question regarding the -censor and -concat option in 3dDeconvolve

Hello,

I have a question regarding the usage of -censor and -concat options in 3dDeconvolve.
Let us say I have 3 runs of data that were concatenated after preprocessing, each with 100 TRs, I understand I can do "-concat '1D: 0 100 200'" to combine them.
My question is, how does this option interact with -the censor? Let us say for each run, I need to censor 10TRs because of high noise. Do I adjust the -concat option to account for the censored TRs: "-concat '1D:0, 90, 180, 270'"?

Thanks,
Kai

Hi Kai,

The -concat option applies to the input, so it has no adjustment for censoring. Just use the '1D: 0 100 200' format.

Consider running your data through afni_proc.py for comparison. Even if you don't end up using it, it is nice for at least verification, error finding, suggested options, QC or additional processing steps.

I guess it would not demonstrate the -concat option, because it never uses it, keeping runs separate through input to 3dDeconvolve.

  • rick