afni_proc.py cleanup and single-run files

AFNI Message Board
1

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?

2

Hi Henry,

Use the -concat option to 3dDeconvolve to specify the run lengths. Note that that you can also use afni_proc.py to generate a modified 3dDeconvolve command, using -write_3dD_script and -write_3dD_prefix. But you would still have to modify -input and -concat.

  • rick
3

Thanks!

Before I spend a few hours struggling over writing this, is there an obvious place to get the output that 3dDeconvolve would need for concat? The 1D_tool.py seems to have a number of options to get the number of TRs per run (as is given by the ss_review) or to turn global TR indices to run indices, but not the reverse.

4

The concatenated dataset was created from some input datasets. How long were those runs? 1d_tool.py is probably not useful here. What are the commands that you ran to create the concatenated dataset?

Once you recall the run lengths, the concat file just as time index offsets, per run. If there are 4 runs of length 150, for example, the concat file might look like:

concat.txt:
0 150 300 450

Then it could be specified as:

-concat concat.txt

Or it could be specified directly on the command line, as:

-concat ‘1D: 0 150 300 450’

  • rick
5

Sorry, my mistake, I was fro some reason assuming that the all_runs would be without the censored TRs, but of course they aren’t which is why we have the censored_$subj_combined file.