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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