ENIGMA MEG Working Group: Difference between revisions

From MEG Core
Jump to navigation Jump to search
Content added Content deleted
No edit summary
 
(20 intermediate revisions by 2 users not shown)
Line 1: Line 1:
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. <br>
http://enigma.ini.usc.edu/


====MEG Working group====
LIST OF PARTICIPATING INSTITUTES


[http://enigma.ini.usc.edu/ The ENIGMA Consortium]<br>
===Singularity Container===
[http://enigma.ini.usc.edu/ongoing/enigma-meg-working-group/ The ENIGMA MEG Working Group]</br>
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. <br>
For more information visit: https://sylabs.io/singularity/


==Enigma Project - MEG working group==
The singularity def file can be found at:
The goal of the ENIGMA MEG Working Group is to explore the spatiotemporal patterns of brain oscillatory activity, and determine how these patterns relate to age, gender, and common genetic variants. Data from numerous modalities have demonstrated a hierarchical organization of the brain from sensory systems to higher cortical areas. There is some evidence that this hierarchical organization may also be reflected in the spatial distribution of intrinsic timescales of activity. This ENIGMA working group intends to explore these patterns across the lifespan. To achieve the highest possible number of subjects, this needs to be done by meta-analysis.<br>
github.com/........ upload


[mailto:nugenta@nih.gov Allison Nugent, PhD], ENIGMA MEG Chair <br>
The singularity container can be downloaded from:
[mailto:jeff.stout@nih.gov Jeff Stout, PhD], Lead Scientist <br>
Under Construction
[mailto:anna.namyst@nih.gov Anna Namyst, BA], Project Coordinator</br>


==MEG Working Group: Participating Institutions==
Calling commands:
[[File:ENIGMA-MEG-WG 12.2021.jpg|frameless|right|500px|600px| Global Participation in the ENIGMA MEG Working Group]]
The singularity container will be provided in a folder that also includes a ./bin folder
* Advent Health for Children
The commands within the bin folder are links to functions in the container
* Arkansas Childrens Hospital
* Aston University, UK
Commands can be called from the full path:
* Cambridge University
e.g.) /home/jstout/enigma/bin/enigma_rel_power -i /data/my_meg_data/subj1_resting_state.ds
* Children's Hospital of Philadephia
Commands can be added to the path and run using the command name:
* DNISC (Università degli Studi G.D'Annunzio Chieti Pescara)
for BASH, add this line to the /home/$USER/.bashrc file and save:
* IRCCS San Camillo Hospital Venice
export PATH=$PATH:/this/is/the/path/to/enigma/bin
* Johannes Gutenberg University, Mainz, Germany (Biomedical statistics and multimodal signal processing Unit)
enigma_rel_power -i /data/my_meg_data/subj1_resting_state.ds
* Macquarie University
* Massachusetts General Hospital
* McGill University, Montreal Neurological Institute
* National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
* Nemours DuPont Hospital for Children
* NeuroSpin
* New York University and NYU Abu Dhabi
* NIH/NICHD
* NIH/NIMH
* Precision Medicine Centre, Hokuto Hospital
* Precision Medicine Centre, Kumagaya General Hospital
* Salisbury VA Medical Center, Wake Forest University, Wake Forest School of Medecine
* The Mind Research Network
* Thomas Jefferson University
* Universiti Sains Malaysia
* Universiti Teknologi PETRONAS
* University of Alabama, Birmingham
* University of Göttingen
* University of Jyväskylä, Finland
* University of Pittsburgh
* University of Pittsburgh
* University of Texas Southwestern
* University of Tübingen


If you are interested in participating in this project, please email the project coordinator, [mailto:anna.namyst@nih.gov Anna Namyst], for more information.
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===
==Data Analysis==
Data analysis will be available in two flavors:
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.
1. Upload coregistered anonymized data to NIH
2. Perform analysis at acquisition site using EnigmaMeg scripts


*[https://github.com/jstout211/enigma_MEG ENIGMA MEG Pipeline on GitHub]
Anatomical Preprocessing:
*[https://megcore.nih.gov/index.php/ENIGMA_MEG_Pipeline_FAQ Processing Pipeline FAQ]
Surface models: Scalp, Outer Skull, Inner Skull, Pial Surface
Coregistration of the MRI and MEG data
Parcel extraction (freesurfer autorecon3)
Subparcel calculation (mne ....)


