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The code below was used in R (v.4.3.3) to plot the cluster-wise values from the RFT and TFCE corrected analyses and validate them with additional mixed linear models.
We produce a figure displaying the thickness of the hippocampal clusters in relation to the group and session variables, in RFT and TFCE models, demonstrating a steeper curve toward group 2:
#We divide the cluster values by their sum to get the average thickness per vertex
dat_beh_ses13$clustCTTFCE=(FINK_Tv_smoothed_ses13 %*% TFCEoutput$pos_mask)/sum(TFCEoutput$pos_mask>0)
dat_beh_ses13$clustRFT=(FINK_Tv_smoothed_ses13 %*% model2_RFT$pos_mask)/sum(model2_RFT$pos_mask>0)
library(ggplot2)
library(ggbeeswarm)
library(cowplot)
a=ggplot(data=dat_beh_ses13,aes(y=clustCTTFCE,x=as.factor(session), color=as.factor(group)))+
geom_quasirandom(dodge.width=0.5)+
geom_line(aes(group=participant_id), alpha=0.2)+
geom_smooth(aes(group=group), method="lm")+
labs(y="Mean thickness (mm)", x="session", color="group")+
guides(colour = "none")+
ggtitle("Positive cluster\n (TFCE-corrected)")+
ylim(1.1, 1.55)
b=ggplot(data=dat_beh_ses13,aes(y=clustRFT,x=as.factor(session), color=as.factor(group)))+
geom_quasirandom(dodge.width=0.5)+
geom_line(aes(group=participant_id), alpha=0.2)+
geom_smooth(aes(group=group), method="lm")+
labs(y="Mean thickness (mm)", x="session", color="group")+
ggtitle("Positive cluster\n(RFT-corrected)")+
scale_color_discrete(name="Group",labels=c("group 1", "group 2"))+
ylim(1.1, 1.55)
png(filename="traj.png", res=300, width=2500,height=1080)
plots=plot_grid(a,b, nrow=1,rel_widths=c(0.3,0.40))
print(plots)
dev.off()
As an additional validation of these results, these significant clusters were extracted as regions-of-interests and fitted in a linear mixed effects model using another R package— lmerTest (Kuznetsova, Brockhoff, and Christensen 2017).
Linear mixed effect testing the effect of session, group, and session * group interaction on the positive RFT clusters’ average thickness value
lme.RFT=lmer(clustRFT~session+group+session*group+(1|participant_id),data =dat_beh_ses13 )
summary(lme.RFT)
## Linear mixed model fit by REML. t-tests use Satterthwaite's method ['lmerModLmerTest']
## Formula: clustRFT ~ session + group + session * group + (1 | participant_id)
## Data: dat_beh_ses13
##
## REML criterion at convergence: -317.1
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.69862 -0.43221 -0.04002 0.42291 2.57082
##
## Random effects:
## Groups Name Variance Std.Dev.
## participant_id (Intercept) 0.004837 0.06955
## Residual 0.000236 0.01536
## Number of obs: 96, groups: participant_id, 48
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 1.326760 0.010717 54.685962 123.801 < 2e-16 ***
## session -0.003450 0.001580 46.000000 -2.183 0.0342 *
## group -0.006877 0.010717 54.685962 -0.642 0.5237
## session:group 0.007645 0.001580 46.000000 4.837 1.51e-05 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) sessin group
## session -0.295
## group -0.125 0.037
## session:grp 0.037 -0.125 -0.295
Linear mixed effect testing the effect of session, group, and session * group interaction on the positive TFCE clusters’ average thickness value
lme.posTFCE=lmer(clustCTTFCE~session+group+session*group+(1|participant_id),data =dat_beh_ses13 )
summary(lme.posTFCE)
## Linear mixed model fit by REML. t-tests use Satterthwaite's method ['lmerModLmerTest']
## Formula: clustCTTFCE ~ session + group + session * group + (1 | participant_id)
## Data: dat_beh_ses13
##
## REML criterion at convergence: -272.9
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.50112 -0.45415 -0.05631 0.49916 1.71410
##
## Random effects:
## Groups Name Variance Std.Dev.
## participant_id (Intercept) 0.0048047 0.06932
## Residual 0.0005989 0.02447
## Number of obs: 96, groups: participant_id, 48
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 1.134943 0.011549 66.462361 98.275 < 2e-16 ***
## session -0.003589 0.002517 46.000000 -1.426 0.160692
## group -0.009920 0.011549 66.462361 -0.859 0.393452
## session:group 0.010234 0.002517 46.000000 4.065 0.000186 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) sessin group
## session -0.436
## group -0.125 0.054
## session:grp 0.054 -0.125 -0.436
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