September 23, 2004 —
Brainstorm 2.0: USC's Widely Used Brain Imaging Software Gets an Upgrade
Thursday, September 23rd, 2004 —
For five years, researchers around the world have explored the activity of the cerebral cortex in both time and space using "Brainstorm" imaging software created by an interdisciplinary partnership led by the University of Southern California.
Reading a mind: a netwok of sensors around a head picks up electrical and magnetic activity through layers of skin and bone from the brain beneath. Software can analyze these signals and locate the areas of the brain that are giving rise to them.
Prof. Richard Leahy at the USC Viterbi School of Engineering says the team, which includes a former USC student and former USC post doctoral researcher, has just completed alpha testing of a complete rewrite of the successful original software. Like its predecessor, Brainstorm 2.0 is an open-source, multipurpose product, which is being distributed free at the Brainstorm web site.
One of Leahy’s collaborators, John Mosher of the Los Alamos National Laboratory, will present the now-beta version software at an Oct. 20, symposium of the Society for Psychophysiological Research’s 44th Annual Meeting in Santa Fe, New Mexico.
Brainstorm 2.0, like the original, synthesizes brain imaging data gathered from Electroencephalograms (EEG), Magnetoencephalograms (MEGs), and functional Magnetic Resonance (fMRIs) scans of activity patterns within the brain.
The software can present the images as maps, as slides or even movies showing changes over time, at a fine-grained (millisecond) time scale. It also offers detailed, 3D renderings of brain surfaces.
The new version is written in the widely used MatLab scientific programming language and retains from the original a striking, colorful, multi-window interface that displays data in numerous forms. This allows researchers to zero in on areas of interest in multiple ways and to easily compare separate imaging records.
The original Brainstorm packaged two basic algorithms; both mathematical schemes for “reconstructing” or deducing what specific areas of the brain cortex are doing from the subtle murmer of electrical and magnetic noise picked up by sensors affixed to the outside of subject's heads.
Brainstorm 2.0 adds more algorithms to the toolbox, including ones to create ‘virtual electrodes’ at designated listening points inside the brain. It also has what Leahy calls “boring but very useful” data management features that enable users to easily and quickly index, search, and classify EEG, MEG and MRI records. It has also added features to quickly import data recorded in various widely used commercial imaging softwares.
“And it is far more stable and less temperamental,” adds the researcher. “Researchers can focus on the brain, not on the software.”
BRAINSTORM INTERFACE: This display is processing one algorithm that provides a precise point source for cerebral activity. The records here are of sense stimulation of a finger: the three center images locate the signal epicenter of the brain activity as a single point. The records on the right side show general signal strength over time. The pull down selections on the left control how the records are analyzed and displayed.
In recent months, users have downloaded some 300 copies of the alpha version. The researchers have received feedback from numerous users at institutions like the University of Wisconsin, Northwestern University, New York University, and the UC-San Francisco.
In the Huntington Medical Research Institute in Pasadena California, clinician William Sutherling, who has been working with Brainstorm for years, is now considering using Brainstorm 2 to supplement existing commercial products for guiding neurosurgery to treat cases of epilepsy that resist management by drugs.
Sylvain Baillet of the French National Scientific Research Center (CNRS) Cognitive Neuroscience and Brain Imaging Laboratory, who built the original Brainstorm when he was a post-doctoral researcher in Leahy’s laboratories at the USC Viterbi School’s Signal and Image Processing Institute, also collaborated on the new software. Mosher is a former Leahy grad student.
Others involved in upgrading Brainstorm included Felix Darvas, Dimitrios Pantazis, Esen Kucukaltun-Yildirim, John Ermer, Alexei Ossadtchi, Belma Dogdas, all at USC; Denis Schwartz, Line Garnero and Antoine Ducorps at CNRS in Paris; and Darren Webe at UC-San Francisco.
Funding for Brainstorm was provided by the National Institute of Mental Health and the National Institute of Biomedical Imaging and Bioengineering.
Leahy is a professor in the Viterbi School's Department of Electrical Engineering and director of the USC NeuroImaging Research Group. He is also won the Viterbi Schools 2003 Outstanding Senior Researcher Award.
ANOTHER VIEW of brain stimulation, this one using a differenttechnique that deduces general areas of activity. Area 1 is the time sequence, with the vertical line showing the precise moment that the record was taken -- the line moves from left to right in millisecond intervals, with displays 2 and 3 changing as the line moves. These records can be displayed as a movie. Display number 2 shows the distribution of the data picked up by EEG electrodes of the MEG helmet. Red shows positve electrical or (for MEG) outward magnetic flux; blue shows negative or inward flux; in this record, as the line moves to the narrow band in 1, the display turns more blue. The display in 3 shows the estimated activity on the white matter cortical surface, with the colored areas those which produce more than the global average.