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                                Subcortical-PFC resting state connectivity
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 significance of p< .05. Next, we inspected the overlap between whole brain connectivity from sample I and sample II using conjunction analyses. Conjunction analyses were performed using the easythresh_conj script in FSL (Nichols et al., 2005), using the same threshold described for the previous analyzes (Z > 3.09, p<0.05) in order to identify regions commonly connected in both samples.
Region of Interest Analysis
To further investigate limbic/subcortical-cortical and limbic/subcortical- subcortical brain connectivity we examined the zstats in predefined ROIs. Since studies have shown that different regions of the PFC have distinct functions, we investigated six specific subdivisions of the PFC (Fig 4a): the ventral and dorsal medial prefrontal cortex (vmPFC, dmPFC), the orbitofrontal cortex (OFC), the dorsal lateral prefrontal cortex (dlPFC), and the ventral and dorsal anterior cingulate cortex (vACC, dACC). All ROIs were bilateral. Regions were based on the Harvard-Oxford cortical structural atlas and were thresholded on ≥25% probability, resulting in the following sizes of anatomical ROIs: vmPFC 1189 voxels; dmPFC 5378 voxels; OFC 3502 voxels; dlPFC 5741 voxels; vACC 1313 voxels; and dACC1925 voxels. The following regions were used: Frontal Medial Cortex for vmPFC, Superior Frontal Gyrus for dmPFC, Frontal Orbital Cortex for OFC, Middle Frontal Gyrus for dlPFC, and the Cingulate Cortex anterior division for the ACC. The ACC was divided in a dorsal and ventral division with a cutoff at y=30.
Since both the VS and AMY also have shown to be connected the hippocampus (HPC) and the thalamus (TH) (Roy et al., 2009; Gabard-Durnam et al., 2014; Fareri et al., 2015), we included exploratory analyses of limbic/subcortical-subcortical connectivity, with additional subcortical ROIs of the TH and HPC (Fig 4b). Regions were based on the Harvard-Oxford subcortical structural atlas and were thresholded on ≥75% probability, resulting in a bilateral, anatomical TH ROI of 1646 voxels and a HPC ROI of 494 voxels. We used a stricter probability for the subcortical regions in order to prevent subcortical regions would overlap. In addition, we investigated functional connectivity between the VS and AMY. Zstats were extracted from subjects’ specific first level for each seed with the different ROIs as a mask using Featquery (as implemented in FSL v5.09). This way we extracted subject-specific connectivity estimates for 12 different subcortical-PFC connections and 5 different subcortical-subcortical connections.
To explore possible outliers, we calculated z-values of the subject specific zstats at the group level. When outliers were detected (Z-value <-3.29 or >3.29), scores were winsorized (Tabachnick and Fidell, 2013). One sample t-tests were used to investigate whether connectivity between a seed and a ROI was significantly different from zero (separately for both samples). Independent sample t-tests were used to test whether there were differences in connectivity
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