Yes, memory is likely the culprit here. Note that several steps attempt to reduce memory usage based on the parts of the image that need to be processed, so the limit can vary from subject to subject. And of course other activities on your computer might limit further the amount of memory you can allocate to Java.

As a note, many of the CBSTools have been ported to Nighres, a python-based library with a slightly smaller memory footprint.