Difference between revisions of "MNE BIDS MEG Anonymization"

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(Initial)
 
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UNDER CONSTRUCTION
UNDER CONSTRUCTION

==== Introduction to Import/Upload Process ====
Datasets must be organized prior to anonymization. <br>
Several organizational options will be provided to assist in recognizing the datasets. <br>
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
#This installs mne_docker / mne-bids / mne-bids-pipeline
git clone git@tako:mne_singularity
git clone git@tako:mne_singularity
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Link freesurfer or build from singularity:
Link freesurfer or build from singularity:
ln -s PATH_TO_FREESURFER ./freesurfer
ln -s PATH_TO_FREESURFER ./freesurfer


==== Create Head Surface to view anonymization ====
#Create
enigma/import/import_mri.sh


==== Data Curating before anonymization ====

=== OPTION 1 ===
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






Revision as of 09:16, 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 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

 #Create 
 enigma/import/import_mri.sh


Data Curating before anonymization

OPTION 1

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 -- https://github.com/mne-tools/mne-docker
 singularity pull docker://ghcr.io/mne-tools/mne-python-jupyter:main