Scripting allows you to:
  • encapsulate common lists of commands in a file
  • automate/batch processes
  • make new flexible and configurable tools
  • understand other people's scripts/tools

"I wish you'd forced me to learn scripting 3 years ago!" - Dr Parry
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  • Common scripting languages include:
    • Shell scripts - sh, bash, csh, tcsh
    • Other scripting languages - TCL, Perl, Python
  • We will look at sh as it is simple, portable, powerful and just like the command line

  • Repeated tasks can be done much faster
  • Scripts act as exact records of what commands were run
  • Scripts avoid small inconsistent errors in processing

  • Knowing scripting helps with any computer tasks, not just analysis
  • Examples of useful tasks:
    • Automatically call BET with several different options
    • Measure image stats/volumes/PEs for a set of subjects with a single command
    • Extract timing info from stimulus / behavioural data files
    • Renaming sets of files
    • Changing the format of a set of files (e.g. png to tiff)
  • In these slides there are several accompanying practicals that are extremely useful and can be found by following the links marked with e at the bottom right (to the left of the navigation arrows)
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    • In order to help scripting (and your own sanity) it is a good idea to give files and directories systematic names.
      • For example:
      • Con0001 , Con0002, Con0003 , ... , Con0020, Pat0001, Pat0002, ... , Pat0020

    • Padding the numbers with zeros like this (Con0020 instead of Con20) helps keep the ordering consistent for scripting

    • In the UK (and other countries) you must not have identifiers (names, dates of birth, even initials) in the filenames

    • Consider renaming your original images to more meaningful (and consistent) names

    • Keep track of your disk usage and delete any analyses that were incorrect (many people have res.feat, res+.feat, res++.feat, res+++.feat , etc. which is confusing and a waste of space)
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    • A bourne shell (sh) script is a list of lines in a file that are executed in the bourne shell (a forerunner of bash); simplest is just commands that could be run at the prompt.

    • The first line in a sh script MUST be   #!/bin/sh

    • Things to remember:
      • always make sure it has executable status
        chmod a+x filename
      • script runs in the current directory (pwd)
      • may not inherit the same environment - esp. if used by others

    • Example:
      bet im1 im1_brain -m
      mv im1_brain_mask.nii.gz mask1.nii.gz

    • A script can be stopped at any point by using return: e.g. return 0
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    • Before learning things systematically, here is a fairly simple script which is very powerful and useful for modifying for many different tasks.
        for filename in *.nii.gz ; do
          fname=`$FSLDIR/bin/remove_ext ${filename}`
          fslmaths ${fname} -s 2 ${fname}_smooth2
          mv ${fname}.nii.gz ${fname}_smooth0.nii.gz

    • What this does:
        For each image (*.nii.gz) it smooths it to make a new one of the same name but ending in _smooth2 and also renames the unsmoothed image to end with _smooth0
    • How this works:
      • The variable filename is used in a for loop to go through each name matching *.nii.gz
      • The variable fname is set to the filename with the ending (e.g. .nii.gz) removed.
          Don't worry about how this works for now - the details will be explained later.
      • ${filename} and ${fname} are used to get the values (contents) of the variables
      • fslmaths is used to do the smoothing.
      • mv is used to do the renaming (notice that .nii.gz is needed here, but not for the fsl tools, as they work with or without the .nii.gz endings).
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    Here are some basic, but useful, tips for writing scripts
    • Put in comments (to jog your memory when you write your paper months/years later)

    • Put in some echo output commands so that you get some feedback on what your script is doing as it runs

    • If your script starts doing something bad (or nothing at all) then use control-C to stop it

    • If your script makes new files, changes files or deletes files then start with a version which uses echo in front of the important commands. When you run this version it will just display the commands to the screen so that you can examine them carefully and make sure they are right. Once you are happy with them then remove the echo from in front of these commands and run this version.

