David E Rex | Search PubMed

PubMed2006

Quantitative evaluation of automated skull-stripping methods applied to contemporary and legacy images: effects of diagnosis, bias correction, and slice location.

Performance of automated methods to isolate brain from nonbrain tissues in magnetic resonance (MR) structural images may be influenced by MR signal inhomogeneities, type of MR image set, regional anatomy, and age and diagnosis of subjects studied. The present study compared the performance of four methods: Brain Extraction Tool (BET; Smith [2002]: Hum Brain Mapp 17:143-155); 3dIntracranial (Ward [1999] Milwaukee: Biophysics Research Institute, Medical College of Wisconsin; in AFNI); a Hybrid Watershed algorithm (HWA, Segonne et al. [2004] Neuroimage 22:1060-1075; in FreeSurfer); and Brain Surface Extractor (BSE, Sandor and Leahy [1997] IEEE Trans Med Imag 16:41-54; Shattuck et al. [2001] Neuroimage 13:856-876) to manually stripped images. The methods were applied to uncorrected and bias-corrected datasets; Legacy and Contemporary T1-weighted image sets; and four diagnostic groups (depressed, Alzheimer's, young and elderly control). To provide a criterion for outcome assessment, two experts manually stripped six sagittal sections for each dataset in locations where brain and nonbrain tissue are difficult to distinguish. Methods were compared on Jaccard similarity coefficients, Hausdorff distances, and an Expectation-Maximization algorithm. Methods tended to perform better on contemporary datasets; bias correction did not significantly improve method performance. Mesial sections were most difficult for all methods. Although AD image sets were most difficult to strip, HWA and BSE were more robust across diagnostic groups compared with 3dIntracranial and BET. With respect to specificity, BSE tended to perform best across all groups, whereas HWA was more sensitive than other methods. The results of this study may direct users towards a method appropriate to their T1-weighted datasets and improve the efficiency of processing for large, multisite neuroimaging studies.

Adult↗

PubMed2005

Lobar distribution of lesion volumes in late-life depression: the Biomedical Informatics Research Network (BIRN).

White matter hyperintense lesions on T2-weighted images are associated with late-life depression. Little work has been carried out examining differences in lesion location between elderly individuals with and without depression. In contrast to previous studies examining total brain white matter lesion volume, this study examined lobar differences in white matter lesion volumes derived from brain magnetic resonance imaging. This study examined 49 subjects with a DSM-IV diagnosis of major depression and 50 comparison subjects without depression. All participants were age 60 years or older. White matter lesion volumes were measured in each hemisphere using a semiautomated segmentation process and localized to lobar regions using a lobar atlas created for this sample using the imaging tools provided by the Biomedical Informatics Research Network (BIRN). The lobar lesion volumes were compared against depression status. After controlling for age and hypertension, subjects with depression exhibited significantly greater total white matter lesion volume in both hemispheres and in both frontal lobes than did control subjects. Although a similar trend was observed in the parietal lobes, the difference did not reach a level of statistical significance. Models of the temporal and occipital lobes were not statistically significant. Older individuals with depression have greater white matter disease than healthy controls, predominantly in the frontal lobes. These changes are thought to disrupt neural circuits involved in mood regulation, thus increasing the risk of developing depression.

Aged↗

PubMed2004

Mapping cortical thickness and gray matter concentration in first episode schizophrenia.

We mapped regional changes in cortical thickness and intensity-based cortical gray matter concentration in first episode schizophrenia. High-resolution magnetic resonance images were obtained from 72 (51 male, 21 female) first episode patients and 78 (37 male, 41 female) healthy subjects similar in age. Cortical pattern matching methods allowed comparisons of cortical thickness and gray matter concentration at thousands of homologous cortical locations between subjects in three dimensions. Principal components analyses reduced measures obtained across the cortex to identify global differences in cortical thickness/gray matter concentration. First principal component factor scores showed significant effects of diagnosis, sex and age for both cortical measures. Diagnosis and age effects remained significant after brain size correction. Cortical thickness and gray matter concentration values were highly correlated. Statistical maps showed significant regional gray matter thinning in frontal, temporal and parietal heteromodal association cortices bilaterally in first episode patients. Regional reductions in cortical gray matter concentration were similar but pronounced in the superior temporal lobe. Regional reductions in cortical thickness and gray matter concentration are present at disease onset in brain regions linked with functional disturbances in schizophrenia. Cortical thickness and gray matter concentration mapping produce similar results, although the concentration metric may be influenced by diagnostic differences in extra-cortical cerebrospinal fluid and surface curvature/complexity.

Adult↗

PubMed2004

Comparing gray matter loss profiles between dementia with Lewy bodies and Alzheimer's disease using cortical pattern matching: diagnosis and gender effects.

