multiple files for -ortvec option

AFNI Message Board
1

AFNI Experts,

I am carrying out “denoising” (using ICA AROMA) separately on each run of the functional dataset. This denoising produces several components (timeseires) which represent noise for that particular run. I want to include these timeseires as confounds in my 3dDeconvolve model. However, since each run may have different number of confound timeseries, I cannot put them in one single text file with the -ortvec option.

My question is: I there a way to provide multiple confound text files (one for each run) with the -ortvec (or any other) option?

Thank you,
Chirag

2

Hi Chirag,

That the number of components varies per run does not really matter. You would not want to simply concatenate them, since that would force the terms that happen to go in the same column to have the same beta weight. They should probably be zero-padded across all runs, and passed using multiple -ortvec options to 3dDeconvolve.

One way to do this would be to loop over the runs using “1d_tool.py -pad_into_many_runs”. See Examples 4a and 4b from the 1d_tool.py -help output.

Does that seem reasonable?

  • rick
3

That makes sense.

Thank you, Rick