Over the course of the last century, the cerebral cortex has been of interest for neuroscientists, and the work with mapping and measuring the cortex started in the early 1900s (Brodmann 1909).The advances in medical imaging over the recent decades has given the opportunity to measure the cortex in vivo, and several algorithms and types of software applications has been developed for this purpose. These software applications can be used to execute complex analysis to determine both cortex thickness and density.The algorithms and software applications presented in this paper are the ones most utilized to measure cortical thickness today, and include four software applications and two algorithms. The basic principles of these tools will be outlined, as well as their strengths and weaknesses.