Hello,

I am conducting a resting-state analysis on a longitudinal dataset that includes two structural and two functional runs for each participant. I have completed the preprocessing steps, but I noticed that the number of output files generated for the first functional run and the second functional run differ from each other.

In the second functional run, I assume that some preprocessing steps were not performed correctly. For example, the functional centralization and segmentation step seems to be missing, as I do not have the centering.mat and c1,c2, and c3 files. I am concerned about whether any preprocessing steps are dependent on each other when running the pipeline together for multiple sessions.

What could be the reason for this? Is it acceptable to rerun the entire preprocessing pipeline just for session 2 to ensure all steps are correctly applied or should I preprocess them together? 

I would appreciate any guidance and recommendations on how to resolve this issue. Thank you!