Hi,
Having run an analysis through afni_proc.py, with the -remove_preproc_files tag, I wanted to do a re-analysis of the single-subject data with a new regression model. However, I now realise that the only timeseries data that is saved is the all_runs file. Obviously I could re-segment the all_runs data, but that's non-trivial given potential TR removal. The other option is to hand the all_runs to 3dDeconvolve, but then, so far as I can tell, I'd have to create my own polynomial regressors (and restructure my stimulus timing files), because there doesn't seem to be a way to tell 3dDeconvolve what the run length is--this is extrapolated from the run files it's handed.
My question is whether, for the future, am I missing an easy solution? Is there a way to tell 3dDeconvolve what the run lengths are, or, alternatively, is there a way (other than doing the cleanup manually) to get afni_proc.py to do a cleanup that leaves the final single-run skull-stripped, aligned, blurred, scaled files?