.. 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_mne_sample.py: ====================================== Convert MNE sample data to BIDS format ====================================== This example demonstrates how to convert your existing files into a BIDS-compatible folder. .. code-block:: default # Authors: Mainak Jas # Alexandre Gramfort # Teon Brooks # License: BSD (3-clause) Let us import mne_bids .. code-block:: default import os.path as op import mne from mne.datasets import sample from mne_bids import write_raw_bids from mne_bids.utils import print_dir_tree And define the paths and event_id dictionary. .. code-block:: default data_path = sample.data_path() event_id = {'Auditory/Left': 1, 'Auditory/Right': 2, 'Visual/Left': 3, 'Visual/Right': 4, 'Smiley': 5, 'Button': 32} raw_fname = op.join(data_path, 'MEG', 'sample', 'sample_audvis_raw.fif') events_data = op.join(data_path, 'MEG', 'sample', 'sample_audvis_raw-eve.fif') output_path = op.join(data_path, '..', 'MNE-sample-data-bids') Finally, we specify the raw_file and events_data .. code-block:: default raw = mne.io.read_raw_fif(raw_fname) bids_basename = 'sub-01_ses-01_task-audiovisual_run-01' write_raw_bids(raw, bids_basename, output_path, events_data=events_data, event_id=event_id, overwrite=True) .. rst-class:: sphx-glr-script-out Out: .. code-block:: none Opening raw data file /home/stefanappelhoff/mne_data/MNE-sample-data/MEG/sample/sample_audvis_raw.fif... Read a total of 3 projection items: PCA-v1 (1 x 102) idle PCA-v2 (1 x 102) idle PCA-v3 (1 x 102) idle Range : 25800 ... 192599 = 42.956 ... 320.670 secs Ready. Current compensation grade : 0 Opening raw data file /home/stefanappelhoff/mne_data/MNE-sample-data/MEG/sample/sample_audvis_raw.fif... Read a total of 3 projection items: PCA-v1 (1 x 102) idle PCA-v2 (1 x 102) idle PCA-v3 (1 x 102) idle Range : 25800 ... 192599 = 42.956 ... 320.670 secs Ready. Current compensation grade : 0 Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/participants.tsv'... age group participant_id sex 0 NaN NaN sub-01 NaN 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 0 meg/sub-01_ses-01_task-audiovisual_run-01_meg.fif 2002-12-03T20:01:10 Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_events.tsv'... onset duration trial_type event_value event_sample 0 3.624618 0.0 Auditory/Right 2 2177 1 4.237323 0.0 Visual/Left 3 2545 2 4.946596 0.0 Auditory/Left 1 2971 3 5.692499 0.0 Visual/Right 4 3419 4 6.413426 0.0 Auditory/Right 2 3852 Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/dataset_description.json'... { "Name": " ", "BIDSVersion": "1.1.1 (draft)" } /home/stefanappelhoff/miniconda3/envs/mne_bids1/lib/python3.6/site-packages/mne_bids-0.1-py3.6.egg/mne_bids/mne_bids.py:431: UserWarning: No line frequency found, defaulting to 50 Hz warn('No line frequency found, defaulting to 50 Hz') Reading 0 ... 166799 = 0.000 ... 277.714 secs... Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_meg.json'... { "TaskName": "audiovisual", "Manufacturer": "Elekta", "PowerLineFrequency": 50, "SamplingFrequency": 600.614990234375, "SoftwareFilters": "n/a", "RecordingDuration": 277.7136813300495, "RecordingType": "continuous", "DewarPosition": "n/a", "DigitizedLandmarks": false, "DigitizedHeadPoints": false, "MEGChannelCount": 306, "MEGREFChannelCount": 0, "EEGChannelCount": 60, "EOGChannelCount": 1, "ECGChannelCount": 0, "EMGChannelCount": 0, "MiscChannelCount": 0, "TriggerChannelCount": 9 } Writing '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_channels.tsv'... name type units description sampling_frequency \ 0 MEG 0113 MEGGRADPLANAR T/m Planar Gradiometer 600.61499 1 MEG 0112 MEGGRADPLANAR T/m Planar Gradiometer 600.61499 2 MEG 0111 MEGMAG T Magnetometer 600.61499 3 MEG 0122 MEGGRADPLANAR T/m Planar Gradiometer 600.61499 4 MEG 0123 MEGGRADPLANAR T/m Planar Gradiometer 600.61499 low_cutoff high_cutoff status 0 0.1 172.1763 good 1 0.1 172.1763 good 2 0.1 172.1763 good 3 0.1 172.1763 good 4 0.1 172.1763 good Copying data files to /home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_meg.fif /home/stefanappelhoff/Desktop/bids/mne-bids/examples/convert_mne_sample.py:44: RuntimeWarning: This filename (/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) 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 event_id=event_id, overwrite=True) Overwriting existing file. Writing /home/stefanappelhoff/mne_data/MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_meg.fif Closing /home/stefanappelhoff/mne_data/MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_meg.fif [done] '/home/stefanappelhoff/mne_data/MNE-sample-data/../MNE-sample-data-bids' 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 |------------------ MNE-sample-data-bids |--------------------- participants.tsv |--------------------- dataset_description.json |--------------------- participants.json |--------------------- sub-01 |------------------------ ses-01 |--------------------------- sub-01_ses-01_scans.tsv |--------------------------- meg |------------------------------ sub-01_ses-01_coordsystem.json |------------------------------ sub-01_ses-01_task-audiovisual_run-01_meg.json |------------------------------ sub-01_ses-01_task-audiovisual_run-01_channels.tsv |------------------------------ sub-01_ses-01_task-audiovisual_run-01_meg.fif |------------------------------ sub-01_ses-01_task-audiovisual_run-01_events.tsv |--------------------------- anat |------------------------------ sub-01_ses-01_T1w.nii.gz |------------------------------ sub-01_ses-01_T1w.json .. rst-class:: sphx-glr-timing **Total running time of the script:** ( 0 minutes 1.347 seconds) .. _sphx_glr_download_auto_examples_convert_mne_sample.py: .. only :: html .. container:: sphx-glr-footer :class: sphx-glr-footer-example .. container:: sphx-glr-download :download:`Download Python source code: convert_mne_sample.py ` .. container:: sphx-glr-download :download:`Download Jupyter notebook: convert_mne_sample.ipynb ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_