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Brain tissue segmentation based on MP2RAGE multi-contrast images in 7 T MRI

We proposed a method for segmentation of brain tissues-gray matter, white matter, and cerebrospinal fluid-using multi-contrast images, including a T1 map and a uniform T1-weighted image, from a magnetization-prepared 2 rapid acquisition gradient echoes (MP2RAGE) sequence at 7 Tesla. The proposed met... Full description

Journal Title: PloS one 2019, Vol.14 (2), p.e0210803-e0210803
Main Author: Choi, Uk-Su
Other Authors: Kawaguchi, Hirokazu , Matsuoka, Yuichiro , Kober, Tobias , Kida, Ikuhiro
Format: Electronic Article Electronic Article
Language: English
Subjects:
Publisher: United States: Public Library of Science
ID: ISSN: 1932-6203
Link: https://www.ncbi.nlm.nih.gov/pubmed/30818328
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title: Brain tissue segmentation based on MP2RAGE multi-contrast images in 7 T MRI
format: Article
creator:
  • Choi, Uk-Su
  • Kawaguchi, Hirokazu
  • Matsuoka, Yuichiro
  • Kober, Tobias
  • Kida, Ikuhiro
subjects:
  • Adult
  • Algorithms
  • Analysis
  • Anatomy
  • Biology and Life Sciences
  • Body Fluids
  • Brain
  • Brain - diagnostic imaging
  • Brain Mapping - methods
  • Brain research
  • Central Nervous System
  • Cerebellum
  • Cerebral Cortex
  • Cerebrospinal Fluid
  • Computer and Information Sciences
  • Diagnostic Medicine
  • Diagnostic Radiology
  • Engineering and Technology
  • Female
  • Gaussian Noise
  • Humans
  • Image segmentation
  • Imaging Techniques
  • Imaging, Three-Dimensional
  • Magnetic Resonance Imaging
  • Male
  • Mathematics
  • Medicine
  • Medicine and Health Sciences
  • Middle Aged
  • Nervous System
  • Neuroimaging
  • Neuroscience
  • Physical Sciences
  • Physiology
  • Radiology and Imaging
  • Research and Analysis Methods
  • Research Article
  • Science
  • Software Engineering
  • Software Tools
  • Statistical Noise
  • Statistics
  • Usage
ispartof: PloS one, 2019, Vol.14 (2), p.e0210803-e0210803
description: We proposed a method for segmentation of brain tissues-gray matter, white matter, and cerebrospinal fluid-using multi-contrast images, including a T1 map and a uniform T1-weighted image, from a magnetization-prepared 2 rapid acquisition gradient echoes (MP2RAGE) sequence at 7 Tesla. The proposed method was evaluated with respect to the processing time and the similarity of the segmented masks of brain tissues with those obtained using FSL, FreeSurfer, and SPM12. The processing time of the proposed method (28 ± 0 s) was significantly shorter than those of FSL and SPM12 (444 ± 4 s and 159 ± 2 s for FSL and SPM12, respectively). In the similarity assessment, the tissue mask of the brain obtained by the proposed method showed higher consistency with those obtained using FSL than with those obtained using SPM12. The proposed method misclassified the subcortical structures and large vessels since it is based on the intensities of multi-contrast images obtained using MP2RAGE, which uses a similar segmentation approach as FSL but is not based on a template image or a parcellated brain atlas, which are used for FreeSurfer and SPM12, respectively. However, the proposed method showed good segmentation in the cerebellum and white matter in the medial part of the brain in comparison with the other methods. Thus, because the proposed method using different contrast images of MP2RAGE sequence showed the shortest processing time and similar segmentation ability as the other methods, it may be useful for both neuroimaging research and clinical diagnosis.
language: eng
source:
identifier: ISSN: 1932-6203
fulltext: no_fulltext
issn:
  • 1932-6203
  • 1932-6203
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descriptionWe proposed a method for segmentation of brain tissues-gray matter, white matter, and cerebrospinal fluid-using multi-contrast images, including a T1 map and a uniform T1-weighted image, from a magnetization-prepared 2 rapid acquisition gradient echoes (MP2RAGE) sequence at 7 Tesla. The proposed method was evaluated with respect to the processing time and the similarity of the segmented masks of brain tissues with those obtained using FSL, FreeSurfer, and SPM12. The processing time of the proposed method (28 ± 0 s) was significantly shorter than those of FSL and SPM12 (444 ± 4 s and 159 ± 2 s for FSL and SPM12, respectively). In the similarity assessment, the tissue mask of the brain obtained by the proposed method showed higher consistency with those obtained using FSL than with those obtained using SPM12. The proposed method misclassified the subcortical structures and large vessels since it is based on the intensities of multi-contrast images obtained using MP2RAGE, which uses a similar segmentation approach as FSL but is not based on a template image or a parcellated brain atlas, which are used for FreeSurfer and SPM12, respectively. However, the proposed method showed good segmentation in the cerebellum and white matter in the medial part of the brain in comparison with the other methods. Thus, because the proposed method using different contrast images of MP2RAGE sequence showed the shortest processing time and similar segmentation ability as the other methods, it may be useful for both neuroimaging research and clinical diagnosis.
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subjectAdult ; Algorithms ; Analysis ; Anatomy ; Biology and Life Sciences ; Body Fluids ; Brain ; Brain - diagnostic imaging ; Brain Mapping - methods ; Brain research ; Central Nervous System ; Cerebellum ; Cerebral Cortex ; Cerebrospinal Fluid ; Computer and Information Sciences ; Diagnostic Medicine ; Diagnostic Radiology ; Engineering and Technology ; Female ; Gaussian Noise ; Humans ; Image segmentation ; Imaging Techniques ; Imaging, Three-Dimensional ; Magnetic Resonance Imaging ; Male ; Mathematics ; Medicine ; Medicine and Health Sciences ; Middle Aged ; Nervous System ; Neuroimaging ; Neuroscience ; Physical Sciences ; Physiology ; Radiology and Imaging ; Research and Analysis Methods ; Research Article ; Science ; Software Engineering ; Software Tools ; Statistical Noise ; Statistics ; Usage
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notesCompeting Interests: HK and TK are employed by Siemens Healthcare. This does not alter our adherence to PLOS ONE policies on sharing data and materials. Siemens Healthcare did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The other authors have declared that no competing interests exist.
abstractWe proposed a method for segmentation of brain tissues-gray matter, white matter, and cerebrospinal fluid-using multi-contrast images, including a T1 map and a uniform T1-weighted image, from a magnetization-prepared 2 rapid acquisition gradient echoes (MP2RAGE) sequence at 7 Tesla. The proposed method was evaluated with respect to the processing time and the similarity of the segmented masks of brain tissues with those obtained using FSL, FreeSurfer, and SPM12. The processing time of the proposed method (28 ± 0 s) was significantly shorter than those of FSL and SPM12 (444 ± 4 s and 159 ± 2 s for FSL and SPM12, respectively). In the similarity assessment, the tissue mask of the brain obtained by the proposed method showed higher consistency with those obtained using FSL than with those obtained using SPM12. The proposed method misclassified the subcortical structures and large vessels since it is based on the intensities of multi-contrast images obtained using MP2RAGE, which uses a similar segmentation approach as FSL but is not based on a template image or a parcellated brain atlas, which are used for FreeSurfer and SPM12, respectively. However, the proposed method showed good segmentation in the cerebellum and white matter in the medial part of the brain in comparison with the other methods. Thus, because the proposed method using different contrast images of MP2RAGE sequence showed the shortest processing time and similar segmentation ability as the other methods, it may be useful for both neuroimaging research and clinical diagnosis.
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