DOI: 10.1016/j.neuroimage.2008.03.037. High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl/6J mice

High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl/6J mice

10.1016/j.neuroimage.2008.03.037

Crossref journal-article

Elsevier BV

NeuroImage (78)

Bibliography

Dorr, A. E., Lerch, J. P., Spring, S., Kabani, N., & Henkelman, R. M. (2008). High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl/6J mice. NeuroImage, 42(1), 60â69.

Authors 5

A.E. Dorr (first)
J.P. Lerch (additional)
S. Spring (additional)
N. Kabani (additional)
R.M. Henkelman (additional)

References 29 Referenced 471

A.I.B.S., Allen Brain Atlas Internet — www.brain-map.org.
10.1016/j.neuroimage.2005.04.017 / NeuroImage / Automated segmentation of neuroanatomical structures in multispectral MR microscopy of the mouse brain by Ali (2005)
10.1002/nbm.1167 / NMR Biomed. / MRI of mouse models of neurological disorders by Anderson (2007)
10.1016/j.neuroimage.2007.05.046 / NeuroImage / Morphometric analysis of the C57BL/6J mouse brain by Badea (2007)
10.1016/j.neuroimage.2006.09.053 / NeuroImage / Neuroanatomical phenotypes in the reeler mouse by Badea (2007)
10.1016/S1474-4422(06)70472-0 / Lancet Neurol. / Translational neuroscience and magnetic-resonance microscopy by Benveniste (2006)
10.1523/JNEUROSCI.5438-05.2006 / J. Neurosci. / In vivo magnetic resonance imaging and semiautomated image analysis extend the brain phenotype for cdf/cdf mice by Bock (2006)
10.1006/nimg.1995.1009 / NeuroImage / NeuroNames Brain Hierarchy by Bowden (1995)
10.1016/j.neuroimage.2005.07.008 / NeuroImage / Neuroanatomical differences between mouse strains as shown by high-resolution 3D MRI by Chen (2006)
10.1097/00004728-199403000-00005 / J. Comput. Assist. Tomogr. / Automatic 3D intersubject registration of MR volumetric data in standardized Talairach space by Collins (1994)
{'key': '10.1016/j.neuroimage.2008.03.037_bib11', 'series-title': 'The Allen Reference Atlas: a Digital Colour Brain Atlas of C57BL/6J Male Mouse', 'author': 'Dong', 'year': '2008'} / The Allen Reference Atlas: a Digital Colour Brain Atlas of C57BL/6J Male Mouse by Dong (2008)
10.1016/j.neuroimage.2006.12.040 / NeuroImage / Three-dimensional cerebral vasculature of the CBA mouse brain: a magnetic resonance imaging and micro computed tomography study by Dorr (2007)
{'key': '10.1016/j.neuroimage.2008.03.037_bib13', 'series-title': 'Comparative cytoarchitectonic atlas of the C57BL/6 and 129/Sv mouse brains', 'author': 'Hof', 'year': '2000'} / Comparative cytoarchitectonic atlas of the C57BL/6 and 129/Sv mouse brains by Hof (2000)
