First off, I am new to conducting connectivity analyses so I apologize if my wording is a little unclear. I'm currently looking to conduct a functional connectivity analysis to examine connectivity between the amygdala and the prefrontal cortex during an emotion regulation task. I created two seed ROIs in the right dmPFC and in the right dorsal amygdala. However, I am having issues designing a template (for use in the FEAT GLM) to examine connectivity due to a jittered fixation gap in between each trial. In some instances, the timing of this fixation (from onset until end) does not line up with the TR (2000 ms) for the task which throws off the alignment of the signal/volume with the appropriate/relevant condition. Is there a way to account for this difference in my template (in the GLM) so that signal lines up with condition appropriately? If so, how would I go about this?
If any further clarification is needed, please let me know.