ENIGMA MEG Working Group: Difference between revisions
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===Singularity Container=== |
===Singularity Container=== |
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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. Being a container, the analysis can be run on any platform (linux, mac, windows, ...). |
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. Being a container, the analysis can be run on any platform (linux, mac, windows, ...). <br> |
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https://sylabs.io/singularity/ |
https://sylabs.io/singularity/ |
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Revision as of 09:47, 2 April 2020
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
Data Analysis
Consistent Processing
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. Being a container, the analysis can be run on any platform (linux, mac, windows, ...).
https://sylabs.io/singularity/
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.
The singularity def file can be found at:
github.com/........ upload
The singularity container can be downloaded from:
Under Construction
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.
Meta-Analysis:
Statistics will be compiled across institutes