Distinct spatial associations of adversity with hippocampal macro- and microstructure in early adolescence

This repository contains scripts to reproduce analyses of the BioRxiv preprint.

Instructions

The scripts can be found under /scripts and their respective folder explained below. The number in the scripts names refer to the order they were run to produce the results found in the paper. Further explanation on required packages, script depencendies and input and output data can be found at the beginning of each script.

Sample and behavioral

Scripts pertaining to sample and behavioral data organization /sample_behavioral.

• hippo-adv_01_agreement: estimates agreement between youth- and caregiver-reported family environment questionnaire items.
• hippo-adv_02_efa: runs the exploratory factor analysis of the selected stress-related questionnaires of the ABCD Study.
• hippo-adv_03_inr: calculates measures of income-to-needs ratio.
• hippo-adv_04_sample_selection: filters participants who fall into the inclusion criteria for structural MRI and have baseline data.
• hippo-adv_10_neuro_sample: filters participants with MRI data that have behavioral and biological data.
• hippo-adv_11_cfa: runs confirmatory factor analysis on the neuroimaging sample and checks for biases.
• hippo-adv_13_traintest_split: splits the data into train and test for confirmatory factor analysis, harmonization and downstream analyses.
• hippo-adv_15_cfa_GE_SIEMENS: reruns confirmatory factor analysis again for the sample with only GE and SIEMENS participants.

Imaging and preprocessing

Scripts pertaining to preprocessing and HippUnfold pipelines /imaging_preprocessing.

• hippo-adv_05_prefreesurfer: runs the Prefreesurfer step of the ABCD-HCP pipeline.
• hippo-adv_06_hippunfold: runs HippUnfold.
• hippo-adv_07_hippunfold_dice: quality control of HippUnfold segmentation output.
• hippo-adv_08a_neuro_generate_dekraker25: generates volumetric DeKraker25 labels.
• hippo-adv_08b_hippunfold_dekraker25: projects DeKraker25 labels onto hippocampal surfaces.
• hippo-adv_09_subfield_surfaces: extracts the hippocampal features across AP and PD axes.
• hippo-adv_12_filter_harmonization: filters participants based on their T1w/T2w ratio values.
• hippo-adv_16_neuroharmonize: harmonizes neuroimaging data before running models.
• hippo-adv_17_sum_biomarkers: sums biomarkers based on the subfields to create total measures.

Analyses

Scripts pertaining to statistical analyses /analyses.

• hippo-adv_14_stats_plot_scanners: runs statistical tests and plots sociodemographical and biological variables across scanners.
• hippo-adv_18_plsr: runs nested PLS-R models for all features across both axes to investigate the effects of single adversity types.
• hippo-adv_19_lmms: runs linear mixed effects models to investigate the effects of cumulative adversity exposure.
• hippo-adv_20_fdr_plsr_extraction: runs global fdr correction for the PLS-R models and extracts the coefficients, VIP scores and first component loadings.

Figures

Scripts pertaining to figures creation /figures.

• hippo-adv_21_plsr_plots: plots PLS-R coefficients, VIP scores and first latent component.
• hippo-adv_22_lmms_fdr_plot: runs global fdr correction for the linear mixed effects models, extracts their beta coefficients and plot effect their effects.
• hippo-adv_23_spatial_features: plots spatial maps across the PD and AP axes for each hippocampal feature.