We used magnetic resonance imaging (MRI) and cortical pattern matching to map differences in cortical gray matter deficits between Alzheimer's disease (AD) and dementia with Lewy bodies (DLB), and explored the possible influence of gender on these patterns. Twenty-nine patients with AD (age 77.9 +/- 5.5), 16 patients with DLB (76.4 +/- 6.7), and 38 controls (75.3 +/- 6.8) were included. Dementia groups were matched for illness severity. Detailed spatial analyses of gray matter were conducted across the entire cerebral cortex by measuring local proportions of gray matter at thousands of homologous cortical surface locations in each subject and between diagnostic groups. To visualize regional changes, statistical differences were mapped at each cortical surface location in 3D. Main effects of diagnosis demonstrated prominent gray matter differences in orbitofrontal and temporal cortices, where AD exhibited the greatest deficits relative to DLB. Main effects of sex showed less gray matter in men within all group comparisons. Exploratory findings for sex by diagnosis interactions suggest greater gray matter loss in the anterior cingulate for men with AD, relative to controls, AD females, and individuals with DLB. Relative preservation of orbitofrontal cortices in addition to temporal structures may contribute to distinguishing DLB from AD. Further investigation of the influence of gender might provide a more comprehensive understanding of the pathophysiological differences underlying the two forms of dementia.

Aged↗

PubMed2004

A meta-algorithm for brain extraction in MRI.

Accurate identification of brain tissue and cerebrospinal fluid (CSF) in a whole-head MRI is a critical first step in many neuroimaging studies. Automating this procedure can eliminate intra- and interrater variance and greatly increase throughput for a labor-intensive step. Many available procedures perform differently across anatomy and under different acquisition protocols. We developed the Brain Extraction Meta-Algorithm (BEMA) to address these concerns. It executes many extraction algorithms and a registration procedure in parallel to combine the results in an intelligent fashion and obtain improved results over any of the individual algorithms. Using an atlas space, BEMA performs a voxelwise analysis of training data to determine the optimal Boolean combination of extraction algorithms to produce the most accurate result for a given voxel. This allows the provided extractors to be used differentially across anatomy, increasing both the accuracy and robustness of the procedure. We tested BEMA using modified forms of BrainSuite's Brain Surface Extractor (BSE), FSL's Brain Extraction Tool (BET), AFNI's 3dIntracranial, and FreeSurfer's MRI Watershed as well as FSL's FLIRT for the registration procedure. Training was performed on T1-weighted scans of 136 subjects from five separate data sets with different acquisition parameters on separate scanners. Testing was performed on 135 separate subjects from the same data sets. BEMA outperformed the individual algorithms, as well as interrater results from a subset of the scans, when compared for the mean Dice coefficient, a rating of the similarity of output masks to the manually defined gold standards.

Adult↗

PubMed2004

Gender differences in cortical complexity.

Cortical complexity, a measure that quantifies the spatial frequency of gyrification and fissuration of the brain surface, has not been thoroughly characterized with respect to gender differences in the human brain. Using a new three-dimensional (3D) analytic technique with magnetic resonance imaging, we found greater gyrification in women than men in frontal and parietal regions. Increased complexity implies more cortical surface area, which may offset gender differences in brain volume and account for behavioral gender differences.

Cerebral Cortex↗

PubMed2003

The LONI Pipeline Processing Environment.

The analysis of raw data in neuroimaging has become a computationally entrenched process with many intricate steps run on increasingly larger datasets. Many software packages exist that provide either complete analyses or specific steps in an analysis. These packages often possess diverse input and output requirements, utilize different file formats, run in particular environments, and have limited abilities with certain types of data. The combination of these packages to achieve more sensitive and accurate results has become a common tactic in brain mapping studies but requires much work to ensure valid interoperation between programs. The handling, organization, and storage of intermediate data can prove difficult as well. The LONI Pipeline Processing Environment is a simple, efficient, and distributed computing solution to these problems enabling software inclusion from different laboratories in different environments. It is used here to derive a T1-weighted MRI atlas of the human brain from 452 normal young adult subjects with fully automated processing. The LONI Pipeline Processing Environment's parallel processing efficiency using an integrated client/server dataflow model was 80.9% when running the atlas generation pipeline from a PC client (Acer TravelMate 340T) on 48 dedicated server processors (Silicon Graphics Inc. Origin 3000). The environment was 97.5% efficient when the same analysis was run on eight dedicated processors.

Brain Mapping↗

PubMed2002

Utility of preoperative functional magnetic resonance imaging for identifying language cortices in patients with vascular malformations.

