Stroke Lesion Segmentation in FLAIR MRI Datasets Using Customized Markov Random Fields
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Stroke Lesion Segmentation in FLAIR MRI Datasets Using Customized Markov Random Fields. / Subbanna, Nagesh K; Rajashekar, Deepthi; Cheng, Bastian; Thomalla, Götz; Fiehler, Jens; Arbel, Tal; Forkert, Nils D.
In: FRONT NEUROL, Vol. 10, 2019, p. 541.Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review
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TY - JOUR
T1 - Stroke Lesion Segmentation in FLAIR MRI Datasets Using Customized Markov Random Fields
AU - Subbanna, Nagesh K
AU - Rajashekar, Deepthi
AU - Cheng, Bastian
AU - Thomalla, Götz
AU - Fiehler, Jens
AU - Arbel, Tal
AU - Forkert, Nils D
PY - 2019
Y1 - 2019
N2 - Robust and reliable stroke lesion segmentation is a crucial step toward employing lesion volume as an independent endpoint for randomized trials. The aim of this work was to develop and evaluate a novel method to segment sub-acute ischemic stroke lesions from fluid-attenuated inversion recovery (FLAIR) magnetic resonance imaging (MRI) datasets. After preprocessing of the datasets, a Bayesian technique based on Gabor textures extracted from the FLAIR signal intensities is utilized to generate a first estimate of the lesion segmentation. Using this initial segmentation, a customized voxel-level Markov random field model based on intensity as well as Gabor texture features is employed to refine the stroke lesion segmentation. The proposed method was developed and evaluated based on 151 multi-center datasets from three different databases using a leave-one-patient-out validation approach. The comparison of the automatically segmented stroke lesions with manual ground truth segmentation revealed an average Dice coefficient of 0.582, which is in the upper range of previously presented lesion segmentation methods using multi-modal MRI datasets. Furthermore, the results obtained by the proposed technique are superior compared to the results obtained by two methods based on convolutional neural networks and three phase level-sets, respectively, which performed best in the ISLES 2015 challenge using multi-modal imaging datasets. The results of the quantitative evaluation suggest that the proposed method leads to robust lesion segmentation results using FLAIR MRI datasets only as a follow-up sequence.
AB - Robust and reliable stroke lesion segmentation is a crucial step toward employing lesion volume as an independent endpoint for randomized trials. The aim of this work was to develop and evaluate a novel method to segment sub-acute ischemic stroke lesions from fluid-attenuated inversion recovery (FLAIR) magnetic resonance imaging (MRI) datasets. After preprocessing of the datasets, a Bayesian technique based on Gabor textures extracted from the FLAIR signal intensities is utilized to generate a first estimate of the lesion segmentation. Using this initial segmentation, a customized voxel-level Markov random field model based on intensity as well as Gabor texture features is employed to refine the stroke lesion segmentation. The proposed method was developed and evaluated based on 151 multi-center datasets from three different databases using a leave-one-patient-out validation approach. The comparison of the automatically segmented stroke lesions with manual ground truth segmentation revealed an average Dice coefficient of 0.582, which is in the upper range of previously presented lesion segmentation methods using multi-modal MRI datasets. Furthermore, the results obtained by the proposed technique are superior compared to the results obtained by two methods based on convolutional neural networks and three phase level-sets, respectively, which performed best in the ISLES 2015 challenge using multi-modal imaging datasets. The results of the quantitative evaluation suggest that the proposed method leads to robust lesion segmentation results using FLAIR MRI datasets only as a follow-up sequence.
U2 - 10.3389/fneur.2019.00541
DO - 10.3389/fneur.2019.00541
M3 - SCORING: Journal article
C2 - 31178820
VL - 10
SP - 541
JO - FRONT NEUROL
JF - FRONT NEUROL
SN - 1664-2295
ER -