10.1016/j.jneumeth.2006.02.020 / J. Neurosci. Methods / 3D volume reconstruction of a mouse brain from histological sections using warp filtering by Ju (2006)
Kale, S.C., Lerch, J.P., Henkelman, R.M., Chen, X.J., in press. Optimization of the SNR-resolution tradeoff for registration of magnetic resonance images. Hum. Brain Mapp. doi:10.1002/hbm.20453. (10.1002/hbm.20453)
10.1093/cercor/bhh165 / Cereb. Cortex / A three-dimensional MRI atlas of the mouse brain with estimates of the average and variability by Kovacevic (2005)
10.1007/s00429-005-0048-y / Anat. Embryol. (Berl.) / Standard atlas space for C57BL/6J neonatal mouse brain by Lee (2005)
10.1038/nature05453 / Nature / Genome-wide atlas of gene expression in the adult mouse brain by Lein (2007)
10.1016/j.neuroscience.2005.07.014 / Neuroscience / A three-dimensional digital atlas database of the adult C57BL/6J mouse brain by magnetic resonance microscopy by Ma (2005)
10.1111/j.1469-7580.2004.00264.x / J. Anat. / A multimodal, multidimensional atlas of the C57BL/6J mouse brain by MacKenzie-Graham (2004)
10.1002/nbm.981 / NMR Biomed. / Magnetic resonance imaging for detection and analysis of mouse phenotypes by Nieman (2005)
{'key': '10.1016/j.neuroimage.2008.03.037_bib22', 'series-title': 'The Mouse Brain in Stereotaxic Coordinates', 'author': 'Paxinos', 'year': '2001'} / The Mouse Brain in Stereotaxic Coordinates by Paxinos (2001)
10.1073/pnas.242746599 / Proc. Natl. Acad. Sci. U. S. A. / Dentate gyrus volume is reduced before onset of plaque formation in PDAPP mice: a magnetic resonance microscopy and stereologic analysis by Redwine (2003)
10.1016/j.neuroimage.2006.04.214 / NeuroImage / A stereotaxic MRI template set for the rat brain with tissue class distribution maps and co-registered anatomical atlas: application to pharmacological MRI by Schwarz (2006)
10.1016/j.neuroimage.2007.08.028 / NeuroImage / Automated segmentation of the actively stained mouse brain using multi-spectral MR microscopy by Sharief (2008)
10.1109/42.668698 / IEEE Trans. Med. Imag. / A nonparametric method for automatic correction of intensity nonuniformity in MRI data by Sled (1998)
10.1016/j.neuroimage.2007.02.023 / NeuroImage / Sexual dimorphism revealed in the structure of the mouse brain using three-dimensional magnetic resonance imaging by Spring (2007)
{'key': '10.1016/j.neuroimage.2008.03.037_bib28', 'series-title': 'Brain Maps: Structure of the Rat Brain', 'author': 'Swanson', 'year': '2004'} / Brain Maps: Structure of the Rat Brain by Swanson (2004)
10.1016/j.neuroimage.2005.08.037 / NeuroImage / Statistical diffusion tensor histology reveals regional dysmyelination effects in the shiverer mouse mutant by Tyszka (2006)

