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MNE Sample Data: BEM from T1 images

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
.

bids_root = "~/mne_data/ds000248"
deriv_root = "~/mne_data/derivatives/mne-bids-pipeline/ds000248_T1_BEM"
subjects_dir = f"{bids_root}/derivatives/freesurfer/subjects"

subjects = ["01"]
conditions = ["Auditory"]

ch_types = ["meg"]

bem_mri_images = "T1"
recreate_bem = True
freesurfer_verbose = True  # Prevent the CI from canceling the job prematurely

Generated output

Summary reports

sub-01_task-audiovisual_report.html