1d_tool.py show different censored TR counts

AFNI Message Board
1

Hi all,

    I am checking the censored TR information from the file func_decon.xmat.1D generated by 3dDeconvolve.
    I have six runs for one subject. Each run has 586 TRs. I concatenated the time series from the six runs and then did GLM analysis with 3dDeconvolve.

    I ran the command below to check censored TRs.
   1d_tool.py -infile func_decon.xmat.1D -show_censor_count -show_trs_censored comma

    The command showed the message as below.
    0,586,1172,1758,2344,2930
    total number of censored TRs = 2925

    The -show_tr_censored showed that the first epoch from each run was censored. But the -show_censor_count returned a different number.
    My question is why the number of censored TRs are different from these options.

    Thanks!

Nan

2

Hi Nan,

Actually, the -show_censor_count is a very simple form
of it that does not evaluate the header of the X-matrix.
It was meant to be used with functions to create censor
or evaluate (binary) censor files).

Maybe I will add explicit versions of that option to be
clear where the censor count is coming from, e.g.
-show_censor_count_xmat
-show_censor_count_simple

Also, I will change the existing option to try to guess,
but will change the examples to use explicit forms.

Thanks for the comment,

  • rick
3

Hi Rick,

    Thank you very much for your comment.
    So, to check the information in the xmat.1D file, -show_trs_censored will return the correct censored TRs.
  • Nan
4

Yes, -show_trs_censored will show the correct (0-based) list.
Until I add a -show_censor_count_xmat option, say, you can
print a space separated list and pipe it through wc, say:

1d_tool.py -show_trs_censored space -infile X.xmat.1D | wc -w

  • rick