Dates

Type	When
Created	17 years, 4 months ago (April 9, 2008, 10:02 a.m.)
Deposited	6 years, 3 months ago (May 9, 2019, 9:48 p.m.)
Indexed	3 days, 12 hours ago (Aug. 27, 2025, 11:32 a.m.)
Issued	17 years ago (Aug. 1, 2008)
Published	17 years ago (Aug. 1, 2008)
Published Print	17 years ago (Aug. 1, 2008)

Funders 0

None

BibTeX

@article{Dorr_2008, title={High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl/6J mice}, volume={42}, ISSN={1053-8119}, url={http://dx.doi.org/10.1016/j.neuroimage.2008.03.037}, DOI={10.1016/j.neuroimage.2008.03.037}, number={1}, journal={NeuroImage}, publisher={Elsevier BV}, author={Dorr, A.E. and Lerch, J.P. and Spring, S. and Kabani, N. and Henkelman, R.M.}, year={2008}, month=aug, pages={60–69} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        8,
        27
      ]
    ],
    "date-time": "2025-08-27T15:32:08Z",
    "timestamp": 1756308728258
  },
  "reference-count": 29,
  "publisher": "Elsevier BV",
  "issue": "1",
  "license": [
    {
      "start": {
        "date-parts": [
          [
            2008,
            8,
            1
          ]
        ],
        "date-time": "2008-08-01T00:00:00Z",
        "timestamp": 1217548800000
      },
      "content-version": "tdm",
      "delay-in-days": 0,
      "URL": "https://www.elsevier.com/tdm/userlicense/1.0/"
    }
  ],
  "content-domain": {
    "domain": [],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        2008,
        8
      ]
    ]
  },
  "DOI": "10.1016/j.neuroimage.2008.03.037",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2008,
        4,
        9
      ]
    ],
    "date-time": "2008-04-09T14:02:25Z",
    "timestamp": 1207749745000
  },
  "page": "60-69",
  "source": "Crossref",
  "is-referenced-by-count": 471,
  "title": "High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl/6J mice",
  "prefix": "10.1016",
  "volume": "42",
  "author": [
    {
      "given": "A.E.",
      "family": "Dorr",
      "sequence": "first",
      "affiliation": []
    },
    {
      "given": "J.P.",
      "family": "Lerch",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "S.",
      "family": "Spring",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "N.",
      "family": "Kabani",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "R.M.",
      "family": "Henkelman",
      "sequence": "additional",
      "affiliation": []
    }
  ],
  "member": "78",
  "reference": [
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib1",
      "unstructured": "A.I.B.S., Allen Brain Atlas Internet \u2014 www.brain-map.org."
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib2",
      "doi-asserted-by": "crossref",
      "first-page": "425",
      "DOI": "10.1016/j.neuroimage.2005.04.017",
      "article-title": "Automated segmentation of neuroanatomical structures in multispectral MR microscopy of the mouse brain",
      "volume": "27",
      "author": "Ali",
      "year": "2005",
      "journal-title": "NeuroImage"
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib3",
      "doi-asserted-by": "crossref",
      "first-page": "200",
      "DOI": "10.1002/nbm.1167",
      "article-title": "MRI of mouse models of neurological disorders",
      "volume": "20",
      "author": "Anderson",
      "year": "2007",
      "journal-title": "NMR Biomed."
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib4",
      "doi-asserted-by": "crossref",
      "first-page": "683",
      "DOI": "10.1016/j.neuroimage.2007.05.046",
      "article-title": "Morphometric analysis of the C57BL/6J mouse brain",
      "volume": "37",
      "author": "Badea",
      "year": "2007",
      "journal-title": "NeuroImage"
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib5",
      "doi-asserted-by": "crossref",
      "first-page": "1363",
      "DOI": "10.1016/j.neuroimage.2006.09.053",
      "article-title": "Neuroanatomical phenotypes in the reeler mouse",
      "volume": "34",
      "author": "Badea",
      "year": "2007",
      "journal-title": "NeuroImage"
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib6",
      "doi-asserted-by": "crossref",
      "first-page": "536",
      "DOI": "10.1016/S1474-4422(06)70472-0",
      "article-title": "Translational neuroscience and magnetic-resonance microscopy",
      "volume": "5",
      "author": "Benveniste",
      "year": "2006",
      "journal-title": "Lancet Neurol."
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib7",
      "doi-asserted-by": "crossref",
      "first-page": "4455",
      "DOI": "10.1523/JNEUROSCI.5438-05.2006",
      "article-title": "In vivo magnetic resonance imaging and semiautomated image analysis extend the brain phenotype for cdf/cdf mice",