    • It doesn't hurt to make a backup of key files before running a script, just in case.
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    • We will now look systematically at the following shell and scripting concepts:
      • Wildmasks
      • Echo (printing to the screen/file)
      • Variables
      • Braces
      • Command Line Arguments
      • Single Quotes and Backslash
      • Double Quotes
      • Backquotes
      • Pipes
      • File Redirection
    • Following this some useful utilities and programming constructs (like the for loop) will be covered.
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    Can use wildmasks for matching patterns in filenames; expand into a list of all filename matches. E.g.:
          * matches any string
          ? matches any one character
          [abgj] matches any one character in this range/list
    $ ls
      sub1_t1.nii.gz sub1_t2.nii.gz sub2_t1.nii.gz sub2_t2.nii.gz sub3_pd.nii.gz
    $ ls sub*
      sub1_t1.nii.gz sub1_t2.nii.gz sub2_t1.nii.gz sub2_t2.nii.gz sub3_pd.nii.gz
    $ ls sub1*
      sub1_t1.nii.gz sub1_t2.nii.gz
    $ ls sub*t1*
      sub1_t1.nii.gz sub2_t1.nii.gz
    $ ls sub[13]*
      sub1_t1.nii.gz sub1_t2.nii.gz sub3_pd.nii.gz
    $ ls sub?_t2.nii.gz
      sub1_t2.nii.gz sub2_t2.nii.gz
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    • echo prints the rest of the line to the screen (standard output).
    • This is useful for providing output or updates in a script.

    • Wildmasks (for filenames) and variables (values) are substituted in the argument before echo prints them.

    • Examples:
      $ echo Hello All!
        Hello All!
      $ echo sub*t1*
        sub1_t1.nii.gz sub2_t1.nii.gz
      $ echo j*k
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    • Like most programming languages, the shell allows items to be stored in variables.
    • All shell variables store strings.

    • A variable is set using:
    • The variable name should start with a letter but can contain numbers and underscores
    • The value of a variable can be returned/used by adding a prefix $

    • Examples:
      $ var1=im1.nii.gz
      $ echo $var1
      $ echo var1
      $ ls $var1
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    • Any name that starts with a letter can be used as a variable name.
    • For instance: v, v1, v1_1, v_filename_4

    • To add a string immediately after a variable name can be confusing.
    • The situation is solved by putting the variable name inside braces.

    • Examples:
      $ v=im1
      $ echo $v_new

      $ echo ${v}_new

    • NB: all unused variables are blank by default (generate no error)
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    • Inside a script the variables $1 $2 $3 etc. store the value of the command line arguments.

    • e.g. if a script called reg_vol is executed as:
      $ reg_vol im1 3 abc
      then $1 = im1, $2 = 3, $3 = abc

    • Other special variables are:
      • $0 = name of the script (often including the path)
      • $# = number of command line arguments given
      • $@ = all the command line arguments
                (i.e. $1 $2 $3 ...)
      • $$ = process ID number (unique to this process)
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    • The shell substitutes variable names and wildmasks before executing the command - sometimes this is undesirable.
    • To avoid substitutions either
      1. prefix the special character (wildmask or $ sign) with a backslash: \
      2. put the desired string in single quotes: '

    • Examples:
      $ var1=im1.nii.gz
      $ echo $var1
      $ echo \$var1
      $ echo '$var1'
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    • To group several strings together as one argument it is necessary to use double quotes: "

    • For example:
      $ v=Hello World
      $ echo $v
      $ v="Hello World"
      $ echo $v
        Hello World

    • NB: Variable substitutions are done inside double quotes but wildmasks are not expanded:
        e.g.   echo "*"   just prints a *
        but   echo "$v"   is the same as   echo $v
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    • The (text) result of any command can be captured using backquotes: `

    • This is very useful for setting variables.

    • Examples:
      $ v=`ls sub[13]*`
      $ echo $v
        sub1_t1.nii.gz sub1_t2.nii.gz sub3_pd.nii.gz
      $ echo `fslval sub1_t1 pixdim2`

    • NB: the result is always treated as a single string, even if it contains spaces
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    • One of the most powerful features of the shell is the ability to chain commands together, each taking its input from the previous command's output.

