Dear experts,

I have been using these wonderful scripts happily. Thanks a lot for all the hard work.

I have a question regarding analyzing seed-based FC with motion outliers. Methods have been proposed to detect time-points with excessive motion (with both SPM and FSL), and marked such time-points as motion outliers. The way to incorporate these motion outliers into FC analysis is to use them as regressors of non-interest (i.e. confound EVs with 1 at motion time-point and 0 for the rest of the time series; if there are 4 motion outliers, there will be 4 columns in the design matrix in addition to the time-course of interests).

I was wondering if there is a easier way to incorporate the motion outliers into the script, especially in 6_sunglesubjectRSFC? Should I generate a ".mat" contrast file instead of the "ideal_file"? Could I still be using 3dfim+ or should I switch to 3dDeconvolve? It will be more complicated if I use FEAT in FSL to accomplish this task. Since I don't have a lot of experience in AFNI, I would really appreciate any suggestions!

Thank you so much for your help!

Best,
Monica