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We used an analysis method that permitted unambiguous assignment of the direction of connectivity, GCA.
Applying directed graphs is a more sophisticated approach since it also provides information about the direction of connectivity.
A limitation of our work is that we did not consider the direction of connectivity, although most of the relationships we extracted have a direction described in the sentence.
The strategy of using multiple measures and searching for a consistent direction of connectivity changes in AD across the methods has the advantage of increasing knowledge on the behavior, such as sensitivity, specificity, availability, and applicability, of the different measures relative to each other.
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Since there are 2 directions of connectivity for each connection (in vs. out) an additional fixed effect of connectivity direction was included in the models.
Indirect methods of assessing cortical connectivity using diffusion imaging and resting state functional connectivity are insensitive to the direction of connections and are limited in estimating the weight of the underlying anatomical connections (Hagmann et al. 2008).
Granger causality spectra were obtained (see Materials and Methods) to test the direction of the connectivity between IC-F and IC-RS in the crossmodal task since significant coherence was observed between these ICs in the task.
Our results are also broadly similar to the direction of structural connectivity differences reported in individuals with schizophrenia [Amad et al., 2014; Cheung et al., 2011].
Although our data cannot resolve the anatomical direction of these connectivity changes, human and animal literature strongly suggest that prefrontal areas can have an inhibitory influence on the amygdala during emotion regulation (Rosenkranz and Grace 2002; Rosenkranz et al. 2003; Quirk et al. 2003; Etkin et al. 2006; Passamonti et al. 2008).
Each Meta-Family was composed of 3 further families in which models were grouped by similarities in the direction of modulation of connectivity.
A further family-level BMS, with models from Meta-Family C divided according to the direction of modulation of connectivity during RS, favored Family C1 (exceedance probability = 0.98) (Fig. 3 B ).
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