Imaging pipeline

//Imaging pipeline
Imaging pipeline 2018-10-05T18:45:24+00:00

Understanding the genetic factors influencing sensitivity to environmental adversity in childhood will help us to identify molecular pathways that produce altered brain structure, dysfunctional behavior, psychopathology, and ultimately targets for novel therapeutics. The promise of finding genetic determinants of psychiatric disorder is identifying etiologic pathways for targeted interventions. We will conduct a G X E GWAS of relevant structural brain phenotypes where childhood trauma is a major risk factor, with the long-term goal of identifying genetic modulators of brain structure that help early prediction and treatment for a range of psychiatric disorders

Current subfield pipeline analyses include: Hippocampal, Cortical Thickness, Subcortical Volume, DTI, Resting State, and Imaging GWAS . Please note that these protocols are subject to improvements as we get more feedback, so please check often for the latest!

Cortical Thickness Pipeline 

View analysis variables:
Sample Cortical Imaging Data
Steps for submitting cortical data for analysis:
Cortical Thickness Data Submission Instructions
See structural image processing protocol under ENIGMA Cortical Quality Control Protocol 2.0 (April 2017):
Cortical Thickness Image Processing Protocol
Read the cortical analysis proposal by Duke University:
Structural Covariance Networks

Subcortical Volume Pipeline 

View analysis variables:
Sample Subcortical Imaging Data
For more info on variables:
Subcortical Variable Explanation
Download steps for submitting subcortical data for analysis:
Subcortical Data Submission Instructions

Hippocampal Subfield Pipeline 

View analysis variables:
Sample Hippocampal Imaging Data
For more info on variables:
Hippocampal Variable Explanation
Steps for submitting hippocampal data for analysis:
Hippocampal Data Submission Instructions
Scripts needed for Hippocampal subfields:
Hippocampal Pipeline Scripts

DTI Analysis Pipeline

View analysis variables:
Sample DTI Imaging Data
For more info on variables:
DTI Variable Explanation
To download ENIGMA protocols on NITRC:
ENIGMA DTI Protocols

Resting State Pipeline

View analysis variables:
Sample Resting State Data
Read the rs-fMRI Analysis Proposal from Duke/Durham VA:
Dynamic Resting State Connectivity - Seed based
Read the rs-fMRI Analysis Proposal from Emory, UWashington, USC, UMaryland & Duke/DurhamVA:
Resting State FC - Seed based and dual-regression
Read the rs-fMRI Analysis Proposal from Stanford:
Resting State FC - Tolerance Intervals

Resting State Pipeline Cont.

Read the rs-fMRI Analysis Proposal from UMichigan:
Connectome Based Neural Network
Read the rs-fMRI Analysis Proposal from Minneapolis VA:
Focal Activity Differences; ReHo, ALFF
Read the rs-fMRI Analysis Proposal from ColumbiaU and UC Boulder:
Data-Driven Multi-Modal Diagnosis of PTSD
Read the rs-fMRI Analysis Proposal from AMC Amsterdam:
Biotypes of PTSD

Imaging GWAS Pipeline

Scripts needed for QWAS analysis:
QWAS Pipeline Analysis

PGC-PTSD ENIGMA Aims

Pipeline for all Imaging and GWAS Sites

Resting State Imaging Pipeline Flow