Difference between revisions of "MNE BIDS MEG Anonymization"

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= Introduction to Import/Upload Process =
= Introduction to Import/Upload Process =
Datasets must be organized prior to anonymization. <br>
Datasets must be organized prior to anonymization. <br>
Several organizational options will be provided to assist in recognizing the datasets. <br>
Several organizational options will be provided to assist in recognizing and linking the datasets. <br>
There are a variety of options ranging from extensive renaming of files to manipulating search expressions (choose the option most appropriate for your lab)
There are a variety of options ranging from extensive renaming of files to manipulating search expressions (choose the option most appropriate for your lab)
Prior to anonymization - a "master_list" will be created linking the appropriate input information.
Prior to anonymization - a "master_list" will be created linking the appropriate input information.

Revision as of 08:58, 31 August 2021

UNDER CONSTRUCTION

Introduction to Import/Upload Process

Datasets must be organized prior to anonymization.
Several organizational options will be provided to assist in recognizing and linking the datasets.
There are a variety of options ranging from extensive renaming of files to manipulating search expressions (choose the option most appropriate for your lab) Prior to anonymization - a "master_list" will be created linking the appropriate input information.

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

 #Create 
 enigma/import/import_mri.sh


Data Curating before anonymization

OPTION 1

This option requires the most space/manual labor, but is easy to troubleshoot

Copy all data into a single folder using the following format:
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