      "volume": "26",
      "author": "Bock",
      "year": "2006",
      "journal-title": "J. Neurosci."
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib8",
      "doi-asserted-by": "crossref",
      "first-page": "63",
      "DOI": "10.1006/nimg.1995.1009",
      "article-title": "NeuroNames Brain Hierarchy",
      "volume": "2",
      "author": "Bowden",
      "year": "1995",
      "journal-title": "NeuroImage"
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib9",
      "doi-asserted-by": "crossref",
      "first-page": "99",
      "DOI": "10.1016/j.neuroimage.2005.07.008",
      "article-title": "Neuroanatomical differences between mouse strains as shown by high-resolution 3D MRI",
      "volume": "29",
      "author": "Chen",
      "year": "2006",
      "journal-title": "NeuroImage"
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib10",
      "doi-asserted-by": "crossref",
      "first-page": "192",
      "DOI": "10.1097/00004728-199403000-00005",
      "article-title": "Automatic 3D intersubject registration of MR volumetric data in standardized Talairach space",
      "volume": "18",
      "author": "Collins",
      "year": "1994",
      "journal-title": "J. Comput. Assist. Tomogr."
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib11",
      "series-title": "The Allen Reference Atlas: a Digital Colour Brain Atlas of C57BL/6J Male Mouse",
      "author": "Dong",
      "year": "2008"
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib12",
      "doi-asserted-by": "crossref",
      "first-page": "1409",
      "DOI": "10.1016/j.neuroimage.2006.12.040",
      "article-title": "Three-dimensional cerebral vasculature of the CBA mouse brain: a magnetic resonance imaging and micro computed tomography study",
      "volume": "35",
      "author": "Dorr",
      "year": "2007",
      "journal-title": "NeuroImage"
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib13",
      "series-title": "Comparative cytoarchitectonic atlas of the C57BL/6 and 129/Sv mouse brains",
      "author": "Hof",
      "year": "2000"
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib14",
      "doi-asserted-by": "crossref",
      "first-page": "84",
      "DOI": "10.1016/j.jneumeth.2006.02.020",
      "article-title": "3D volume reconstruction of a mouse brain from histological sections using warp filtering",
      "volume": "156",
      "author": "Ju",
      "year": "2006",
      "journal-title": "J. Neurosci. Methods"
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib15",
      "doi-asserted-by": "crossref",
      "unstructured": "Kale, S.C., Lerch, J.P., Henkelman, R.M., Chen, X.J., in press. Optimization of the SNR-resolution tradeoff for registration of magnetic resonance images. Hum. Brain Mapp. doi:10.1002/hbm.20453.",
      "DOI": "10.1002/hbm.20453"
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib16",
      "doi-asserted-by": "crossref",
      "first-page": "639",
      "DOI": "10.1093/cercor/bhh165",
      "article-title": "A three-dimensional MRI atlas of the mouse brain with estimates of the average and variability",
      "volume": "15",
      "author": "Kovacevic",
      "year": "2005",
      "journal-title": "Cereb. Cortex"
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib17",
      "doi-asserted-by": "crossref",
      "first-page": "245",
      "DOI": "10.1007/s00429-005-0048-y",
      "article-title": "Standard atlas space for C57BL/6J neonatal mouse brain",
      "volume": "210",
      "author": "Lee",
      "year": "2005",
      "journal-title": "Anat. Embryol. (Berl.)"
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib18",
      "doi-asserted-by": "crossref",
      "first-page": "168",
      "DOI": "10.1038/nature05453",
      "article-title": "Genome-wide atlas of gene expression in the adult mouse brain",
      "volume": "445",
      "author": "Lein",
      "year": "2007",
      "journal-title": "Nature"
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib19",
      "doi-asserted-by": "crossref",
      "first-page": "1203",
      "DOI": "10.1016/j.neuroscience.2005.07.014",
      "article-title": "A three-dimensional digital atlas database of the adult C57BL/6J mouse brain by magnetic resonance microscopy",
      "volume": "135",
      "author": "Ma",
      "year": "2005",
      "journal-title": "Neuroscience"
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib20",
      "doi-asserted-by": "crossref",
      "first-page": "93",
      "DOI": "10.1111/j.1469-7580.2004.00264.x",
      "article-title": "A multimodal, multidimensional atlas of the C57BL/6J mouse brain",
      "volume": "204",
      "author": "MacKenzie-Graham",
      "year": "2004",
