Hi Alfonso, 

I have an error for the set up step (see below) for previously concatenated files. They were concatenated in CONN as you previously advised (https://www.nitrc.org/forum/message.php?...). There are 500 files in total but once they were concatenated there are 5 files (100 each). Could you please help?

Here is the error message:
Ready to run Setup pipeline
overwrite existing results (re-compute for all subjects/ROIs)
steps : [1 1 0 1]
local processing (run on this computer)
CONN: RUNNING SETUP STEP
Step 1/7: Checking data completeness
warning: Subject 1 Session 2 functional data has only 5 time-points (scans) defined
warning: Subject 2 Session 2 functional data has only 5 time-points (scans) defined
warning: Subject 3 Session 2 functional data has only 5 time-points (scans) defined
warning: Subject 4 Session 2 functional data has only 5 time-points (scans) defined
spm @ C:\spm12
conn @ C:\conn
SOME ERRORS FOUND!: Please revise the Setup information
ERROR DESCRIPTION:

ERROR: Subject 1 Session 2 first-level covariate realignment mismatched dimensions (500 rows, while functional data has 5 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 1 Session 2 first-level covariate QC_timeseries mismatched dimensions (500 rows, while functional data has 5 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 1 Session 2 first-level covariate scrubbing mismatched dimensions (500 rows, while functional data has 5 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 2 Session 2 first-level covariate realignment mismatched dimensions (500 rows, while functional data has 5 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 2 Session 2 first-level covariate QC_timeseries mismatched dimensions (500 rows, while functional data has 5 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 2 Session 2 first-level covariate scrubbing mismatched dimensions (500 rows, while functional data has 5 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 3 Session 2 first-level covariate realignment mismatched dimensions (500 rows, while functional data has 5 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 3 Session 2 first-level covariate QC_timeseries mismatched dimensions (500 rows, while functional data has 5 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 3 Session 2 first-level covariate scrubbing mismatched dimensions (500 rows, while functional data has 5 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 4 Session 2 first-level covariate realignment mismatched dimensions (500 rows, while functional data has 5 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 4 Session 2 first-level covariate QC_timeseries mismatched dimensions (500 rows, while functional data has 5 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 4 Session 2 first-level covariate scrubbing mismatched dimensions (500 rows, while functional data has 5 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
CONN19.c
SPM12 + DEM FieldMap MEEGtools
Matlab v.2019a
project: CONN19.c
storage: 187.3Gb available

Thanks in advance, 
Best,
Amy