Smoothing in functional connectivity analysis

Dear experts,

I would like to run a functional connectivity ROI-to-ROI analysis with AFNI (first level analysis).

First, I would extract the mean value of the seed-ROI in each subject.
Then, I would calculate FC between these seed-ROI values and the 250 EPI volumes masked by the target-ROI.

Should I use the 250 EPI volumes that are masked by the target-ROI with smoothing?
Or is it better to do the correlation with these volumes without smoothing?

And finally, to be sure, I shouldn’t apply smoothing before calculating the mean values of the seed-ROI, right?

Thank you in advance!
Best regards,

Hi, Marina-

For an ROI-based analysis, I don’t think I would smooth- it would only smear data across ROI boundaries.

Do you want an functional connectivity matrix output? Have you looked at 3dNetCorr, whose inputs are:

  • a map of ROIs
  • an EPI (or other 4D) dataset
    and whose output would be a functional connectivity matrix?