Quickstart: mkh5 to EEGLAB

Converting mkh5 to EEGLAB .set requires MNE Python under the hood.

An apparatus map with standard mkh5 Right Anterior Superior (RAS) electrode locations is required and rotated automatically to the EEGLAB default coordinates. This can be included in the .yhdr YAML file when creating the mkh5 file or added later when converting to EEGLAB as shown here. The apparatus map format is the same.

Note

The first time you load the .set file into EEGLAB clean up the EEGLAB events and center the channel locations with spherical coordinates. In MATLAB

>> eeglab
>> EEG = pop_loadset('filename','sub00.set')
>> EEG = eeg_checkset(EEG, 'eventconsistency')
>> pop_chanedit(EEG)

FYI … environment and versions.

import os
import mne
import mkpy
from mkpy.io import mkh5eeglab, mkh5mne


print("conda env", os.environ["CONDA_DEFAULT_ENV"])
for pkg in [mkpy, mne]:
    print(pkg.__name__, pkg.__version__)

Out:

conda env env_3.8
mkpy 0.2.7
mne 1.0.3

`mkh5eeglab.mkh5_to_set()`

Convert an mkh5 file into an EEGLAB format .set file

Adding epochs_name is optional, it adds the event tags from the named epochs table to EEG.events and EEG.urevents.
Adding garv_annotations is optional but adds “boundary” events to EEG.events and EEG.urevents

The sample data is a single subject mkh5 data file for an auditory oddball paradigm.

Minimal export: EEG data, datablock labels and boundaries, and log event codes. The mkh5 file has electrode locations baked in via the YAML .yhdr

mkh5eeglab.mkh5_to_set("../mkh5_data/sub000p3.h5", "sub000p3.set")

Out:

../mkh5_data/sub000p3.h5
looking up data block paths, larger files take longer ...
ok
checking info, montage sub000/dblock_1
checking info, montage sub000/dblock_2
checking info, montage sub000/dblock_3
checking info, montage sub000/dblock_4
Creating RawArray with float64 data, n_channels=39, n_times=31232
    Range : 0 ... 31231 =      0.000 ...   124.924 secs
Ready.
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting positions of 5 eog channels found in montage:
['lle', 'lhz', 'HEOG', 'rle', 'rhz']
Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
  raw_dblock.set_montage(montage)
sub000/dblock_0 setting mkh5 epochs table ms100 events and metadata
sub000/dblock_0 setting mkh5 epochs table ms10000 events and metadata
sub000/dblock_0 setting mkh5 epochs table ms1500 events and metadata
sub000/dblock_0 setting mkh5 epochs table ms3000 events and metadata
Creating RawArray with float64 data, n_channels=39, n_times=32768
    Range : 0 ... 32767 =      0.000 ...   131.068 secs
Ready.
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting positions of 5 eog channels found in montage:
['lle', 'lhz', 'HEOG', 'rle', 'rhz']
Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
  raw_dblock.set_montage(montage)
sub000/dblock_1 setting mkh5 epochs table ms100 events and metadata
sub000/dblock_1 setting mkh5 epochs table ms10000 events and metadata
sub000/dblock_1 setting mkh5 epochs table ms1500 events and metadata
sub000/dblock_1 setting mkh5 epochs table ms3000 events and metadata
Creating RawArray with float64 data, n_channels=39, n_times=31744
    Range : 0 ... 31743 =      0.000 ...   126.972 secs
Ready.
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting positions of 5 eog channels found in montage:
['lle', 'lhz', 'HEOG', 'rle', 'rhz']
Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
  raw_dblock.set_montage(montage)
sub000/dblock_2 setting mkh5 epochs table ms100 events and metadata
sub000/dblock_2 setting mkh5 epochs table ms10000 events and metadata
sub000/dblock_2 setting mkh5 epochs table ms1500 events and metadata
sub000/dblock_2 setting mkh5 epochs table ms3000 events and metadata
Creating RawArray with float64 data, n_channels=39, n_times=32512
    Range : 0 ... 32511 =      0.000 ...   130.044 secs
Ready.
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting positions of 5 eog channels found in montage:
['lle', 'lhz', 'HEOG', 'rle', 'rhz']
Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
  raw_dblock.set_montage(montage)
sub000/dblock_3 setting mkh5 epochs table ms100 events and metadata
sub000/dblock_3 setting mkh5 epochs table ms10000 events and metadata
sub000/dblock_3 setting mkh5 epochs table ms1500 events and metadata
sub000/dblock_3 setting mkh5 epochs table ms3000 events and metadata
Creating RawArray with float64 data, n_channels=39, n_times=28416
    Range : 0 ... 28415 =      0.000 ...   113.660 secs
Ready.
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting positions of 5 eog channels found in montage:
['lle', 'lhz', 'HEOG', 'rle', 'rhz']
Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
  raw_dblock.set_montage(montage)
sub000/dblock_4 setting mkh5 epochs table ms100 events and metadata
sub000/dblock_4 setting mkh5 epochs table ms10000 events and metadata
sub000/dblock_4 setting mkh5 epochs table ms1500 events and metadata
sub000/dblock_4 setting mkh5 epochs table ms3000 events and metadata
EEG data marked as already having the desired reference.

