Hi Teodora,
I did not realize that you were running 3dDeconvovle with the '-stim_nptr' option.
In this case with '-stim_nptr k n', minlag and maxlag should be set in multiples of TR/n. Since your TR = 10 seconds, and n = 10, you should set something like this:
-stim_minlag k x -stim_maxlag k y
With x and y in the above setup you want a delay of x seconds and a duration of (y-x) seconds.
For example, if you want no delay and a duration of 10 seconds, it goes like:
3dDeconvolve -input allruns+orig -mask mask+orig \
-censor censoraug21.1D -concat concat.1D \
-polort 1 -nfirst 0 -num_stimts 5 \
-stim_file 1 'idealaug21.1D[0]' -stim_label 1 stim1 \
-stim_file 2 'idealaug21.1D[1]' -stim_label 2 stim2 \
-stim_file 3 'idealaug21.1D[2]' -stim_label 3 stim3 \
-stim_file 4 'idealaug21.1D[3]' -stim_label 4 stim4 \
-stim_file 5 'idealaug21.1D[4]' -stim_label 5 stim5 \
-stim_minlag 1 0 -stim_maxlag 1 10 \
-stim_minlag 2 0 -stim_maxlag 2 10\
-stim_minlag 3 0 -stim_maxlag 3 10\
-stim_minlag 4 0 -stim_maxlag 4 10\
-stim_minlag 5 0 -stim_maxlag 5 10\
-stim_nptr 1 10 \
-stim_nptr 2 10 \
-stim_nptr 3 10 \
-stim_nptr 4 10 \
-stim_nptr 5 10 \
-num_glt 3 \
-glt 1 c1vc2.glt -glt_label 1 1v2 \
-glt 1 c3vc4.glt -glt_label 2 3v4 \
-glt 1 c1vc5.glt -glt_label 3 1v5 \
-fout -tout -bucket test_Decon
This will probably make the non-invertibility problem gone.
Gang
