The -censor option looks for a file that is just a list of time indexes, with no run indexes allowed. It is not that similar to the -CENSORTR option.

However, you can put the -CENSORTR values into a file, then call that out onto the command line, as in

file.censor contains these lines:
2:19
2:80
4:90

and then the command to use would look something like this:

3dDeconvolve -CENSORTR `cat file.censor` ...

Note the use of the backward quote -- the string inside those quotes is executed as a command, then the output that would normally go to the terminal is captured and put on the command line there. So this would be exactly the same as

3dDeconvolve -CENSORTR 2:19 2:80 4:90 ...

and in fact 3dDeconvolve itself would never see the `cat file.censor` construction, since that would be replaced before 3dDeconvolve is even started up.

Note that line breaks in the output of the `cat file.censor` command are replaced by blanks on the re-configured 3dDeconvolve command line, which is just what you want.