Structural MR image processing using the BRAINS2 toolbox

Mental Health Clinical Research Center, The University of Iowa Hospitals and Clinics, Room 2911 JPP, 200 Hawkins Drive, Iowa City, IA 52242, USA.
Computerized Medical Imaging and Graphics (Impact Factor: 1.22). 07/2002; 26(4):251-64. DOI: 10.1016/S0895-6111(02)00011-3
Source: PubMed


Medical imaging has opened a new door into biomedical research. In order to study various diseases of the brain and detect their impact on brain structure, robust and user friendly image processing packages are required. These packages must be multi-faceted to distinguish variations in size, shape, volume, and the ability to detect longitudinal changes over the course of an illness. This paper describes the BRAINS2 image processing package, which contains both manual and automated tools for structural identification, methods for tissue classification and cortical surface generation. These features are described in detail, as well as the reliability of these procedures.

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    • "Both hippocampus and amygdala were manually segmented by trained raters (Hipocampus: SP; Amygdala: RC). First, raw image data had to be converted to BRAINS2 (Magnotta et al., 2002) readable format using the MRIcro free software package. The employed standardized segmentation protocol for the hippocampus (Malykhin et al., 2007) is state of the art according to review articles (Geuze et al., 2005; Konrad et al., 2009). "
    • "Automated processing of the anatomical images was performed using BRAINS2 software ( Magnotta et al . , 2002 ) . The BRAINS2 software includes automated AC – PC alignment , image alignment , image intensity standardization , tissue classification , and brain extraction . The BRAINS2 method for white matter segmentation has shown reliability with manual raters and adequately addresses concerns of partial volume contamination ( Harris et al . , "
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    Frontiers in Human Neuroscience 07/2015; 9. DOI:10.3389/fnhum.2015.00408 · 2.99 Impact Factor
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    • "The images were processed using the software BRAINS2 (Imaging Processing Lab, The University of Iowa Hospitals and Clinics, Iowa City, Iowa) (Andreasen et al., 1992, 1996; Magnotta et al., 2002). In brief, the T1-weighted images were spatially normalized and resampled to 1.0-mm 3 voxels. "
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