ENIGMA MEG Working Group

UNDER CONSTRUCTION

Enigma Project - MEG working group

The enigma project is a large scale neuroimaging project to leverage data across multiple institutes to identify neuroimaging findings that are generally not possible at a single institute.
http://enigma.ini.usc.edu/

MEG Working group

LIST OF PARTICIPATING INSTITUTES

MEG Subcommitees

 Healthy Volunteers
 Epilepsy
 Alzheimer's and dementia
 Motor Analysis
 Language Processing
 Anxiety Disorders
 Schizophrenia and related disorders
 Developmental disorders
 Traumatic Brain Injury
 Stroke

Singularity Container

Singularity is a container technology (similar to Docker). We are using containers to allow for easy distribution of the analysis pipeline and analysis consistency. Singularity was chosen becuase it does not require administrative priveledges during runtime and can be run on an HPC system or local computing resources. Being a container, the analysis can be run on any platform (linux, mac, windows, ...) with singularity installed.
For more information visit: https://sylabs.io/singularity/

The singularity def file can be found at:

 github.com/........ upload

 To build from scratch:
 sudo singularity build enigma_meg.sif enigma_meg.def

The pre-built singularity container can be downloaded from (recommended/easier):

 Under Construction

Calling commands:

 The singularity container will be provided in a folder that also includes a ./bin folder
 The commands within the bin folder are links to functions in the container
 
 Commands can be called from the full path:
 e.g.) /home/jstout/enigma/bin/enigma_rel_power -i /data/my_meg_data/subj1_resting_state.ds 
 Commands can be added to the path and run using the command name:
 for BASH, add this line to the /home/$USER/.bashrc file and save:
   export PATH=$PATH:/this/is/the/path/to/enigma/bin
 enigma_rel_power -i /data/my_meg_data/subj1_resting_state.ds 

 Freesurfer related operations require a license file (download from https://surfer.nmr.mgh.harvard.edu/fswiki/License).  You will need to put your license file in the enigma folder and call it fs_license.txt

Resting State Analysis

The analysis routine has been implemented in MNE python (https://mne.tools/stable/index.html) and packaged into a singularity container. This guarantees that differences in software dependencies and operating system configurations have been eliminated.

Anatomical Preprocessing:

 Surface models: Scalp, Outer Skull, Inner Skull, Pial Surface
 Coregistration of the MRI and MEG data
 Parcel extraction (freesurfer autorecon3)
 Subparcel calculation (mne ....)

The resting state analysis steps:

 Check data type and load data
 Downsample to 200Hz
 Split to 1 second epochs
 Reject sensor level data at a specific threshold
 Calculate broad band dSPM inverse solution
 Filter the data into bands (1-3, 3-6, 8-12, 13-35, 35-55)
 Project the data to parcels and create parcel time series
 Calculate relative power in each band and parcel

Outputs:

 The outputs of the analysis will result in a csv file
 A csv file for each subject will be created in the subfolder of the singularity directory
 A final command can be run to calculate the summary statistics
 

Submission of Results:

 After calculating the local institutes summary statistics, the group csv file will be uploaded to the NIMH.
 The group csv will have mean and standard deviation for each parcel and frequency band
 A separate demographic csv will also be created with the demographic summary statistics 

Meta-Analysis:

 Statistics will be compiled across institutes