I am relatively new to working with fMRI data and have a basic question regarding usage of connectivity toolboxes.
I have 2 groups of sample data: Patient and Control; both processed using the same steps; and to analyse the resultant data I have decided to compare the output from two different toolboxes.
I am comparing resultant analysis data from two toolboxes; one of which is CONN and the other being DPARSF.
I have used the 1st level bivariate correlation ROI-to-ROI analysis in CONN folllowed by 2nd level FDR corrected two sided p value computation to compare functional connectivity patterns between control and group.
In DPARSF, I have used only the Functional connectivity option to obtain the correlation coefficients for each subject. Following which I have used Matlab to compute Mean, Standard deviation for the two groups and subsequent two sided T test to compute the p value.

According to my knowledge, both the analysis methods appear to be similar, but the results from both are largely different; with DPARSF showing mainly only left ROI to right corresponding ROI higher functional connectivity.
Any clarification and assistance in the following matter would be greatly appreciated in order to understand this better.