==Upload Data to be analyzed on NIH Biowulf cluster==
The resting state analysis steps:
Check data type and load data
Instructions for data preparation and upload: <br>
[https://megcore.nih.gov/index.php/ENIGMA_MEG_data_upload ENIGMA MEG Data Upload]
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


==Potential MEG Subanalyses==
Outputs:
Healthy Volunteers
The outputs of the analysis will result in a csv file
Epilepsy
A csv file for each subject will be created in the subfolder of the singularity directory
Alzheimer's and dementia
A final command can be run to calculate the summary statistics
Motor Analysis
Language Processing
Submission of Results:
Anxiety Disorders
After calculating the local institutes summary statistics, the group csv file will be uploaded to the NIMH.
Schizophrenia and related disorders
The group csv will have mean and standard deviation for each parcel and frequency band
Developmental disorders
A separate demographic csv will also be created with the demographic summary statistics
Traumatic Brain Injury

Stroke
Meta-Analysis:
Statistics will be compiled across institutes

Latest revision as of 16:48, 14 February 2024


The ENIGMA Consortium
The ENIGMA MEG Working Group

Enigma Project - MEG working group

The goal of the ENIGMA MEG Working Group is to explore the spatiotemporal patterns of brain oscillatory activity, and determine how these patterns relate to age, gender, and common genetic variants. Data from numerous modalities have demonstrated a hierarchical organization of the brain from sensory systems to higher cortical areas. There is some evidence that this hierarchical organization may also be reflected in the spatial distribution of intrinsic timescales of activity. This ENIGMA working group intends to explore these patterns across the lifespan. To achieve the highest possible number of subjects, this needs to be done by meta-analysis.

Allison Nugent, PhD, ENIGMA MEG Chair
Jeff Stout, PhD, Lead Scientist
Anna Namyst, BA, Project Coordinator

MEG Working Group: Participating Institutions

Global Participation in the ENIGMA MEG Working Group
Global Participation in the ENIGMA MEG Working Group
  • Advent Health for Children
  • Arkansas Childrens Hospital
  • Aston University, UK
  • Cambridge University
  • Children's Hospital of Philadephia
  • DNISC (Università degli Studi G.D'Annunzio Chieti Pescara)
  • IRCCS San Camillo Hospital Venice
  • Johannes Gutenberg University, Mainz, Germany (Biomedical statistics and multimodal signal processing Unit)
  • Macquarie University
  • Massachusetts General Hospital
  • McGill University, Montreal Neurological Institute
  • National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
  • Nemours DuPont Hospital for Children
  • NeuroSpin
  • New York University and NYU Abu Dhabi
  • NIH/NICHD
  • NIH/NIMH
  • Precision Medicine Centre, Hokuto Hospital
  • Precision Medicine Centre, Kumagaya General Hospital
  • Salisbury VA Medical Center, Wake Forest University, Wake Forest School of Medecine
  • The Mind Research Network
  • Thomas Jefferson University
  • Universiti Sains Malaysia
  • Universiti Teknologi PETRONAS
  • University of Alabama, Birmingham
  • University of Göttingen
  • University of Jyväskylä, Finland
  • University of Pittsburgh
  • University of Pittsburgh
  • University of Texas Southwestern
  • University of Tübingen
If you are interested in participating in this project, please email the project coordinator, Anna Namyst, for more information.

Data Analysis

Data analysis will be available in two flavors: 1. Upload coregistered anonymized data to NIH 2. Perform analysis at acquisition site using EnigmaMeg scripts

Upload Data to be analyzed on NIH Biowulf cluster

Instructions for data preparation and upload: 

 ENIGMA MEG Data Upload

Potential MEG Subanalyses

 Healthy Volunteers
 Epilepsy
 Alzheimer's and dementia
 Motor Analysis
 Language Processing
 Anxiety Disorders
 Schizophrenia and related disorders
 Developmental disorders
 Traumatic Brain Injury
 Stroke
Retrieved from "https://megcore.nih.gov/index.php?title=ENIGMA_MEG_Working_Group&oldid=5585"