Hi Jana,
The quick but lousy answer first... Use ctrl-s to suspend the terminal
process, which will do nothing until you tell it to continue, usually
via ctrl-q.
---
The better answer... Never run commands to process your data without
storing the output in a file. It is quite common to need to see the
output later (such as this case), and quite difficult to read all of it
as it flies by on the screen. To do this, pipe stdout and stderr through
the 'tee' program, which sends output both back to the terminal window
and to the text file that you specify.
For example, suppose my 3dDeconvolve command is in the file run.3dDecon
(and let us assume that any shell syntax is in tcsh, not bash). Then I
would execute the script via:
tcsh -x run.3dDecon |& tee output.run.3dDecon
The '-x' option to 3dDeconvolve will echo the commands to the terminal
before actually executing them (so your actual 3dDeconvolve command will
be saved in the output, too).
The '|&' symbol pair means to pipe both stdout and stderr. Normally one
just plays with stdout via '|'. But often error/warning messages are
sent to the stderr file stream, and they are most important to catch.
So stdout and stderr are both piped to the 'tee' program, which simply
duplicates the input, sending it both back to the screen (so the user
gets to see it) and to whatever file the user specified (output.run.3dDecon
in this case).
So after the command is done, 'output.run.3dDecon' will contain all of the
commands, plus their output. It is just a text file, so it can be viewed
with an editor or maybe with the 'less' (or more) program.
- rick
