FreeSurfer— the software package— may not be a household name in the beach bum community but it has become an essential tool for researchers in a range of disciplines who work with neuroimaging data. Introduced and continuousy developed and refined by investigators in the MGH Martinos Center in Boston, the suite has helped to provide ever-deeper insights into the structures of the brain, and thus has played an integral role in advancing our understandings of the brain in both health and disease.
But what does it do exactly?
Stated simply, FreeSurfer provides automated anatomical analysis of the brain. While it brings together a number of different tools for use with neuroimaging data, it is best known for— and named after— the first of these to be introduced, a tool designed for analysis of the surface of the cortex in the brain.
Martinos Center investigator Doug Greve offers a simple analogy to explain what this means for the typical neuroscientist; Greve joined the Center in the late 1990s and has been working with FreeSurfer since not long after. The analogy begins, as few in the neurosciences do, with a paper bag.
“ The cortex is inherently a highly folded two-dimensional structure, like a paper bag that has been wadded up into a ball to fit inside a skull,” he says. With MRI, data is collected as a series of single images, in effect cutting the wadded-up bag into slices. If something were written on the bag— say, a topographic map, an image of the world as we perceive it projected onto the cortex— it would be nearly impossible to read from looking at the slices.
This is where the software package comes in.“ FreeSurfer essentially stitches these sections together to reconstruct the folded bag, then unfolds it. The natural language of the cortex is written on the bag, so unfolding it makes it much easier to interpret.”
One might ask: Why is this important? In what ways can FreeSurfer actually help people? Even beyond the many benefits it confers for research applications, where it can help to make sense of functional neuroimaging studies by providing anatomical context, the software can bolster healthcare applications. t has been used to track changes in disease due to pharmaceutical
Speakers at the 2017 FreeSurfer Symposium react to a one-liner. From L to R: Marty Sereno, David Salat, Arthur Liu( with his head in his hand), Bruce Fischl, Anastasia Yendiki and Doug Greve. Photo by Caroline Magnain.
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