      "journal-title": "J. Anat."
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib21",
      "doi-asserted-by": "crossref",
      "first-page": "447",
      "DOI": "10.1002/nbm.981",
      "article-title": "Magnetic resonance imaging for detection and analysis of mouse phenotypes",
      "volume": "18",
      "author": "Nieman",
      "year": "2005",
      "journal-title": "NMR Biomed."
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib22",
      "series-title": "The Mouse Brain in Stereotaxic Coordinates",
      "author": "Paxinos",
      "year": "2001"
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib23",
      "doi-asserted-by": "crossref",
      "first-page": "1381",
      "DOI": "10.1073/pnas.242746599",
      "article-title": "Dentate gyrus volume is reduced before onset of plaque formation in PDAPP mice: a magnetic resonance microscopy and stereologic analysis",
      "volume": "100",
      "author": "Redwine",
      "year": "2003",
      "journal-title": "Proc. Natl. Acad. Sci. U. S. A."
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib24",
      "doi-asserted-by": "crossref",
      "first-page": "538",
      "DOI": "10.1016/j.neuroimage.2006.04.214",
      "article-title": "A stereotaxic MRI template set for the rat brain with tissue class distribution maps and co-registered anatomical atlas: application to pharmacological MRI",
      "volume": "32",
      "author": "Schwarz",
      "year": "2006",
      "journal-title": "NeuroImage"
    },
    {
      "issue": "1",
      "key": "10.1016/j.neuroimage.2008.03.037_bib25",
      "doi-asserted-by": "crossref",
      "first-page": "136",
      "DOI": "10.1016/j.neuroimage.2007.08.028",
      "article-title": "Automated segmentation of the actively stained mouse brain using multi-spectral MR microscopy",
      "volume": "39",
      "author": "Sharief",
      "year": "2008",
      "journal-title": "NeuroImage"
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib26",
      "doi-asserted-by": "crossref",
      "first-page": "87",
      "DOI": "10.1109/42.668698",
      "article-title": "A nonparametric method for automatic correction of intensity nonuniformity in MRI data",
      "volume": "17",
      "author": "Sled",
      "year": "1998",
      "journal-title": "IEEE Trans. Med. Imag."
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib27",
      "doi-asserted-by": "crossref",
      "first-page": "1424",
      "DOI": "10.1016/j.neuroimage.2007.02.023",
      "article-title": "Sexual dimorphism revealed in the structure of the mouse brain using three-dimensional magnetic resonance imaging",
      "volume": "35",
      "author": "Spring",
      "year": "2007",
      "journal-title": "NeuroImage"
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib28",
      "series-title": "Brain Maps: Structure of the Rat Brain",
      "author": "Swanson",
      "year": "2004"
    },
    {
      "key": "10.1016/j.neuroimage.2008.03.037_bib29",
      "doi-asserted-by": "crossref",
      "first-page": "1058",
      "DOI": "10.1016/j.neuroimage.2005.08.037",
      "article-title": "Statistical diffusion tensor histology reveals regional dysmyelination effects in the shiverer mouse mutant",
      "volume": "29",
      "author": "Tyszka",
      "year": "2006",
      "journal-title": "NeuroImage"
    }
  ],
  "container-title": "NeuroImage",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://api.elsevier.com/content/article/PII:S1053811908002504?httpAccept=text/xml",
      "content-type": "text/xml",
      "content-version": "vor",
      "intended-application": "text-mining"
    },
    {
      "URL": "https://api.elsevier.com/content/article/PII:S1053811908002504?httpAccept=text/plain",
      "content-type": "text/plain",
      "content-version": "vor",
      "intended-application": "text-mining"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2019,
        5,
        10
      ]
    ],
    "date-time": "2019-05-10T01:48:39Z",
    "timestamp": 1557452919000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://linkinghub.elsevier.com/retrieve/pii/S1053811908002504"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2008,
        8
      ]
    ]
  },
  "references-count": 29,
  "journal-issue": {
    "issue": "1",
    "published-print": {
      "date-parts": [
        [
          2008,
          8
        ]
      ]
    }
  },
  "alternative-id": [
    "S1053811908002504"
  ],
  "URL": "http://dx.doi.org/10.1016/j.neuroimage.2008.03.037",
  "relation": {},
  "ISSN": [
    "1053-8119"
  ],
  "subject": [],
  "container-title-short": "NeuroImage",
  "published": {
    "date-parts": [
      [
        2008,
        8
      ]
    ]
  }
}