These instructions use FA images to create an FA template using the software package ANTs (http://stnava.github.io/ANTs/); the process should work well with other image modalities. First we can use FLIRT to register a group of 4 brains (semi-randomly chosen by looking … Continue reading
With neuroimaging analyses we deal with a lot of text files. These are often the result of program or scripts running on the MRI data; they can be statistics, volumes, error logs, or any number of other outputs. Let’s say … Continue reading
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 … Continue reading
I’ve written about Bash scripting previously, as it applies to neuroimaging. Scripting is extremely useful; it can save hours worth of work. But what if you want to do something that is repetitive but do not really need to create … Continue reading
You can skip this first paragraph if you do not want to read a personal aside. One useful thing about becoming familiar with the command line interface (Terminal in OS X) is that a little scripting can save you days … Continue reading
Understanding the bash environment and simple bash scripting can really speed up your neuroimaging work. While I am not an expert in scripting, I have learned a few tricks that can make life easier. If you are interested in learning … Continue reading