Three-dimensional hippocampal MR morphometry with high-dimensional transformation of a neuroanatomic atlas.

Haller, John; Banerjee, Ayananshu; Christensen, Gary E.; Gado, Mokhtar H.; Joshi, Sarang; Miller, Michael I.; Sheline, Yvette I.; Vannier, Michael W.; Csernansky, John G.

doi:10.1148/radiology.202.2.9015081

Cited by 201 publications

(204 citation statements)

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“…The method proposed by Webb et al 130 involves warping an atlas (obtained by manual volumetrics of 30 individuals) to the individual MR image. Another important automated method is the method used by Haller and co-workers, [131][132][133][134] which uses a high-dimensional fluid transformation to warp a template of the hippocampus and surrounding anatomical structures to an individual MR image. This method has also been validated, and was found to have less variability than manual tracing.…”

Section: Discussionmentioning

confidence: 99%

MR-based in vivo hippocampal volumetrics: 1. Review of methodologies currently employed

2004

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The advance of neuroimaging techniques has resulted in a burgeoning of studies reporting abnormalities in brain structure and function in a number of neuropsychiatric disorders. Measurement of hippocampal volume has developed as a useful tool in the study of neuropsychiatric disorders. We reviewed the literature and selected all English-language, human subject, data-driven papers on hippocampal volumetry, yielding a database of 423 records. From this database, the methodology of all original manual tracing protocols were studied. These protocols differed in a number of important factors for accurate hippocampal volume determination including magnetic field strength, the number of slices assessed and the thickness of slices, hippocampal orientation correction, volumetric correction, software used, inter-rater reliability, and anatomical boundaries of the hippocampus. The findings are discussed in relation to optimizing determination of hippocampal volume.

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Section: Discussionmentioning

confidence: 99%

MR-based in vivo hippocampal volumetrics: 1. Review of methodologies currently employed

2004

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“…In full-brain registration, small structures may be poorly aligned because they contribute a small portion to the overall objective function optimized by the registration. When augmented by expertdefined landmarks, registration methods can achieve very high accuracy in structures like the hippocampus (Haller et al, 1997) but, without effective low cost software tools, they may lose their fully automatic appeal. Methods based on registration are also very computationally intensive, which may discourage their routine use in the clinical environment.…”

Section: Previous Workmentioning

confidence: 99%

“…The spectrum of available segmentation approaches is broad, ranging from manual outlining of structures in 2D cross-sections to cutting-edge methods that use deformable registration to find optimal correspondences between 3D images and a labeled atlas (Haller et al, 1997;Goldszal et al, 1998). Amid this spectrum lie semiautomatic approaches that combine the efficiency and repeatability of automatic segmentation with the sound judgement that can only come from human expertise.…”

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confidence: 99%

User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability

Yushkevich¹,

Piven²,

Hazlett³

et al. 2006

NeuroImage

7,385

4,931

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Active contour segmentation and its robust implementation using level set methods are well established theoretical approaches that have been studied thoroughly in the image analysis literature. Despite the existence of these powerful segmentation methods, the needs of clinical research continue to be fulfilled, to a large extent, using slice-by-slice manual tracing. To bridge the gap between methodological advances and clinical routine, we developed an open source application called ITK-SNAP, which is intended to make level set segmentation easily accessible to a wide range of users, including those with little or no mathematical expertise. This paper describes the methods and software engineering philosophy behind this new tool and provides the results of validation experiments performed in the context of an ongoing child autism neuroimaging study. The validation establishes SNAP intra/interrater reliability and overlap error statistics for the caudate nucleus and finds that SNAP is a highly reliable and efficient alternative to manual tracing.Analogous results for lateral ventricle segmentation are provided.

