TY - GEN
T1 - Subcortical structure segmentation using probabilistic atlas priors
AU - Gouttard, Sylvain
AU - Styner, Martin
AU - Joshi, Sarang
AU - Smith, Rachel G.
AU - Hazlett, Heather Cody
AU - Gerig, Guido
PY - 2007
Y1 - 2007
N2 - The segmentation of the subcortical structures of the brain is required for many forms of quantitative neuroanatomy analysis. The volumetric and shape parameters of structures such as lateral ventricles, putamen, caudate, hippocampus, pallidus and amygdala are employed to characterize a disease or its evolution. This paper presents a fully automatic segmentation of these structures via a non-rigid registration of a probabilistic atlas prior and alongside a comprehensive validation. Our approach is based on an unbiased diffeomorphic atlas with probabilistic spatial priors built from a training set of MR images with corresponding manual segmentations. The atlas building computes an average image along with transformation fields mapping each training case to the average image. These transformation fields are applied to the manually segmented structures of each case in order to obtain a probabilistic map on the atlas. When applying the atlas for automatic structural segmentation, an MR image is first intensity inhomogeneity corrected, skull stripped and intensity calibrated to the atlas. Then the atlas image is registered to the image using an affine followed by a deformable registration matching the gray level intensity. Finally, the registration transformation is applied to the probabilistic maps of each structures, which are then thresholded at 0.5 probability. Using manual segmentations for comparison, measures of volumetric differences show high correlation with our results. Furthermore, the dice coefficient, which quantifies the volumetric overlap, is higher than 62% for all structures and is close to 80% for basal ganglia. The intraclass correlation coefficient computed on these same datasets shows a good inter-method correlation of the volumetric measurements. Using a dataset of a single patient scanned 10 times on 5 different scanners, reliability is shown with a coefficient of variance of less than 2 percents over the whole dataset. Overall, these validation and reliability studies show that our method accurately and reliably segments almost all structures. Only the hippocampus and amygdala segmentations exhibit relative low correlation with the manual segmentation in at least one of the validation studies, whereas they still show appropriate dice overlap coefficients.
AB - The segmentation of the subcortical structures of the brain is required for many forms of quantitative neuroanatomy analysis. The volumetric and shape parameters of structures such as lateral ventricles, putamen, caudate, hippocampus, pallidus and amygdala are employed to characterize a disease or its evolution. This paper presents a fully automatic segmentation of these structures via a non-rigid registration of a probabilistic atlas prior and alongside a comprehensive validation. Our approach is based on an unbiased diffeomorphic atlas with probabilistic spatial priors built from a training set of MR images with corresponding manual segmentations. The atlas building computes an average image along with transformation fields mapping each training case to the average image. These transformation fields are applied to the manually segmented structures of each case in order to obtain a probabilistic map on the atlas. When applying the atlas for automatic structural segmentation, an MR image is first intensity inhomogeneity corrected, skull stripped and intensity calibrated to the atlas. Then the atlas image is registered to the image using an affine followed by a deformable registration matching the gray level intensity. Finally, the registration transformation is applied to the probabilistic maps of each structures, which are then thresholded at 0.5 probability. Using manual segmentations for comparison, measures of volumetric differences show high correlation with our results. Furthermore, the dice coefficient, which quantifies the volumetric overlap, is higher than 62% for all structures and is close to 80% for basal ganglia. The intraclass correlation coefficient computed on these same datasets shows a good inter-method correlation of the volumetric measurements. Using a dataset of a single patient scanned 10 times on 5 different scanners, reliability is shown with a coefficient of variance of less than 2 percents over the whole dataset. Overall, these validation and reliability studies show that our method accurately and reliably segments almost all structures. Only the hippocampus and amygdala segmentations exhibit relative low correlation with the manual segmentation in at least one of the validation studies, whereas they still show appropriate dice overlap coefficients.
KW - Segmentation
KW - Shape
KW - Shape analysis
KW - Validation
UR - http://www.scopus.com/inward/record.url?scp=36248980391&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=36248980391&partnerID=8YFLogxK
U2 - 10.1117/12.708626
DO - 10.1117/12.708626
M3 - Conference contribution
AN - SCOPUS:36248980391
SN - 0819466301
SN - 9780819466303
T3 - Progress in Biomedical Optics and Imaging - Proceedings of SPIE
BT - Medical Imaging 2007
T2 - Medical Imaging 2007: Image Processing
Y2 - 18 February 2007 through 20 February 2007
ER -