Email

cnievergelt@ucsd.edu

Imaging pipeline

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!

Pipeline Instructions & Variables

Cortical Thickness Pipeline 

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

Subcortical Volume Pipeline 

For more info on variables:
Subcortical Variable Explanation
Steps for submitting subcortical data for analysis:
Subcortical Data Submission Instructions

Hippocampal Subfield Pipeline 

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

For more info on variables:
DTI Variable Explanation
To download ENIGMA protocols on NITRC:
ENIGMA DTI Protocols

Imaging GWAS Pipeline

Scripts needed for QWAS analysis:
QWAS Pipeline Analysis

Sample Data

Cortical Thickness Pipeline 

View analysis variables:
Sample Cortical Imaging Data

Subcortical Volume Pipeline 

View analysis variables:
Sample Subcortical Imaging Data

Hippocampal Subfield Pipeline 

View analysis variables:
Sample Hippocampal Imaging Data

DTI Analysis Pipeline

View analysis variables:
Sample DTI Imaging Data

Resting State Pipeline

View analysis variables:
Sample Resting State Data

Analysis Proposals

Read the cortical analysis proposal by Duke University:
Structural Covariance Networks
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 Analysis Proposal:
Brain Aging in PTSD
Read the rs-fMRI proposal from UW-Milwaukee:
Dynamic RS FC - data driven connectivity states
Read the rs-fMRI proposal from UW-Madison:
RS resolution limit-free community detection
Read the harmonization proposal from Duke:
Harmonization of cross-platform data
Read the rs-fMRI Analysis Proposal from Stanford:
Resting State FC - Tolerance Intervals
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 amygdala Analysis Proposal from University of Cape Town:
Amygdala Subregions: Heritability and PTSD
Read the rs-fMRI and Machine Learning Proposal from Brown University:
Clinical Feature Prediction
Read the domain-focused approach from Columbia University:
Intrusive re-experiencing domain
Read the hierarchical multi-site ICA model proposal from Emory University:
Multi-site ICA Model
Read the default mode network subsystems for PTSD proposal from Boston University School of Medicine:
DMN Subsystems in PTSD
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
Read the Analysis Proposal from Stanford and USC:
Childhood Trauma and Brain Structure
Read the Analysis Proposal from Duke:
Structural Covariance with Cortical Thickness Reduction
Read the Analysis Proposal from Duke:
Thalamic Nuclei Volumes
Read the Analysis Proposal from USC:
PTSD and Bipolar Cross-Disorder Machine Learning
Read the Analysis Proposal from Stanford:
Tolerance intervals in neuro-biological abnormalities

PGC-PTSD ENIGMA Aims

Pipeline for all Imaging and GWAS Sites

Resting State Imaging Pipeline Flow