Article

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: 1.5). 07/2002; 26(4):251-64. DOI: 10.1016/S0895-6111(02)00011-3
Source: PubMed

ABSTRACT 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.

1 Follower
 · 
101 Views
  • Source
    • "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). "
  • Source
    • ") was used to process the MRI scans. This involves an automated procedure in BRAINS image analysis software (Magnotta et al., 2002) and artificial neural networks (Powell et al., 2008). Total regional brain volume which included the sum of the gray and white matter volume (but not cerebral spinal fluid, CSF) of the right and left side of each brain region was computed for the hippocampus, caudate, and putamen (Fig. 1). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Exercise has been shown to increase hippocampal volume in healthy older adults. Observations from animal models of diabetes and hypertension suggest that the combination of exercise and caloric restriction may exert greater neuroprotection in the hippocampus than either behavior alone. Yet, in humans, the effects of exercise and caloric restriction on the hippocampus are not known. We measured the volume of the hippocampus prior to clinical treatment in women with anorexia nervosa (AN) who were restricting calories and engaging in excessive exercise, women with AN who did not exercise excessively, and healthy women who did not engage in either behavior. Women with AN were also examined longitudinally (once weight was restored and six months later). In the present report, we found that women with AN engaged in caloric restriction and excessive exercising prior to clinical treatment had larger hippocampal volumes than healthy comparison women. After weight restoration, women with AN who had engaged in food restriction and excessive exercise prior to treatment had hippocampal volumes similar to that of women with AN who only engaged in caloric restriction. These results advance the field by showing for the first time that hippocampal volume may be increased by exercise alone or exercise interacting with food restriction in AN.
    Psychiatry Research Neuroimaging 10/2014; 232(2). DOI:10.1016/j.pscychresns.2014.10.013 · 2.83 Impact Factor
  • Source
    • "The amygdalae and the hippocampi were outlined using the software BRAINS2 (Magnotta et al. 2002 "
    [Show abstract] [Hide abstract]
    ABSTRACT: Fear conditioning is a basic learning process which involves the association of a formerly neutral conditioned stimulus (CS) with a biologically relevant aversive unconditioned stimulus (US). Previous studies conducted in brain-lesioned patients have shown that while the acquisition of autonomic fear responses requires an intact amygdala, a spared hippocampus is necessary for the development of the CS-US contingency awareness. Although these data have been supported by studies using functional neuroimaging techniques in healthy people, attempts to extend these findings to the morphological aspects of amygdala and hippocampus are missing. Here we tested the hypothesis that amygdalar and hippocampal volumes play dissociable roles in determining autonomic responses and contingency awareness during fear conditioning. Fifty-two healthy individuals (mean age 21.83) underwent high-resolution magnetic resonance imaging. We used a differential delay fear conditioning paradigm while assessing skin conductance responses (SCRs), subjective ratings of CS-US contingency, as well as emotional valence and perceived arousal. Left amygdalar volume significantly predicted the magnitude of differential SCRs during fear acquisition, but had no impact on contingency learning. Conversely, bilateral hippocampal volumes were significantly related to contingency ratings, but not to SCRs. Moreover, left amygdalar volume predicted SCRs to the reinforced CS alone, but not those elicited by the US. Our findings bridge the gap between previous lesion and functional imaging studies, by showing that amygdalar and hippocampal volumes differentially modulate the acquisition of conditioned fear. Further, our results reveal that the morphology of these limbic structures moderate learning and memory already in healthy persons.
    Brain Structure and Function 06/2014; DOI:10.1007/s00429-014-0807-8 · 4.57 Impact Factor
Show more