Inter Unix 1. Practice some basic commands, and note the $HOME variable.
Commands and descriptions:
cd : change directories
ls : list directory contents
-a : list all files (include those starting with '.')
-l : long listing (show file type, ownership, size, date)
pwd : show the Present Working Directory
cat : display the contents of a file (usually a short text file)
echo : echo given text to the terminal window
A. In a terminal window, go to the $HOME directory. The 'cd' command
(without any arguments) will do this.
Commands:
- go to the $HOME directory
- display the present working directory
- echo the value of the $HOME variable
- list the basic contents of that directory
cd
pwd
echo $HOME
ls
The output for this will vary.
There is no output from a 'cd' command (except for perhaps a change in
the prompt). The output from 'pwd' should show the path to the user's
home directory (as will the output from 'echo $HOME), while the output
from 'ls' should include AFNI_data6.
B. Compare the simple listing of files with the listing of all files and
the long-format listing. Just for fun, try both options.
ls
ls -a
ls -l
The 'ls' command, as above, should show a handful of files and
directories, including AFNI_data6.
With the -a option, all files (and directories) are shown, including
those starting with a '.' (which includes '.' and '..', the current
and parent directories). There is nothing special about such files,
except that they are named starting with '.'. They are typically
configuration files for various programs (such as .afnirc for AFNI
programs and .sumarc for SUMA programs).
C. Move into the AFNI_data6/afni director and see what is there.
cd AFNI_data6/afni
pwd
ls
There are anatomical, EPI, statistical and mask datasets here, along
with scripts (text files of commands, such as rall_regress) and stimulus
timing files (text files of times in seconds, such as stim_AV1_vis.txt).
D. Look at the contents of some of the text files. Enter one command at a
time and note the result. What follows is meant to provide understanding
of the contents of each file.
cat stim_AV1_vis.txt
cat rall_regress
cat quick.s1.afni_proc
file stim_AV1_vis.txt:
The timing file stim_AV1_vis.txt has 3 rows of real numbers, which are
onset times for stimulus events across 3 runs. The first 60 means the
visual stimulus class (AV1_vis) had its first event 60.0 seconds into
the first run. In the third run, that stimulus was given at the very
beginning of the run, at time 0.
file rall_regress:
The file rall_regress contains a single AFNI command, 3dDeconvolve.
The command is used to model the EPI data via linear regression, where
the model is specified by the user.
From the Unix perspective, there are a few key points to make.
1. This is actually 1 long command. A '\' character (when it is
the very last character on a line) tells the shell that the
current command continues on the following line. So
3dDeconvolve -input ... -bucket rall_fun -jobs 2
is considered one command.
2. As usual, command options start with '-' and are followed by
zero or more parameters. For example, the -num_stimts option
takes one parameter (the number of stimulus timing files to be
specified), and in this case 8 is specified. Note that the
subsequent 8 lines describe those timing files.
Alternatively, the -stim_times option takes 3 paramters (the
stimulus index, the name of the timing file, and the basis
function). But our focus is on the Unix aspect, so we just note
the option and parameter grouping is:
-stim_times 1 stim_AV1_vis.txt 'BLOCK(20,1)'
What that option means is saved for a class on 3dDeconvolve.
See the output from "3dDeconvolve -help" for details.
3. Quotes are used for multiple reasons in this one command.
The quotes around '1D: 0 150 300' have the shell pass that text
as a single parameter, instead of 4. So 3dDeconvolve sees
"-concat" as one parameter, and then "1D: 0 150 300" as the next.
It does not see -concat then 1D: then 0 then 150 then 300.
Quotes are used again this way with the -gltsym option.
Another way to view this is that the quotes hide the spaces from
from the shell, so that they are not processed as parameter
separation characters. Which leads us to the other use of the
quotes here...
The stim_times option takes a basis function as its third
parameter, e.g. 'BLOCK(20,1)'. But the () characters are
special to the shell. So to hide those characters from the
shell and let 3dDeconvolve see them, they are put within quotes.
That way 3dDeconvolve reads BLOCK(20,1) as the basis function.
Similarly, [] are special to the shell (for wildcard matching).
But we want to pass motion.1D[0] to 3dDeconvolve (using the
-stim_file option). And to prevent the shell from trying to use
[0] for wildcard file name matching, it is put in quotes, as in:
-stim_file 3 motion.1D'[0]'
Note that the quotes could go in multiple places, they are used
to hide []. So this would work as well:
-stim_file 3 'motion.1D[0]'
file quick.s1.afni_proc:
Like rall_regress, this file contains a script with just one command.
The afni_proc.py command is used to generate a single subject FMRI
processing script, and in this case, execute it.
This script has line continuation characters '\' as before, as well
as single quotes hiding special charcters from the shell in the option
-regress_basis 'BLOCK(20,1)'.
From a Unix perspective, the additional aspect of this script is the
pound/sharp character '#'. When used in a script, this character says
that the rest of the line is to be ignored. Effectively, the script
does not see anything from '#' to the end of the line.
Such lines are generally used as comment lines, a way to tell/remind
the reader the purpose of the following line or lines in the script.
In this example, the comment describes what the afni_proc.py command
will end up doing (creating and then executing a processing script).
Comment(s):
1. Get in the habit of using 'ls' after any 'cd', i.e. see what is in any
directory that you enter.
2. The 'echo' command is mostly used in processing scripts, to inform the
user of something.
3. The 'cat' command is only useful for short files. For longer files,
'less' is much more useful ('less' will be covered in another tutorial).