the script produced by @RetinoProc

AFNI Message Board
1

Hi AFNI Gurus,
Similar to the situation that “afni_proc.py” saves out a specific script (e.g. “proc.FT”) for step-by-step data analysis, I am wondering if @RetinoProc can save out a specific script that an user can view and modify.

I want to use @RetinoProc, but need to know what exactly it does in each one of its processing steps.

Thank you for your help!

2

Hi, Zhihao-

I don’t think @RetinoProc can be retrofitted with that capability too easily without re-writing the whole thing.

Note that it does have an “echo_edu” option, so that each AFNI program will display on the command line its exact set of options; that could be combined with piping+teeing to an output text file, to see what each command is doing exactly. There is also the “-x” option when running a tcsh command echos all commands to the terminal before they are executed; that way, several variable settings would be apparent.

Of course, this will lack the extremely nice features of afni_proc.py-produced scripts, such as having huge numbers of comments and clarity in variables, etc… but would that suffice (there are some comments that get dropped out from the script, too)?

–pt

3

Thank you Paul, your response is very helpful!

4

Note that the -x option is effectively handled with -echo. If you provide that, the script will go into full echo mode.

  • rick