Export with alternate electrode locations

mkh5eeglab.mkh5_to_set(
    "../mkh5_data/sub000p3.h5",
    "sub000p3.set",
    apparatus_yaml="ras_32chan_xyz_spherical.yml",
)

Out:

../mkh5_data/sub000p3.h5
looking up data block paths, larger files take longer ...
ok
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_0 with sensor locations from ras_32chan_xyz_spherical.yml
  warnings.warn(msg)
checking info, montage sub000/dblock_1
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_1 with sensor locations from ras_32chan_xyz_spherical.yml
  warnings.warn(msg)
checking info, montage sub000/dblock_2
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_2 with sensor locations from ras_32chan_xyz_spherical.yml
  warnings.warn(msg)
checking info, montage sub000/dblock_3
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_3 with sensor locations from ras_32chan_xyz_spherical.yml
  warnings.warn(msg)
checking info, montage sub000/dblock_4
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_4 with sensor locations from ras_32chan_xyz_spherical.yml
  warnings.warn(msg)
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_0 with sensor locations from ras_32chan_xyz_spherical.yml
  warnings.warn(msg)
Creating RawArray with float64 data, n_channels=39, n_times=31232
    Range : 0 ... 31231 =      0.000 ...   124.924 secs
Ready.
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting position of 1 eog channel found in montage:
['HEOG']
Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
  raw_dblock.set_montage(montage)
sub000/dblock_0 setting mkh5 epochs table ms100 events and metadata
sub000/dblock_0 setting mkh5 epochs table ms10000 events and metadata
sub000/dblock_0 setting mkh5 epochs table ms1500 events and metadata
sub000/dblock_0 setting mkh5 epochs table ms3000 events and metadata
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_1 with sensor locations from ras_32chan_xyz_spherical.yml
  warnings.warn(msg)
Creating RawArray with float64 data, n_channels=39, n_times=32768
    Range : 0 ... 32767 =      0.000 ...   131.068 secs
Ready.
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting position of 1 eog channel found in montage:
['HEOG']
Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
  raw_dblock.set_montage(montage)
sub000/dblock_1 setting mkh5 epochs table ms100 events and metadata
sub000/dblock_1 setting mkh5 epochs table ms10000 events and metadata
sub000/dblock_1 setting mkh5 epochs table ms1500 events and metadata
sub000/dblock_1 setting mkh5 epochs table ms3000 events and metadata
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_2 with sensor locations from ras_32chan_xyz_spherical.yml
  warnings.warn(msg)
Creating RawArray with float64 data, n_channels=39, n_times=31744
    Range : 0 ... 31743 =      0.000 ...   126.972 secs
Ready.
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting position of 1 eog channel found in montage:
['HEOG']
Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
  raw_dblock.set_montage(montage)
sub000/dblock_2 setting mkh5 epochs table ms100 events and metadata
sub000/dblock_2 setting mkh5 epochs table ms10000 events and metadata
sub000/dblock_2 setting mkh5 epochs table ms1500 events and metadata
sub000/dblock_2 setting mkh5 epochs table ms3000 events and metadata
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_3 with sensor locations from ras_32chan_xyz_spherical.yml
  warnings.warn(msg)
Creating RawArray with float64 data, n_channels=39, n_times=32512
    Range : 0 ... 32511 =      0.000 ...   130.044 secs
Ready.
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting position of 1 eog channel found in montage:
['HEOG']
Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
  raw_dblock.set_montage(montage)
sub000/dblock_3 setting mkh5 epochs table ms100 events and metadata
sub000/dblock_3 setting mkh5 epochs table ms10000 events and metadata
sub000/dblock_3 setting mkh5 epochs table ms1500 events and metadata
sub000/dblock_3 setting mkh5 epochs table ms3000 events and metadata
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_4 with sensor locations from ras_32chan_xyz_spherical.yml
  warnings.warn(msg)
Creating RawArray with float64 data, n_channels=39, n_times=28416
    Range : 0 ... 28415 =      0.000 ...   113.660 secs
Ready.
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting position of 1 eog channel found in montage:
['HEOG']
Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
  raw_dblock.set_montage(montage)
sub000/dblock_4 setting mkh5 epochs table ms100 events and metadata
sub000/dblock_4 setting mkh5 epochs table ms10000 events and metadata
sub000/dblock_4 setting mkh5 epochs table ms1500 events and metadata
sub000/dblock_4 setting mkh5 epochs table ms3000 events and metadata
EEG data marked as already having the desired reference.