    • This is done using the pipe symbol: |

    • Examples (using the wordcount utility):
      $ cat .bashrc | wc
        7   83   534
      $ echo "Hello World" | wc
        1   2   12

    • Technically this redirects standard output of one command to be the standard input of another.
    • Error messages that are printed to standard error are not redirected with the pipe.
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    • Command input can be taken from a file with: <

    • Command output can be redirected to a file with: >

    • Command output can be appended to a file with: >>

    • Examples:
      $ echo "smoothing=10mm" > settings.txt
      $ echo "No lowpass" >> settings.txt
      $ cat settings.txt
      No lowpass
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    • Some common and nearly essential utilities/programs for shell scripting are:

        Basic Advanced
      • test (or [ ] )
      • if
      • for
      • while
      • grep (search)
      • bc (calculator)
      • sed (find and replace)
      • awk (select columns)

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    • The command test allows two strings or two integers to be compared.
    • A shorthand version uses [ and ] around the arguments.
      WARNING: be very careful to put the spaces in correctly!
    • The syntax is very different for comparing numbers or strings (see help test for the syntax options).
    • test can also be used to check the status of files (whether they exist, are writable, etc.)
      test $a = my         string equality
      [ $a = my ] as above
      [ $a -eq 2 ] tests numerical equality
      [ 11 -gt 2 ] compares numbers (greater than)
      [ 11 > 2 ] does NOT do numerical comparison
      [ -e im1.nii.gnii.gz ] tests if file exists
      Note: for non-integer numerical comparisons, see bc
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    • The if command works like in most programming languages.

    • It usually uses the result of the test command and its syntax is:
      if [ EXPRESSION ] ; then
      COMMANDS ;
      COMMANDS2 ;
    • The else part is optional.

    • For example:
       if [ $a = 2 ] ; then
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    • The for command executes a set of commands for every word in a list of words.
    • Syntax:
      for VARIABLE in LIST OF VALUES ; do
          COMMANDS ;

    • The commands are executed once for each entry in the words list.
    • Each time the variable specified is equal to the current word.

    • Example:
      for filename in im1 im2 im3 ; do
          bet $filename ${filename}_brain ;
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    • The bc command acts like a calculator.

    • It is usually used to set variables, using echo, pipe and backquotes.
    • Use the -l option to get accurate floating-point arithmetic.

    • Example:
      $ a=2;
      $ a=`echo "3 * $a + 1" | bc -l`;
      $ echo $a

    • Note: the double quotes stop the * being used as a wildmask for filenames.
    • Numerical comparisons of non-integers can be done with bc where 0 is returned for false and 1 for true.
        e.g.   echo "-1.2 < 0.5" | bc gives 1
        e.g.   echo "-1.2 > 0.5" | bc gives 0
      So in an if statement do something like:
        if [ `echo "$a < $b" | bc -l` = 1 ] ; then ...
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    • The while command executes a set of commands as long as the condition is true.
    • Syntax:
      while CONDITION ; do
          COMMANDS ;

    • The condition is usually a test statement.

    • Example:
      while [ $a -lt 4 ] ; do
          bet im$a brain$a ;
          a=`echo $a + 1 | bc` ;
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    • The grep command finds patterns in strings.

    • It is usually used to extract lines from a file that contain a given word or phrase.

    • This is a very powerful tool when used together with pipes to filter outputs.

    • Example:
      Find the value of pixdim1 from the fslhd output
      fslhd im1 | grep pixdim1
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    • The awk command is a very general pattern matching facility.
    • One simple but useful capability is to pick out columns of text.
    • This is particularly handy for manipulating tabular information such as in stimulus files.

    • Syntax for selecting column N is:
        awk '{print $N}'

    • Note that the exact syntax (quotes and braces) must be used.
    • Example:
      $ v="im*.nii.gz"
      $ echo $v
        im1.nii.gz im2.nii.gz im3.nii.gz
      $ echo $v | awk '{print $2}'
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    • The sed command performs string substitutions.
    • It is usually used to add, remove or change parts of a string.
    • This is often invaluable for modifying variables.

