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MNE Sample Data: Using the fsaverage template MRI

Demonstrated features

Feature This example
MEG processing ✅
EEG processing ❌
Maxwell filter ❌
Frequency filter ✅
Artifact regression ❌
SSP ❌
ICA ❌
Evoked contrasts ✅
Time-by-time decoding ✅
Time-generalization decoding ❌
CSP decoding ❌
Time-frequency analysis ❌
BEM surface creation ❌
Template MRI ✅

Dataset source

This dataset was acquired from https://openneuro.org/datasets/ds000248

How to download this dataset

Run in your terminal:

Run in your terminal
openneuro-py download \
             --dataset=ds000248 \
             --include=sub-01 \
             --include=sub-emptyroom \
             --include=derivatives/freesurfer/subjects \
             --exclude=derivatives/freesurfer/subjects/fsaverage/mri/aparc.a2005s+aseg.mgz \
             --exclude=derivatives/freesurfer/subjects/fsaverage/mri/aparc+aseg.mgz \
             --exclude=derivatives/freesurfer/subjects/fsaverage/mri/aparc.a2009s+aseg.mgz \
             --exclude=derivatives/freesurfer/subjects/fsaverage/xhemi/mri/aparc+aseg.mgz \
             --exclude=derivatives/freesurfer/subjects/sub-01/mri/aparc+aseg.mgz \
             --exclude=derivatives/freesurfer/subjects/sub-01/mri/aparc.DKTatlas+aseg.mgz \
             --exclude=derivatives/freesurfer/subjects/sub-01/mri/aparc.DKTatlas+aseg.mgz \
             --exclude=derivatives/freesurfer/subjects/sub-01/mri/aparc.a2009s+aseg.mgz

Note that we have to explicitly exclude files due to a problem with OpenNeuro's storage.

Configuration

Click to expand
Python
.

study_name = "ds000248"
bids_root = "~/mne_data/ds000248"
deriv_root = "~/mne_data/derivatives/mne-bids-pipeline/ds000248_no_mri"
subjects_dir = f"{bids_root}/derivatives/freesurfer/subjects"

subjects = ["01"]
rename_events = {"Smiley": "Emoji", "Button": "Switch"}
conditions = ["Auditory", "Visual", "Auditory/Left", "Auditory/Right"]
contrasts = [("Auditory/Right", "Auditory/Left")]

ch_types = ["meg"]
use_maxwell_filter = False
process_empty_room = False

use_template_mri = "fsaverage"
adjust_coreg = True