The First 20 (Plus) Years of FreeSurfer It’s a sunny day in Southern California and the developers of FreeSurfer—a suite of software tools used to analyze data from neuroimaging studies—are preparing for a training session to introduce scientists to the many benefits of the package. To help the scientists find the classroom, they have hung “FreeSurfer Course” signs around the outside of the building, a stone’s throw from the beach and the restless waves of the Pacific. They switch on the computers as they await the attendees’ arrival. The door opens and a gentleman drifts in. He’s young and tanned and dressed—if dressed is the right word—in flip flops and a tank top. It’s not your typical look for a neuroscientist but no matter. All are welcome here. He looks around the room in a quizzical sort of way and, after a moment, asks a single question. “Is this the free surfer course?” FreeSurfer—the software package—may not be a household name in the beach bum community but it has become an essential tool for researchers working in the field of neuroimaging. Introduced and continuously developed and refined by Martinos Center investigators, the suite has helped 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?
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Stated simply, FreeSurfer provides automated analysis of the anatomy of the brain. What does this mean for the typical neuroscientist? Longtime Martinos researcher Doug Greve offers a simple analogy by way of explanation. “The cortex is 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—a topographic map, for example; that is, 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,” Greve adds. “The natural language of the cortex is written on the bag, so unfolding it makes it much easier to interpret.” All of this may sound a bit esoteric, really only applying in a rarefied realm of lab coats and science fiction-like technologies. But FreeSurfer also delivers in myriad, real-world ways. Even beyond its many benefits for research applications, where it helps make sense of neuroimaging studies by literally unfolding the mysteries of the brain’s anatomy, the software can bolster a wide range of healthcare applications. For example, researchers have used it