    • Syntax for changing STRING1 to STRING2 is:
        sed s/STRING1/STRING2/g

    • Example:
      $ v="im*.nii.gz"
      $ v=`echo $v | sed s/im/Subject/g`
      $ echo $v
        Subject1.nii.gz Subject2.nii.gz Subject3.nii.gz

    • Warning: The characters . * [ ] / have special meaning in the first string unless preceded by a backslash
    • Tip: Any character can be used instead of /
      e.g.   sed s@STRING1@STRING2@g
      which can be very handy when dealing with directories/files
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    • Like other languages, functions can be defined in shell scripts.
    • Useful for splitting up scripts into understandable, reusable pieces.
    • Functions can be called like independent scripts.

    • Syntax for creating a function is:
        function NAME { COMMANDS ; }
      or the short form:
        NAME () { COMMANDS ; }

    • Example:
      $ function hi { echo "Hi! $1" ; }
      $ hi
      $ hi There
        Hi! There
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    • Regular expressions are a form of pattern matching syntax which many commands use. (e.g. grep, sed)
    • They are very flexible and not quickly learnt.
    • Some basic forms are easy to learn and very useful.
    • Not the same as shell wildmasks, although some are similar.
    • Special characters used in regular expressions include:
      . matches any one character
      * matches zero or more of the last character
      .* matches any string
      [ ] matches any character in the range
      ^ represents the start of the line
      $ represents the end of the line
      [^ ]   matches any character not in the range
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    • Examples:
      $ echo "Hello world" | sed 's/w.*/X/g'
        Hello X
      $ echo "Hello world" | sed 's/w*/X/g'
        XHXeXlXlXoX XXoXrXlXdX
      $ echo "Hello world" | sed 's/^.* /X/g'
      $ echo "Hello world" | sed 's/.$/X/g'
        Hello worlX
      $ echo "Hello world" | sed 's/[wo]/X/g'
        HellX XXrld
      $ echo "Hello world" | sed 's/[^wo]/X/g'
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    • There are many fsl command line utilities, but there are also specific utilities to assist with scripting:
      1. remove_ext
          this removes only image specific extensions: .nii.gz .nii .hdr .img .hdr.gz .img.gz
          e.g. remove_ext /Volumes/MJ/img1.nii.gz gives /Volumes/MJ/img1
      2. imtest
          this returns the character 1 if the specified file exists and is an image, or 0 otherwise
          e.g. imtest ../img1 gives 1 if ../img1.nii.gz exists (or if ../img1.hdr exists, etc.)
      3. imglob
          this expands into a list of full filenames for images only
          e.g. imglob * lists only the images out of all matches for *
      4. imcp, immv, imrm, imln
          these do cp, mv, rm and ln for images, without needing to specify the extensions (useful when dealing with Analyze or nifti files without needing to know which)
          e.g. imcp im1 im1_orig would be the same as cp im1.nii.gz im1_orig.nii.gz for nifti files, but would do cp im1.hdr im1_orig.hdr and cp im1.img im1_orig.img for Analyze files
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    • There are many other commands which are useful. For example:
      • basename
          removes all leading directory info and specified extensions
          e.g. basename /tmp/epi.nii.gz .nii.gz   gives   epi
      • dirname
          just returns the directory path to the specified file
          e.g. dirname /tmp/epi.nii.gz   gives   /tmp
      • sort
          sorts files (by line) according to alphabetic or numerical order
      • which
          reports where an executable file can be found
          e.g. which flirt   gives   /usr/local/fsl/bin/flirt
      • head
          prints the first n lines of a file
      • tail
          prints the last n lines of a file
      • touch
          creates an empty file
      • paste
          merges files together (horizontally)

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    • For more image analysis command line tools see:

    • To get details about a specific command:
      • run man or help on that command

    • To learn more about general commands and scripting try:
      • searching the web
      • looking at other scripts (e.g. in $FSLDIR/bin)
          Note: check if they are scripts by running file on them
      • apropos searches for any commands with matching keywords in their description
          e.g. apropos merge shows all commands that have something to do with merging
      • books on unix, shell and scripting (though many of them are very technical)
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