ImageNomer: Description of a functional connectivity and omics analysis tool and case study identifying a race confound

A Demographic-Conditioned Variational Autoencoder for fMRI Distribution Sampling and Removal of Confounds

Objective

fMRI and derived measures such as functional connectivity (FC) have been used to predict brain age, general fluid intelligence, psychiatric disease status, and preclinical neurodegenerative disease. However, it is not always clear that all demographic confounds, such as age, sex, and race, have been removed from fMRI data. Additionally, many fMRI datasets are restricted to authorized researchers, making dissemination of these valuable data sources challenging.

Methods

We create a variational autoencoder (VAE)-based model, DemoVAE, to decorrelate fMRI features from demographics and generate high-quality synthetic fMRI data based on user-supplied demographics. We train and validate our model using two large, widely used datasets, the Philadelphia Neurodevel-opmental Cohort (PNC) and Bipolar and Schizophrenia Network for Intermediate Phenotypes (BSNIP).

Results

We find that DemoVAE recapitulates group differences in fMRI data while capturing the full breadth of individual variations. Significantly, we also find that most clinical and computerized battery fields that are correlated with fMRI data are not correlated with DemoVAE latents. An exception are several fields related to schizophrenia medication and symptom severity.

Conclusion

Our model generates fMRI data that captures the full distribution of FC better than traditional VAE or GAN models. We also find that most prediction using fMRI data is dependent on correlation with, and prediction of, demographics.

Significance

Our DemoVAE model allows for generation of high quality synthetic data conditioned on subject demographics as well as the removal of the confounding effects of demographics. We identify that FC-based prediction tasks are highly influenced by demographic confounds.

A Demographic-Conditioned Variational Autoencoder for fMRI Distribution Sampling and Removal of Confounds

Objective

fMRI and derived measures such as functional connectivity (FC) have been used to predict brain age, general fluid intelligence, psychiatric disease status, and preclinical neurodegenerative disease. However, it is not always clear that all demographic confounds, such as age, sex, and race, have been removed from fMRI data. Additionally, many fMRI datasets are restricted to authorized researchers, making dissemination of these valuable data sources challenging.

Methods

We create a variational autoencoder (VAE)-based model, DemoVAE, to decorrelate fMRI features from demographics and generate high-quality synthetic fMRI data based on user-supplied demographics. We train and validate our model using two large, widely used datasets, the Philadelphia Neurodevelopmental Cohort (PNC) and Bipolar and Schizophrenia Network for Intermediate Phenotypes (BSNIP).

Results

We find that DemoVAE recapitulates group differences in fMRI data while capturing the full breadth of individual variations. Significantly, we also find that most clinical and computerized battery fields that are correlated with fMRI data are not correlated with DemoVAE latents. An exception are several fields related to schizophrenia medication and symptom severity.

Conclusion

Our model generates fMRI data that captures the full distribution of FC better than traditional VAE or GAN models. We also find that most prediction using fMRI data is dependent on correlation with, and prediction of, demographics.

Significance

Our DemoVAE model allows for generation of high quality synthetic data conditioned on subject demographics as well as the removal of the confounding effects of demographics. We identify that FC-based prediction tasks are highly influenced by demographic confounds.

Somatomotor-visual resting state functional connectivity increases after 2 years in the UK Biobank longitudinal cohort

Purpose

Functional magnetic resonance imaging (fMRI) and functional connectivity (FC) have been used to follow aging in both children and older adults. Robust changes have been observed in children, in which high connectivity among all brain regions changes to a more modular structure with maturation. We examine FC changes in older adults after 2 years of aging in the UK Biobank (UKB) longitudinal cohort.

Approach

We process fMRI connectivity data using the Power264 atlas and then test whether the average internetwork FC changes in the 2722-subject longitudinal cohort are statistically significant using a Bonferroni-corrected t -test. We also compare the ability of Power264 and UKB-provided, independent component analysis (ICA)-based FC to determine which of a longitudinal scan pair is older. Finally, we investigate cross-sectional FC changes as well as differences due to differing scanner tasks in the UKB, Philadelphia Neurodevelopmental Cohort, and Alzheimer's Disease Neuroimaging Initiative datasets.

Results

We find a 6.8% average increase in somatomotor network (SMT)-visual network (VIS) connectivity from younger to older scans (corrected p < 10 - 15 ) that occurs in male, female, older subject (> 65 years old), and younger subject (< 55 years old) groups. Among all internetwork connections, the average SMT-VIS connectivity is the best predictor of relative scan age. Using the full FC and a training set of 2000 subjects, one is able to predict which scan is older 82.5% of the time using either the full Power264 FC or the UKB-provided ICA-based FC.

Conclusions

We conclude that SMT-VIS connectivity increases with age in the UKB longitudinal cohort and that resting state FC increases with age in the UKB cross-sectional cohort.