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“…For this reason, our comparisons in this study are slightly different as they do not involve a separation of the amygdala and hippocampus, because we evaluated the amygdala-hippocampal complex (one structure) for both the volume and shape measures. 1992; Brechbühler et al, 1992;Hill and Taylor, 1992;Hill et al, 1992;Talbot and Vincent, 1992;Cootes et al, 1993;Gee et al, 1993;Grenander, 1993;Christensen et al, 1994Christensen et al, , 1996Christensen et al, , 1997Attali and Montanvert, 1994;Brechbühler et al, 1995;Haller et al, 1996Haller et al, , 1997Drury et al, 1996;Székely et al, 1996;Näf et al, 1996Näf et al, , 1997Bookstein, 1997a, b , c ;Joshi et al, 1997;Morse et al, 1998;Pizer et al, 1998;Angenent et al, 1999;Kelemen et al, 1999). Such descriptions have involved the use of a skeleton or medial axis to extract shape features (e.g.…”

Section: Introductionmentioning

confidence: 99%

“…A clear trend in shape analysis is toward the movement from summary measures of whole structures or objects to measures of regional differences in shape, thus incorporating more information about the properties of shape than more simple volumetric measures. Shape descriptions that are represented as high-dimensional features (Haller et al, 1996(Haller et al, , 1997Csernansky et al, 1998;Hogan et al, 2000;Wang et al, 2001) or features derived from a projection onto basis functions (Kelemen et al, 1999) are examples of this trend.…”

Section: Introductionmentioning

confidence: 99%

Amygdala–hippocampal shape differences in schizophrenia: the application of 3D shape models to volumetric MR data

Shenton

Gerig

McCarley

et al. 2002

Psychiatry Research: Neuroimaging

125

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Evidence suggests that some structural brain abnormalities in schizophrenia are neurodevelopmental in origin. There is also growing evidence to suggest that shape deformations in brain structure may reflect abnormalities in neurodevelopment. While many magnetic resonance (MR) imaging studies have investigated brain area and volume measures in schizophrenia, fewer have focused on shape deformations. In this MR study we used a 3D shape representation technique, based on spherical harmonic functions, to analyze left and right amygdala-hippocampus shapes in each of 15 patients with schizophrenia and 15 healthy controls matched for age, gender, handedness and parental socioeconomic status. Left/right asymmetry was also measured for both shape and volume differences. Additionally, shape and volume measurements were combined in a composite analysis. There were no differences between groups in overall volume or shape. Left/right amygdalahippocampal asymmetry, however, was significantly larger in patients than controls for both relative volume and shape. The local brain regions responsible for the left/right asymmetry differences in patients with schizophrenia were in the tail of the hippocampus (including both the inferior aspect adjacent to parahippocampal gyrus and the superior aspect adjacent to the lateral geniculate nucleus and more anteriorly to the cerebral peduncles) and in portions of the amygdala body (including the anterior-superior aspect adjacent to the basal nucleus). Also, in patients, increased volumetric asymmetry tended to be correlated with increased left/right shape asymmetry. Furthermore, a combined analysis of volume and shape asymmetry resulted in improved differentiation between groups. Classification function analyses correctly classified 70% of cases using volume, 73.3% using shape, and 87% using combined volume and shape measures. These findings suggest that shape provides important new information toward characterizing the pathophysiology of schizophrenia, and that combining volume and shape measures provides improved group discrimination in studies investigating brain abnormalities in schizophrenia. An evaluation of shape deformations also suggests local abnormalities in the amygdala-hippocampal complex in schizophrenia.

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Three-dimensional hippocampal MR morphometry with high-dimensional transformation of a neuroanatomic atlas.

Abstract: The automated method estimates hippocampal volumes with less variability (ie, lower variance) than that of manual out-lining.

Cited by 201 publications

References 0 publications

MR-based in vivo hippocampal volumetrics: 1. Review of methodologies currently employed

MR-based in vivo hippocampal volumetrics: 1. Review of methodologies currently employed

User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability

Amygdala–hippocampal shape differences in schizophrenia: the application of 3D shape models to volumetric MR data

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