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

Hi Alfonso,
could you please help (see below)?
Thanks,
Best,
Amy

Hi Amy,

Sorry about that, it seems that CONN was not interpreting correctly the number of acquisitions (500) from your 5 files, could you please use the attached patch and try again? (this patch is for release 19c, to install it simply copy the file to your conn distribution folder overwriting the file with the same name there). After installing the file please run the following commands to have CONN re-interpret correctly the number of acquisitions (alternatively, you may also simply re-import the functional data from the GUI):

   files = conn_module('get','functionals'); 
   conn_module('set','functionals', files);

Let me know if you still run into any issues
Alfonso
Originally posted by Amy Bouchard:

Dear Alfonso,

There seems to be a problem with this patch. I applied it and preprocessed my data again and received the error message that I wrote to you in my recent post: https://www.nitrc.org/forum/reply.php?msg_id=31269&group_id=279

After replacing the patch with the file that comes with CONN 19c, I have this error now:

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)
ERROR: Subject 13 Session 2 first-level covariate scrubbing mismatched dimensions (600 rows, while functional data has 500 scans; the number of rows of a first-level covariate should equal the number of scans for this subject/session)
ERROR: Subject 13 Session 5 first-level covariate scrubbing mismatched dimensions (600 rows, while functional data has 500 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: 4169.8Gb available
spm @ C:\spm12
conn @ C:\conn

Thanks for your help,
Amy