| IDL Aids Noninvasive Brain Research
Noninvasive Brain Imaging
Prior to the advent of modern brain imaging methods, patients had to accept the risk of exposure to ionizing radiation from x-rays. Today, neuroimaging researchers use noninvasive methods to view both brain anatomy and brain function, taking advantage of advanced software tools like RSI’s IDL to study the brain while protecting patients from ill side effects.
The Human Brain Project, spearheaded by Los Alamos National Lab’s (LANL) Biophysics Group, is dedicated to noninvasive neuroimaging research to understand general brain function as well as aid in clinical applications such as neurosurgery planning, epilepsy and stroke recovery. To further advance the project’s research, the Biophysics Group created custom software using IDL to combine gigabyte-sized data files from multiple imaging systems—including magnetic resonance imaging (MRI), electroencephalography (EEG) and magnetoencephalography (MEG)—and then display and visualize the data intuitively.
Mapping Brain Activity: The Challenge of Medical Image Data
A number of medical imaging systems are required to obtain brain data, including anatomical and functional MRI, and MEG and EEG time-series data. These data sets range in size from tens of megabytes to more than a gigabyte. Because working with extraordinarily large data sets in a variety of formats presents a unique challenge, the Biophysics Group needed a software solution that would be up to the task.
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A magnetic field resulting from the brain’s response to a visual stimulus is shown as a color contour map on a head surface reconstructed from MRI data. The disks represent sensor locations in a full-head MEG system. The fields shown are an averaged response from repeating the same visual task 100 times. Red represents a magnetic field emanating from the head, blue entering the head. |
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The Magic of MRIVIEW and IDL
Equipped with IDL’s programming power, the Biophysics Group developed a software tool called MRIVIEW for viewing and manipulating volumetric MRI head data. MRIVIEW supplies methods for reading in raw MRI data, viewing this data in two and three dimensions, segmenting structures in the data, reconciling coordinate systems between the MRI data volume and data obtained from brain functional modalities, and viewing combinations of anatomical and functional information.
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This view shows the 3D Model Viewer being used to combine 2 volumes with 2 sets of geometric data. Model 1 contains the MRI head data, Model 2 contains the MRI brain data, Model 3 contains the arrows, and Model 4 contains the contoured MEG data on the helmet inner surface. |
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CSST results from an MEG visual study, showing the range of visualization options of the Source Plotting interface. All text, plot, 2D images and 3D renderings are modifiable. They can be moved, resized, recolored, added or deleted from the viewing window. |
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MRIVIEW includes a MEG inverse solver called Cortical Start Spatial-Temporal (CSST). CSST uses Message Passing Interface to start multiple IDL analyses on a Linux cluster, then gather and save the results. Where multiprocessor machines are present, CSST will also use IDL’s multi-threading capabilities to further speed up computations. Used on a single processor, this type of analysis might require several days, so “this parallel processing capability using IDL has been very useful,” according to Ranken.
Ranken also prizes IDL for the flexibility it allows when working with other commercial programming packages and languages. “With IDL, I can quickly integrate MRIVIEW with other software developed here and elsewhere because IDL allows simple links to other packages written in IDL, C, Fortran, and MATLAB.”
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