Complete export with codemap event tags from epochs table “ms1500” and garv annotations for those events.

mkh5eeglab.mkh5_to_set(
    "../mkh5_data/sub000p3.h5",  # file to convert
    "sub000p3.set",  # eeglab file
    apparatus_yaml="ras_32chan_xyz_spherical.yml",  # electrode locations
    epochs_name="ms1500",  # epochs table with tagged events
    garv_annotations={
        "event_channel": "ms1500",  # mark garv artifacts for tagged events
        "tmin": -750,
        "tmax": 750,
        "units": "ms",
    },
)

Out:

../mkh5_data/sub000p3.h5
looking up data block paths, larger files take longer ...
ok
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_0 with sensor locations from ras_32chan_xyz_spherical.yml
  warnings.warn(msg)
checking info, montage sub000/dblock_1
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_1 with sensor locations from ras_32chan_xyz_spherical.yml
  warnings.warn(msg)
checking info, montage sub000/dblock_2
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_2 with sensor locations from ras_32chan_xyz_spherical.yml
  warnings.warn(msg)
checking info, montage sub000/dblock_3
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_3 with sensor locations from ras_32chan_xyz_spherical.yml
  warnings.warn(msg)
checking info, montage sub000/dblock_4
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_4 with sensor locations from ras_32chan_xyz_spherical.yml
  warnings.warn(msg)
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_0 with sensor locations from ras_32chan_xyz_spherical.yml
  warnings.warn(msg)
Creating RawArray with float64 data, n_channels=39, n_times=31232
    Range : 0 ... 31231 =      0.000 ...   124.924 secs
Ready.
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting position of 1 eog channel found in montage:
['HEOG']
Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
  raw_dblock.set_montage(montage)
sub000/dblock_0 setting mkh5 epochs table ms100 events and metadata
sub000/dblock_0 setting mkh5 epochs table ms10000 events and metadata
sub000/dblock_0 setting mkh5 epochs table ms1500 events and metadata
sub000/dblock_0 setting mkh5 epochs table ms3000 events and metadata
annotating garv artifacts {'event_channel': 'ms1500', 'tmin': -750, 'tmax': 750, 'units': 'ms'}
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_1 with sensor locations from ras_32chan_xyz_spherical.yml
  warnings.warn(msg)
Creating RawArray with float64 data, n_channels=39, n_times=32768
    Range : 0 ... 32767 =      0.000 ...   131.068 secs
Ready.
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting position of 1 eog channel found in montage:
['HEOG']
Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
  raw_dblock.set_montage(montage)
sub000/dblock_1 setting mkh5 epochs table ms100 events and metadata
sub000/dblock_1 setting mkh5 epochs table ms10000 events and metadata
sub000/dblock_1 setting mkh5 epochs table ms1500 events and metadata
sub000/dblock_1 setting mkh5 epochs table ms3000 events and metadata
annotating garv artifacts {'event_channel': 'ms1500', 'tmin': -750, 'tmax': 750, 'units': 'ms'}
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_2 with sensor locations from ras_32chan_xyz_spherical.yml
  warnings.warn(msg)
Creating RawArray with float64 data, n_channels=39, n_times=31744
    Range : 0 ... 31743 =      0.000 ...   126.972 secs
Ready.
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting position of 1 eog channel found in montage:
['HEOG']
Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
  raw_dblock.set_montage(montage)
sub000/dblock_2 setting mkh5 epochs table ms100 events and metadata
sub000/dblock_2 setting mkh5 epochs table ms10000 events and metadata
sub000/dblock_2 setting mkh5 epochs table ms1500 events and metadata
sub000/dblock_2 setting mkh5 epochs table ms3000 events and metadata
annotating garv artifacts {'event_channel': 'ms1500', 'tmin': -750, 'tmax': 750, 'units': 'ms'}
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_3 with sensor locations from ras_32chan_xyz_spherical.yml
  warnings.warn(msg)
Creating RawArray with float64 data, n_channels=39, n_times=32512
    Range : 0 ... 32511 =      0.000 ...   130.044 secs
Ready.
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting position of 1 eog channel found in montage:
['HEOG']
Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
  raw_dblock.set_montage(montage)
sub000/dblock_3 setting mkh5 epochs table ms100 events and metadata
sub000/dblock_3 setting mkh5 epochs table ms10000 events and metadata
sub000/dblock_3 setting mkh5 epochs table ms1500 events and metadata
sub000/dblock_3 setting mkh5 epochs table ms3000 events and metadata
annotating garv artifacts {'event_channel': 'ms1500', 'tmin': -750, 'tmax': 750, 'units': 'ms'}
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_4 with sensor locations from ras_32chan_xyz_spherical.yml
  warnings.warn(msg)
Creating RawArray with float64 data, n_channels=39, n_times=28416
    Range : 0 ... 28415 =      0.000 ...   113.660 secs
Ready.
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting position of 1 eog channel found in montage:
['HEOG']
Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
  raw_dblock.set_montage(montage)
sub000/dblock_4 setting mkh5 epochs table ms100 events and metadata
sub000/dblock_4 setting mkh5 epochs table ms10000 events and metadata
sub000/dblock_4 setting mkh5 epochs table ms1500 events and metadata
sub000/dblock_4 setting mkh5 epochs table ms3000 events and metadata
annotating garv artifacts {'event_channel': 'ms1500', 'tmin': -750, 'tmax': 750, 'units': 'ms'}
EEG data marked as already having the desired reference.

Total running time of the script: ( 1 minutes 3.451 seconds)

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Quickstart: mkh5 to EEGLAB

mkh5eeglab.mkh5_to_set()

`mkh5eeglab.mkh5_to_set()`