I’ve written about shell scripting before (see here and here). Scripting is necessary for efficient neuroimage processing. At the very least, it can provide a way to keep track of how you did something. While there are a number of ways to script – Bash, Perl, or Python, for example – I’ve done most of my scripting in Bash so far. I’m currently branching out to Perl and Python but I haven’t re-written any of my Bash scripts in Perl or Python yet.
Here is a great, in-depth introduction to Bash scripting. That link takes you to a directory where you can select the format of the guide: HTML, PDF, or a few others. I did not create that guide or have any role in its creation. It was created by people affiliated with The Linux Documentation Project.
The guide might be more in-depth than you might need for your neuroimaging scripting needs but it is a great resource if you want to brush up on your scripting. Then, if you branch out to a language like Perl, it will likely be easier to learn.