I am trying to denoise a single subject's data but I am running into errors.

The subject was scanned for 5 separate sessions, and in each session, multiple functional scans were taken (either 3 or 4 scans per session). I loaded these multiple functional scans for each session in Setup.Functional and I was able to preprocess this data through the default pipeline. The realignment parameters generated by this pipeline were written to a single file for each session, where the number of rows corresponds to the number of total frames across all 3 or 4 scans (e.g. for session 1 there are 3 scans at 124 frames each, so there are 372 rows), and the columns correspond to the 6 realignment parameters. 

When I try to move on to the Denoising step , I get the following errors:

"ERROR: Subject 1 Session 1 first-level covariate realignment mismatched dimensions (372 rows, while functional data has 3 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session).
ERROR: Subject 1 Session 1 first-level covariate QC_timeseries mismatched dimensions (372 rows, while functional data has 3 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session).
ERROR: Subject 1 Session 1 first-level covariate scrubbing mismatched dimensions (372 rows, while functional data has 3 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)."

Can you please advise? How should I load data with multiple acquisitions per session?
All the best,
Emily