MNE BIDS MEG Anonymization

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Revision as of 09:17, 31 August 2021 by Jstout (talk | contribs)
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Introduction to Import/Upload Process

Datasets must be organized prior to anonymization.
Several organizational options will be provided to assist in recognizing the datasets.
There are a variety of options ranging from high levels of renaming files to high level of search expressions.

Setup Container

 #This installs mne_docker / mne-bids / mne-bids-pipeline
 git clone git@tako:mne_singularity
 cd mne_singularity 
 sudo singularity build singularity_build.sif singularity_build.def 

Link freesurfer or build from singularity:

 ln -s PATH_TO_FREESURFER ./freesurfer

Create Head Surface to view anonymization


Data Curating before anonymization


Organize all data into the same folder. All MRIs must be of .nii or .mgz All MEG datasets must be single files or directories: .ds, .fif, .sqd, 4D-dataset (?)

 MRIs and MEG datasets must have the same prefix.   
 EG - Subj1.ds  Subj1.nii   OR  LastName_FirstName.fif  LastName_FirstName.nii   OR 

For admin setup

 # From the mne docker website --
 singularity pull docker://