Note
Go to the end to download the full example code.
Getting averaging info from .fif files#
Parse averaging information defined in Elekta Vectorview/TRIUX DACQ (data acquisition). Extract and average epochs accordingly. Modify some averaging parameters and get epochs.
# Author: Jussi Nurminen (jnu@iki.fi)
#
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.
import os
import mne
from mne.datasets import multimodal
fname_raw = os.path.join(multimodal.data_path(), "multimodal_raw.fif")
print(__doc__)
Read raw file
Opening raw data file /home/circleci/mne_data/MNE-multimodal-data/multimodal_raw.fif...
Read a total of 7 projection items:
grad_ssp_upright.fif : PCA-v1 (1 x 306) idle
grad_ssp_upright.fif : PCA-v2 (1 x 306) idle
mag_ssp_upright.fif : PCA-v1 (1 x 306) idle
mag_ssp_upright.fif : PCA-v2 (1 x 306) idle
mag_ssp_upright.fif : PCA-v3 (1 x 306) idle
mag_ssp_upright.fif : PCA-v4 (1 x 306) idle
mag_ssp_upright.fif : PCA-v5 (1 x 306) idle
Range : 183600 ... 576599 = 305.687 ... 960.014 secs
Ready.
Check DACQ defined averaging categories and other info
print(raw.acqparser)
<AcqParserFIF | categories: 20 (8 in use), events: 17 (8 in use)
Averaging categories:
1: "Visual Upper right"
2: "Visual Lower right"
3: "Visual Lower left"
4: "Visual Upper left"
5: "Somato right"
6: "Somato left"
7: "Auditory right"
8: "Auditory left">
Extract epochs corresponding to a category
cond = raw.acqparser.get_condition(raw, "Auditory right")
epochs = mne.Epochs(raw, **cond)
epochs.average().plot_topo(background_color="w")
Not setting metadata
104 matching events found
Setting baseline interval to [-0.09989760657919393, 0.0] s
Applying baseline correction (mode: mean)
Created an SSP operator (subspace dimension = 7)
7 projection items activated
Get epochs from all conditions, average
evokeds = []
for cat in raw.acqparser.categories:
cond = raw.acqparser.get_condition(raw, cat)
# copy (supported) rejection parameters from DACQ settings
epochs = mne.Epochs(
raw, reject=raw.acqparser.reject, flat=raw.acqparser.flat, **cond
)
evoked = epochs.average()
evoked.comment = cat["comment"]
evokeds.append(evoked)
# save all averages to an evoked fiff file
# fname_out = 'multimodal-ave.fif'
# mne.write_evokeds(fname_out, evokeds)
Not setting metadata
118 matching events found
Setting baseline interval to [-0.09989760657919393, 0.0] s
Applying baseline correction (mode: mean)
Created an SSP operator (subspace dimension = 7)
7 projection items activated
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0123', 'MEG 0812', 'MEG 0942', 'MEG 2232']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812', 'MEG 0942', 'MEG 2232']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Not setting metadata
129 matching events found
Setting baseline interval to [-0.09989760657919393, 0.0] s
Applying baseline correction (mode: mean)
Created an SSP operator (subspace dimension = 7)
7 projection items activated
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812', 'MEG 0942']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812', 'MEG 2232']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on GRAD : ['MEG 0812', 'MEG 0942', 'MEG 2232']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Not setting metadata
115 matching events found
Setting baseline interval to [-0.09989760657919393, 0.0] s
Applying baseline correction (mode: mean)
Created an SSP operator (subspace dimension = 7)
7 projection items activated
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0123', 'MEG 0812', 'MEG 0942', 'MEG 2232']
Rejecting epoch based on GRAD : ['MEG 0123', 'MEG 0812', 'MEG 0942', 'MEG 2232']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0123', 'MEG 0812', 'MEG 0942', 'MEG 2232']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Not setting metadata
133 matching events found
Setting baseline interval to [-0.09989760657919393, 0.0] s
Applying baseline correction (mode: mean)
Created an SSP operator (subspace dimension = 7)
7 projection items activated
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812', 'MEG 0942']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0123', 'MEG 0812', 'MEG 0942', 'MEG 2232']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Not setting metadata
107 matching events found
Setting baseline interval to [-0.09989760657919393, 0.0] s
Applying baseline correction (mode: mean)
Created an SSP operator (subspace dimension = 7)
7 projection items activated
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Not setting metadata
118 matching events found
Setting baseline interval to [-0.09989760657919393, 0.0] s
Applying baseline correction (mode: mean)
Created an SSP operator (subspace dimension = 7)
7 projection items activated
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812', 'MEG 2232']
Rejecting epoch based on GRAD : ['MEG 0812', 'MEG 2232']
Rejecting epoch based on GRAD : ['MEG 0812', 'MEG 0942', 'MEG 2232']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812', 'MEG 2232']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812', 'MEG 0942', 'MEG 2232']
Rejecting epoch based on GRAD : ['MEG 0123', 'MEG 0812', 'MEG 0942', 'MEG 2232']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812', 'MEG 0942', 'MEG 2232']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Not setting metadata
104 matching events found
Setting baseline interval to [-0.09989760657919393, 0.0] s
Applying baseline correction (mode: mean)
Created an SSP operator (subspace dimension = 7)
7 projection items activated
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812', 'MEG 0942']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Not setting metadata
117 matching events found
Setting baseline interval to [-0.09989760657919393, 0.0] s
Applying baseline correction (mode: mean)
Created an SSP operator (subspace dimension = 7)
7 projection items activated
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on GRAD : ['MEG 0812', 'MEG 0942']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Make a new averaging category
newcat = dict()
newcat["comment"] = "Visual lower left, longer epochs"
newcat["event"] = 3 # reference event
newcat["start"] = -0.2 # epoch start rel. to ref. event (in seconds)
newcat["end"] = 0.7 # epoch end
newcat["reqevent"] = 0 # additional required event; 0 if none
newcat["reqwithin"] = 0.5 # ...required within .5 s (before or after)
newcat["reqwhen"] = 2 # ...required before (1) or after (2) ref. event
newcat["index"] = 9 # can be set freely
cond = raw.acqparser.get_condition(raw, newcat)
epochs = mne.Epochs(raw, reject=raw.acqparser.reject, flat=raw.acqparser.flat, **cond)
epochs.average().plot(time_unit="s")
Not setting metadata
115 matching events found
Setting baseline interval to [-0.19979521315838786, 0.0] s
Applying baseline correction (mode: mean)
Created an SSP operator (subspace dimension = 7)
7 projection items activated
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0123', 'MEG 0812', 'MEG 0942', 'MEG 2232']
Rejecting epoch based on GRAD : ['MEG 0123', 'MEG 0812', 'MEG 0942', 'MEG 2232']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0123', 'MEG 0812', 'MEG 0942', 'MEG 2232']
Rejecting epoch based on GRAD : ['MEG 0812', 'MEG 0942', 'MEG 2232']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on GRAD : ['MEG 0812']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Rejecting epoch based on EOG : ['EOG 061']
Total running time of the script: (0 minutes 14.802 seconds)
Estimated memory usage: 9 MB