Dear Sai Prasanna,
Since you have time series as input, you should use the Functional pipelines, such as Pipeline functional comparison WU/BUD/BUT. In that case, you should arrange the files of each subject in the format 196 (rows) x 111 (columns)
Here you can see how to organize your subjects’ files to use functional pipelines: http://braph.org/tutorials/general/functional-data-format/
The connectivity pipelines are to be used with already connectivity matrices of each subject as input (111×111)
Best,
Anna