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