.fif.gz or raw_tsss.fif.gz overwrite=True) Overwriting existing file. Writing /home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-3_meg.fif Closing /home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-3_meg.fif [done] Opening raw data file /home/stefanappelhoff/mne_data/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/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 Writing '/home/stefanappelhoff/mne_data/ds000117-bids/participants.tsv'... participant_id age sex group 0 sub-01 10 M n/a 1 sub-1 10 M n/a Writing '/home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/sub-01_ses-01_scans.tsv'... filename acq_time 0 meg/sub-01_ses-01_task-VisualFaces_run-1_meg.fif 2009-04-07T16:39:35 1 meg/sub-01_ses-01_task-VisualFaces_run-2_meg.fif 2009-04-07T16:52:59 2 meg/sub-01_ses-01_task-VisualFaces_run-3_meg.fif 2009-04-07T17:02:25 0 meg/sub-01_ses-01_task-VisualFaces_run-4_meg.fif 2009-04-07T17:17:45 4 meg/sub-01_ses-01_task-VisualFaces_run-5_meg.fif 2009-04-07T17:27:38 294 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/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-4_events.tsv'... onset duration trial_type event_value event_sample 0 25.407273 0.0 face/unfamiliar/first 13 27948 1 26.219091 0.0 NaN 269 28841 2 28.498182 0.0 face/unfamiliar/immediate 14 31348 3 29.337273 0.0 NaN 270 32271 4 31.789091 0.0 face/unfamiliar/first 13 34968 Writing '/home/stefanappelhoff/mne_data/ds000117-bids/dataset_description.json'... { "Name": " ", "BIDSVersion": "1.1.1 (draft)" } Reading 0 ... 543399 = 0.000 ... 493.999 secs... Writing '/home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_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/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-4_channels.tsv'... name type units description sampling_frequency \ 0 MEG0113 MEGGRADPLANAR T/m Planar Gradiometer 1100.0 1 MEG0112 MEGGRADPLANAR T/m Planar Gradiometer 1100.0 2 MEG0111 MEGMAG T Magnetometer 1100.0 3 MEG0122 MEGGRADPLANAR T/m Planar Gradiometer 1100.0 4 MEG0123 MEGGRADPLANAR T/m Planar Gradiometer 1100.0 low_cutoff high_cutoff status 0 0.0 356.399994 good 1 0.0 356.399994 good 2 0.0 356.399994 good 3 0.0 356.399994 good 4 0.0 356.399994 good Copying data files to /home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-4_meg.fif /home/stefanappelhoff/Desktop/bids/mne-bids/examples/convert_group_studies.py:76: RuntimeWarning: This filename (/home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-4_meg.fif) does not conform to MNE naming conventions. All raw files should end with raw.fif, raw_sss.fif, raw_tsss.fif, raw.fif.gz, raw_sss.fif.gz or raw_tsss.fif.gz overwrite=True) Overwriting existing file. Writing /home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-4_meg.fif Closing /home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-4_meg.fif [done] Opening raw data file /home/stefanappelhoff/mne_data/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/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 Writing '/home/stefanappelhoff/mne_data/ds000117-bids/participants.tsv'... participant_id age sex group 0 sub-01 10 M n/a 1 sub-1 10 M n/a Writing '/home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/sub-01_ses-01_scans.tsv'... filename acq_time 0 meg/sub-01_ses-01_task-VisualFaces_run-1_meg.fif 2009-04-07T16:39:35 1 meg/sub-01_ses-01_task-VisualFaces_run-2_meg.fif 2009-04-07T16:52:59 2 meg/sub-01_ses-01_task-VisualFaces_run-3_meg.fif 2009-04-07T17:02:25 3 meg/sub-01_ses-01_task-VisualFaces_run-4_meg.fif 2009-04-07T17:17:45 0 meg/sub-01_ses-01_task-VisualFaces_run-5_meg.fif 2009-04-07T17:27:38 292 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/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-5_events.tsv'... onset duration trial_type event_value event_sample 0 25.717273 0.0 face/famous/first 5 28289 1 26.469091 0.0 NaN 261 29116 2 29.023636 0.0 scrambled/first 17 31926 3 29.599091 0.0 NaN 273 32559 4 32.130909 0.0 scrambled/immediate 18 35344 Writing '/home/stefanappelhoff/mne_data/ds000117-bids/dataset_description.json'... { "Name": " ", "BIDSVersion": "1.1.1 (draft)" } Reading 0 ... 536799 = 0.000 ... 487.999 secs... Writing '/home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_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/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-5_channels.tsv'... name type units description sampling_frequency \ 0 MEG0113 MEGGRADPLANAR T/m Planar Gradiometer 1100.0 1 MEG0112 MEGGRADPLANAR T/m Planar Gradiometer 1100.0 2 MEG0111 MEGMAG T Magnetometer 1100.0 3 MEG0122 MEGGRADPLANAR T/m Planar Gradiometer 1100.0 4 MEG0123 MEGGRADPLANAR T/m Planar Gradiometer 1100.0 low_cutoff high_cutoff status 0 0.0 356.399994 good 1 0.0 356.399994 good 2 0.0 356.399994 good 3 0.0 356.399994 good 4 0.0 356.399994 good Copying data files to /home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-5_meg.fif /home/stefanappelhoff/Desktop/bids/mne-bids/examples/convert_group_studies.py:76: RuntimeWarning: This filename (/home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-5_meg.fif) does not conform to MNE naming conventions. All raw files should end with raw.fif, raw_sss.fif, raw_tsss.fif, raw.fif.gz, raw_sss.fif.gz or raw_tsss.fif.gz overwrite=True) Overwriting existing file. Writing /home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-5_meg.fif Closing /home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-5_meg.fif [done] Opening raw data file /home/stefanappelhoff/mne_data/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/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 Writing '/home/stefanappelhoff/mne_data/ds000117-bids/participants.tsv'... participant_id age sex group 0 sub-01 10 M n/a 1 sub-1 10 M n/a Writing '/home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/sub-01_ses-01_scans.tsv'... filename acq_time 0 meg/sub-01_ses-01_task-VisualFaces_run-1_meg.fif 2009-04-07T16:39:35 1 meg/sub-01_ses-01_task-VisualFaces_run-2_meg.fif 2009-04-07T16:52:59 2 meg/sub-01_ses-01_task-VisualFaces_run-3_meg.fif 2009-04-07T17:02:25 3 meg/sub-01_ses-01_task-VisualFaces_run-4_meg.fif 2009-04-07T17:17:45 4 meg/sub-01_ses-01_task-VisualFaces_run-5_meg.fif 2009-04-07T17:27:38 296 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/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-6_events.tsv'... onset duration trial_type event_value event_sample 0 25.204545 0.0 face/famous/first 5 27725 1 25.850000 0.0 NaN 261 28435 2 28.345455 0.0 scrambled/first 17 31180 3 29.024545 0.0 NaN 273 31927 4 31.470000 0.0 face/famous/first 5 34617 Writing '/home/stefanappelhoff/mne_data/ds000117-bids/dataset_description.json'... { "Name": " ", "BIDSVersion": "1.1.1 (draft)" } Reading 0 ... 544499 = 0.000 ... 494.999 secs... Writing '/home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_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/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-6_channels.tsv'... name type units description sampling_frequency \ 0 MEG0113 MEGGRADPLANAR T/m Planar Gradiometer 1100.0 1 MEG0112 MEGGRADPLANAR T/m Planar Gradiometer 1100.0 2 MEG0111 MEGMAG T Magnetometer 1100.0 3 MEG0122 MEGGRADPLANAR T/m Planar Gradiometer 1100.0 4 MEG0123 MEGGRADPLANAR T/m Planar Gradiometer 1100.0 low_cutoff high_cutoff status 0 0.0 356.399994 good 1 0.0 356.399994 good 2 0.0 356.399994 good 3 0.0 356.399994 good 4 0.0 356.399994 good Copying data files to /home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-6_meg.fif /home/stefanappelhoff/Desktop/bids/mne-bids/examples/convert_group_studies.py:76: RuntimeWarning: This filename (/home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-6_meg.fif) does not conform to MNE naming conventions. All raw files should end with raw.fif, raw_sss.fif, raw_tsss.fif, raw.fif.gz, raw_sss.fif.gz or raw_tsss.fif.gz overwrite=True) Overwriting existing file. Writing /home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-6_meg.fif Closing /home/stefanappelhoff/mne_data/ds000117-bids/sub-01/ses-01/meg/sub-01_ses-01_task-VisualFaces_run-6_meg.fif [done] Now let's see the structure of the BIDS folder we created. .. code-block:: default print_dir_tree(output_path) .. rst-class:: sphx-glr-script-out Out: .. code-block:: none |------------ 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 |--------------- sub-01 |------------------ ses-01 |--------------------- sub-01_ses-01_scans.tsv |--------------------- meg |------------------------ sub-01_ses-01_task-VisualFaces_run-1_meg.fif |------------------------ sub-01_ses-01_task-VisualFaces_run-2_meg.fif |------------------------ sub-01_ses-01_coordsystem.json |------------------------ sub-01_ses-01_task-VisualFaces_run-5_events.tsv |------------------------ sub-01_ses-01_task-VisualFaces_run-6_channels.tsv |------------------------ sub-01_ses-01_task-VisualFaces_run-5_channels.tsv |------------------------ sub-01_ses-01_task-VisualFaces_run-4_channels.tsv |------------------------ sub-01_ses-01_task-VisualFaces_run-6_events.tsv |------------------------ sub-01_ses-01_task-VisualFaces_run-6_meg.fif |------------------------ sub-01_ses-01_task-VisualFaces_run-2_meg.json |------------------------ sub-01_ses-01_task-VisualFaces_run-3_channels.tsv |------------------------ sub-01_ses-01_task-VisualFaces_run-4_events.tsv |------------------------ sub-01_ses-01_task-VisualFaces_run-4_meg.json |------------------------ sub-01_ses-01_task-VisualFaces_run-2_channels.tsv |------------------------ sub-01_ses-01_task-VisualFaces_run-2_events.tsv |------------------------ sub-01_ses-01_task-VisualFaces_run-1_meg.json |------------------------ sub-01_ses-01_task-VisualFaces_run-3_meg.json |------------------------ sub-01_ses-01_task-VisualFaces_run-4_meg.fif |------------------------ sub-01_ses-01_task-VisualFaces_run-1_channels.tsv |------------------------ sub-01_ses-01_task-VisualFaces_run-6_meg.json |------------------------ sub-01_ses-01_task-VisualFaces_run-3_meg.fif |------------------------ sub-01_ses-01_task-VisualFaces_run-3_events.tsv |------------------------ sub-01_ses-01_task-VisualFaces_run-1_events.tsv |------------------------ sub-01_ses-01_task-VisualFaces_run-5_meg.json |------------------------ sub-01_ses-01_task-VisualFaces_run-5_meg.fif .. rst-class:: sphx-glr-timing **Total running time of the script:** ( 0 minutes 35.246 seconds) .. _sphx_glr_download_auto_examples_convert_group_studies.py: .. only :: html .. container:: sphx-glr-footer :class: sphx-glr-footer-example .. container:: sphx-glr-download :download:`Download Python source code: convert_group_studies.py ` .. container:: sphx-glr-download :download:`Download Jupyter notebook: convert_group_studies.ipynb ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_