Dear Aishvarya

The beta/T stats represent the results from a two-sample t-test comparing cases>controls, so the signs of the beta/T values will be positive if connectivity is higher in cases compared to controls and negative otherwise (the stats are two-sided / two-tailed so the p-values will not change when evaluating controls>cases but the sign of the beta/T statistics will of course flip). The color of the lines, on the other hand, simply represents the sign of the connectivity on average in both cases and controls, so that will not change when testing cases>controls vs. controls>cases (in your case, for example, FP and Putamen show positive connectivity on average, with higher connectivity in controls compared to cases; in the example GUI shown in your attachment you may switch your contrast from 'Difference cases > controls' to 'Any effects (F-test)' if you want to see a bar display of the connectivity within cases and controls separately)

Hope this helps
Alfonso

Dear Alfonso,

Thank you so much! Doubts cleared :))

I should also mention that your name is the one which I see in most of the replies. Thanks from all of us for being there and helping us out. 

Regards,

Aishvarya