publication . Article . 2013

aBEAT: A Toolbox for Consistent Analysis of Longitudinal Adult Brain MRI

Laura L. Boles Ponto; Andrew Saykin; li wang; Adrian Preda;
Open Access English
  • Published: 03 Apr 2013 Journal: PLoS ONE (issn: 1932-6203, Copyright policy)
  • Publisher: Public Library of Science (PLoS)
  • Country: Algeria
Abstract
Longitudinal brain image analysis is critical for revealing subtle but complex structural and functional changes of brain during aging or in neurodevelopmental disease. However, even with the rapid increase of clinical research and trials, a software toolbox dedicated for longitudinal image analysis is still lacking publicly. To cater for this increasing need, we have developed a dedicated 4D Adult Brain Extraction and Analysis Toolbox (aBEAT) to provide robust and accurate analysis of the longitudinal adult brain MR images. Specially, a group of image processing tools were integrated into aBEAT, including 4D brain extraction, 4D tissue segmentation, and 4D brai...
Subjects
free text keywords: Medicine, R, Science, Q, General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine
Related Organizations
Funded by
NIH| Alzheimers Disease Neuroimaging Initiative
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1U01AG024904-01
  • Funding stream: NATIONAL INSTITUTE ON AGING
,
NIH| Development and Dissemination of Robust Brain MRI Measurement Tools
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01EB006733-03
  • Funding stream: NATIONAL INSTITUTE OF BIOMEDICAL IMAGING AND BIOENGINEERING
,
NIH| Continued Development of 4-dimensional Image Warping and Registration Software
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1R01EB008374-01A2
  • Funding stream: NATIONAL INSTITUTE OF BIOMEDICAL IMAGING AND BIOENGINEERING
,
CIHR
Project
  • Funder: Canadian Institutes of Health Research (CIHR)
,
NIH| Quantifying Brain Abnormality by Multimodality Neuroimage Analysis
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01AG041721-05
  • Funding stream: NATIONAL INSTITUTE ON AGING
48 references, page 1 of 4

1 Toga AW, Thompson PM (2003) Temporal dynamics of brain anatomy. Annual review of biomedical engineering 5: 119–145.

2 Chetelat G, Landeau B, Eustache F, Mezenge F, Viader F, et al (2005) Using voxel-based morphometry to map the structural changes associated with rapid conversion in MCI: a longitudinal MRI study. Neuroimage 27: 934–946.15979341 [OpenAIRE] [PubMed]

3 Nakamura M, Salisbury DF, Hirayasu Y, Bouix S, Pohl KM, et al (2007) Neocortical gray matter volume in first-episode schizophrenia and first-episode affective psychosis: a cross-sectional and longitudinal MRI study. Biol Psychiatry 62: 773–783.17586477 [OpenAIRE] [PubMed]

4 Thambisetty M, Wan J, Carass A, An Y, Prince JL, et al (2010) Longitudinal changes in cortical thickness associated with normal aging. Neuroimage 52: 1215–1223.20441796 [OpenAIRE] [PubMed]

5 Li Y, Wang Y, Xue Z, Shi F, Lin W, et al (2010) Consistent 4D cortical thickness measurement for longitudinal neuroimaging study. Med Image Comput Comput Assist Interv 13: 133–142.20879308 [OpenAIRE] [PubMed]

6 Li Y, Wang YP, Wu GR, Shi F, Zhou LP, et al.. (2012) Discriminant analysis of longitudinal cortical thickness changes in Alzheimer’s disease using dynamic and network features. Neurobiol ogy Of Aging 33.

7 Eskildsen SF, Coupe P, Fonov V, Manjon JV, Leung KK, et al (2012) BEaST: Brain extraction based on nonlocal segmentation technique. Neuroimage 59: 2362–2373.21945694 [PubMed]

8 Bonne O, Brandes D, Gilboa A, Gomori JM, Shenton ME, et al (2001) Longitudinal MRI study of hippocampal volume in trauma survivors with PTSD. The American journal of psychiatry 158: 1248–1251.11481158 [OpenAIRE] [PubMed]

9 Schuff N, Woerner N, Boreta L, Kornfield T, Shaw LM, et al (2009) MRI of hippocampal volume loss in early Alzheimer’s disease in relation to ApoE genotype and biomarkers. Brain 132: 1067–1077.19251758 [OpenAIRE] [PubMed]

10 Ibanez L, Schroeder W, Ng L, JC (2003) The ITK Software Guide: The Insight Segmentation and Registration Toolkit (version 1.4). Kitware, Inc.

11 Smith SM, Jenkinson M, Woolrich MW, Beckmann CF, Behrens TEJ, et al (2004) Advances in functional and structural MR image analysis and implementation as FSL. Neuroimage 23: S208–S219.15501092 [PubMed]

12 Fischl B, Salat DH, Busa E, Albert M, Dieterich M, et al (2002) Whole brain segmentation: automated labeling of neuroanatomical structures in the human br ain. Neuron 33: 341–355.11832223 [PubMed]

13 Friston K, Ashburner J, Kiebel S, Nichols T, Penny W (2007) Statistical Parametric Mapping: The Analysis of Functional Brain Images. Academic Press.