OBJECT: The goal of this study was to evaluate the utility of preoperative functional magnetic resonance (fMR) imaging in the prediction of whether a given cortical area would be deemed essential for language processing by electrocortical stimulation mapping (ESM). METHODS: The authors studied patients with vascular malformations, specifically arteriovenous malformations (AVMs) and cavernous angiomas, in whom blood-flow patterns are not normal and in whom a perfusion-dependent mapping signal may be questionable. Ten patients were studied (seven harboring AVMs and three with cavernous angiomas). The authors used a battery of linguistic tasks, including visual object naming, word generation, auditory responsive naming, visual responsive naming, and sentence comprehension, to identify brain regions that were consistently activated across expression and comprehension linguistic tasks. In a comparison of ESM and fMR imaging activations, the authors varied the matching criteria (overlapping activations, adjacent activations, and deep activations) and the radii of influence of ESM (2.5, 5, and 10 mm) to determine the effects of these factors on the sensitivity and specificity of fMR imaging. The sensitivity and specificity of fMR imaging were dependent on the task, lobe, and matching criterion. For the population studied, the sensitivity and specificity of fMR imaging activations during expressive linguistic tasks were found to be up to 100 and 66.7%, respectively, in the frontal lobe, and during comprehension linguistic tasks up to 96.2 and 69.8%, respectively, in the temporal and parietal lobes. The sensitivity and specificity of each disease population (patients with AVMs and those with cavernous angiomas) and of individuals were consistent with those values reported for the entire population studied. CONCLUSIONS: The authors conclude that preoperative fMR imaging is a highly sensitive preoperative planning tool for the identification of which cortical areas are essential for language and that this imaging modality may play a future role in presurgical planning for patients with vascular malformations.

Cerebral Cortex↗

PubMed2002

Multiwavelength optical intrinsic signal imaging of cortical spreading depression.

Cortical spreading depression (CSD) is an important disease model for migraine and cerebral ischemia. In this study, we exploit the high temporal and spatial resolution of optical imaging to characterize perfusion-dependent and -independent changes in response to CSD and to investigate the etiology of reflectance changes during CSD. In this experiment, we characterized the optical response to CSD at wavelengths that emphasize perfusion-related changes (610 and 550 nm), and we compared these results with 850 nm and blood volume data. Blood volume changes during CSD were recorded using an intravascular fluorescent dye, Texas Red dextran. We observed triphasic optical signals at 850 and 550 nm characterized by spreading waves of increased, decreased, then increased reflectance (Fig. 1) which expanded at a rate of approximately 3-5 mm/min. The signal at 610 nm had a similar initial phase, but the phase 2 response was slightly more complex, with a parenchymal decrease in reflectance but a vascular increase in reflectance. Reflectance values decreased in phase three. Blood volume signals were delayed relative to the optical intrinsic signals and corresponded temporally to phases 2 and 3. This is the first study to characterize optical imaging of intrinsic signal responses to CSD, in vivo, at multiple wavelengths. The data presented here suggest that changes in light scattering precede perfusion responses, the blood volume increase (phase 2) is accompanied by a reduction in deoxyhemoglobin, and the blood volume decrease (phase 3) is accompanied by an increase in deoxyhemoglobin. Previous studies have suggested the oligemia of spreading depression was a result of decreased metabolic demand. This study suggests that during the oligemic period there is a greater reduction in oxygen delivery than in demand.

Animals↗

PubMed2002

Utility of preoperative functional magnetic resonance imaging for identifying language cortices in patients with vascular malformations.

OBJECT: The goal of this study was to evaluate the utility of preoperative functional magnetic resonance (fMR) imaging in the prediction of whether a given cortical area would be deemed essential for language processing by electrocortical stimulation mapping (ESM). METHODS: The authors studied patients with vascular malformations, specifically arteriovenous malformations (AVMs) and cavernous angiomas, in whom blood-flow patterns are not normal and in whom a perfusion-dependent mapping signal may be questionable. Ten patients were studied (seven harboring AVMs and three with cavernous angiomas). The authors used a battery of linguistic tasks, including visual object naming, word generation, auditory responsive naming, visual responsive naming, and sentence comprehension, to identify brain regions that were consistently activated across expression and comprehension linguistic tasks. In a comparison of ESM and fMR imaging activations, the authors varied the matching criteria (overlapping activations, adjacent activations, and deep activations) and the radii of influence of ESM (2.5, 5, and 10 mm) to determine the effects of these factors on the sensitivity and specificity of fMR imaging. The sensitivity and specificity of fMR imaging were dependent on the task, lobe, and matching criterion. For the population studied, the sensitivity and specificity of fMR imaging activations during expressive linguistic tasks were found to be up to 100 and 66.7%, respectively, in the frontal lobe, and during comprehension linguistic tasks up to 96.2 and 69.8%, respectively, in the temporal and parietal lobes. The sensitivity and specificity of each disease population (patients with AVMs and those with cavernous angiomas) and of individuals were consistent with those values reported for the entire population studied. CONCLUSIONS: The authors conclude that preoperative fMR imaging is a highly sensitive preoperative planning tool for the identification of which cortical areas are essential for language and that this imaging modality may play a future role in presurgical planning for patients with vascular malformations.

Brain Mapping↗