A Great Resource for Advanced Bash Scripting

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.

About Jared Tanner

I have a PhD in Clinical and Health Psychology with an emphasis in neuropsychology at the University of Florida. I previously studied at Brigham Young University. I am currently a Research Assistant Professor at the University of Florida. I spend the bulk of my research time dealing with structural magnetic resonance images of the brain. My specialty is with traditional structural MR images, such as T1-weighted and T2-weighted images, as well as diffusion weighted images. I also look at the cognitive and behavioral functioning of individuals with PD and older adults undergoing orthopedic surgery. Funding for the images came from NINDS K23NS060660 (awarded to Catherine Price, University of Florida). Brain images may not be used without my written permission (grant and software requirements).