14 Thompson PM, Hayashi KM, de Zubicaray G, Janke AL, Rose SE, et al (2003) Dynamics of gray matter loss in Alzheimer’s disease. J Neurosci 23: 994–1005.12574429 [OpenAIRE] [PubMed]

15 Shattuck DW, Leahy RM (2001) Automated graph-based analysis and correction of cortical volume topology. Ieee Transactions on Medical Imaging 20: 1167–1177.11700742 [PubMed]

48 references, page 1 of 4
Abstract
Longitudinal brain image analysis is critical for revealing subtle but complex structural and functional changes of brain during aging or in neurodevelopmental disease. However, even with the rapid increase of clinical research and trials, a software toolbox dedicated for longitudinal image analysis is still lacking publicly. To cater for this increasing need, we have developed a dedicated 4D Adult Brain Extraction and Analysis Toolbox (aBEAT) to provide robust and accurate analysis of the longitudinal adult brain MR images. Specially, a group of image processing tools were integrated into aBEAT, including 4D brain extraction, 4D tissue segmentation, and 4D brai...
Subjects
free text keywords: Medicine, R, Science, Q, General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine
Related Organizations
Funded by
NIH| Alzheimers Disease Neuroimaging Initiative
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1U01AG024904-01
  • Funding stream: NATIONAL INSTITUTE ON AGING
,
NIH| Development and Dissemination of Robust Brain MRI Measurement Tools
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01EB006733-03
  • Funding stream: NATIONAL INSTITUTE OF BIOMEDICAL IMAGING AND BIOENGINEERING
,
NIH| Continued Development of 4-dimensional Image Warping and Registration Software
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1R01EB008374-01A2
  • Funding stream: NATIONAL INSTITUTE OF BIOMEDICAL IMAGING AND BIOENGINEERING
,
CIHR
Project
  • Funder: Canadian Institutes of Health Research (CIHR)
,
NIH| Quantifying Brain Abnormality by Multimodality Neuroimage Analysis
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01AG041721-05
  • Funding stream: NATIONAL INSTITUTE ON AGING
48 references, page 1 of 4

1 Toga AW, Thompson PM (2003) Temporal dynamics of brain anatomy. Annual review of biomedical engineering 5: 119–145.

2 Chetelat G, Landeau B, Eustache F, Mezenge F, Viader F, et al (2005) Using voxel-based morphometry to map the structural changes associated with rapid conversion in MCI: a longitudinal MRI study. Neuroimage 27: 934–946.15979341 [OpenAIRE] [PubMed]

3 Nakamura M, Salisbury DF, Hirayasu Y, Bouix S, Pohl KM, et al (2007) Neocortical gray matter volume in first-episode schizophrenia and first-episode affective psychosis: a cross-sectional and longitudinal MRI study. Biol Psychiatry 62: 773–783.17586477 [OpenAIRE] [PubMed]

4 Thambisetty M, Wan J, Carass A, An Y, Prince JL, et al (2010) Longitudinal changes in cortical thickness associated with normal aging. Neuroimage 52: 1215–1223.20441796 [OpenAIRE] [PubMed]

5 Li Y, Wang Y, Xue Z, Shi F, Lin W, et al (2010) Consistent 4D cortical thickness measurement for longitudinal neuroimaging study. Med Image Comput Comput Assist Interv 13: 133–142.20879308 [OpenAIRE] [PubMed]

6 Li Y, Wang YP, Wu GR, Shi F, Zhou LP, et al.. (2012) Discriminant analysis of longitudinal cortical thickness changes in Alzheimer’s disease using dynamic and network features. Neurobiol ogy Of Aging 33.

7 Eskildsen SF, Coupe P, Fonov V, Manjon JV, Leung KK, et al (2012) BEaST: Brain extraction based on nonlocal segmentation technique. Neuroimage 59: 2362–2373.21945694 [PubMed]

8 Bonne O, Brandes D, Gilboa A, Gomori JM, Shenton ME, et al (2001) Longitudinal MRI study of hippocampal volume in trauma survivors with PTSD. The American journal of psychiatry 158: 1248–1251.11481158 [OpenAIRE] [PubMed]

9 Schuff N, Woerner N, Boreta L, Kornfield T, Shaw LM, et al (2009) MRI of hippocampal volume loss in early Alzheimer’s disease in relation to ApoE genotype and biomarkers. Brain 132: 1067–1077.19251758 [OpenAIRE] [PubMed]

10 Ibanez L, Schroeder W, Ng L, JC (2003) The ITK Software Guide: The Insight Segmentation and Registration Toolkit (version 1.4). Kitware, Inc.

11 Smith SM, Jenkinson M, Woolrich MW, Beckmann CF, Behrens TEJ, et al (2004) Advances in functional and structural MR image analysis and implementation as FSL. Neuroimage 23: S208–S219.15501092 [PubMed]

12 Fischl B, Salat DH, Busa E, Albert M, Dieterich M, et al (2002) Whole brain segmentation: automated labeling of neuroanatomical structures in the human br ain. Neuron 33: 341–355.11832223 [PubMed]

13 Friston K, Ashburner J, Kiebel S, Nichols T, Penny W (2007) Statistical Parametric Mapping: The Analysis of Functional Brain Images. Academic Press.

14 Thompson PM, Hayashi KM, de Zubicaray G, Janke AL, Rose SE, et al (2003) Dynamics of gray matter loss in Alzheimer’s disease. J Neurosci 23: 994–1005.12574429 [OpenAIRE] [PubMed]

15 Shattuck DW, Leahy RM (2001) Automated graph-based analysis and correction of cortical volume topology. Ieee Transactions on Medical Imaging 20: 1167–1177.11700742 [PubMed]

48 references, page 1 of 4
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