INTRODUCTION

  • 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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