Connectivity matrix for task data

Dear CONN experts,

I have a question regarding the calculation of connecitivity matrices in CONN. I am analysing task data with two conditions: during one scanning session, participants experience periods of a task and rest. I understand that I can find the connectivity matrices for each participant and each condition in the results/firstlevel folder.

Now my question: how are these connectivity matrices calculated for the different conditions? For example, how is the time of task onset determined - is the HRF taken into consideration for this? Are the 1st level covariates taken into consideration when calculating the matrices? For example, is the correlation matrix calculated using the BOLD signal with motion signals regressed out? 

I apologise if this is a very basic question, however I was looking through the documentation and forum and unfortunately I could not find an answer.

Best
Judi