Oh, and from spacing out the command, I think I see the issue: "-ortvec .." takes 2 parameters after it, not 1. From the 3dDeconvolve help:
-ortvec fff lll This option lets you input a rectangular array
of 1 or more baseline vectors from file 'fff',
which will get the label 'lll'. Functionally,
it is the same as using '-stim_file' on each
column of 'fff' separately (plus '-stim_base').
This method is just a faster and simpler way to
include a lot of baseline regressors in one step.
-->>**N.B.: This file is NOT included in the '-num_stimts'
count that you provide.
*N.B.: These regression matrix columns appear LAST
in the matrix, after everything else.
*N.B.: You can use column '[..]' and/or row '{..}'
selectors on the filename 'fff' to pick out
a subset of the numbers in that file.
*N.B.: The q-th column of 'fff' will get a label
like 'lll[q]' in the 3dDeconvolve results.
*N.B.: This option is known as the 'Inati Option'.
*N.B.: Unlike the original 'Inati' (who is unique), it
is allowed to have more than one '-ortvec' option.
*N.B.: Program 1dBport is one place to generate a file
for use with '-ortvec'; 1deval might be another.
So, if you changed:
-ortvec /mnt/analysis/sub-${subject}/func/confound_test.1D \
... to:
-ortvec /mnt/analysis/sub-${subject}/func/confound_test.1D ORT_LABEL \
... does that sort that error message out?
Note some of the other points in the other reply might still apply and be useful to address, too.
--pt