MNE BIDS MEG Anonymization: Difference between revisions
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UNDER CONSTRUCTION |
UNDER CONSTRUCTION |
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==== Introduction to Import/Upload Process ==== |
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Datasets must be organized prior to anonymization. <br> |
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Several organizational options will be provided to assist in recognizing the datasets. <br> |
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There are a variety of options ranging from high levels of renaming files to high level of search expressions. |
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==== Setup Container ==== |
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#This installs mne_docker / mne-bids / mne-bids-pipeline |
#This installs mne_docker / mne-bids / mne-bids-pipeline |
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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: |
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ln -s PATH_TO_FREESURFER ./freesurfer |
ln -s PATH_TO_FREESURFER ./freesurfer |
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==== Create Head Surface to view anonymization ==== |
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#Create |
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enigma/import/import_mri.sh |
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==== Data Curating before anonymization ==== |
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=== OPTION 1 === |
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Organize all data into the same folder. |
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All MRIs must be of .nii or .mgz |
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All MEG datasets must be single files or directories: .ds, .fif, .sqd, 4D-dataset (?) |
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MRIs and MEG datasets must have the same prefix. |
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EG - Subj1.ds Subj1.nii OR LastName_FirstName.fif LastName_FirstName.nii OR |
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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