A diffusion MRI tractography connectome of the mouse brain and comparison with neuronal tracer data
Open accessAbstract
Interest in structural brain connectivity has grown with the understanding that abnormal neural connections may play a role in neurologic and psychiatric diseases. Small animal connectivity mapping techniques are particularly important for identifying aberrant connectivity in disease models. Diffusion magnetic resonance imaging tractography can provide nondestructive, 3D, brain-wide connectivity maps, but has historically been limited by low spatial resolution, low signal-to-noise ratio, and the difficulty in estimating multiple fiber orientations within a single image voxel. Small animal diffusion tractography can be substantially improved through the combination of ex vivo MRI with exogenous contrast agents, advanced diffusion acquisition and reconstruction techniques, and probabilistic fiber tracking. Here, we present a comprehensive, probabilistic tractography connectome of the mouse brain at microscopic resolution, and a comparison of these data with a neuronal tracer-based connectivity data from the Allen Brain Atlas. This work serves as a reference database for future tractography studies in the mouse brain, and demonstrates the fundamental differences between tractography and neuronal tracer data.
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Opting against SIFT2 provides a more direct comparison between our results and similar studies that used Allen tracer data without reference to spatial embedding.
“This also provides a more direct comparison between our results and those of similar studies that have used the Allen tracer data to benchmark tractography performance without reference to the role of spatial embedding (Aydogan et al., 2018; Calabrese et al., 2015; Chen et al., 2015).”
From The role of spatial embedding in mouse brain networks constructed from diffusion tractography and tracer injections (2021) · cites this paper as Calabrese et al., 2015
DTI-based connectomes correspond poorly with neuron tracer data.
“DTI-based connectomes have particular limitations, as they have been shown to correspond poorly with neuron tracer data (Calabrese, Badea, Cofer, Qi, & Johnson, 2015).”
From Functional and structural connectome properties in the 5XFAD transgenic mouse model of Alzheimer’s disease (2018) · cites this paper as Calabrese, Badea, Cofer, Qi, & Johnson, 2015
Structure-function modeling using MRI data suffers from inherent limitations in DWI-tractography that have not been overcome by state-of-the-art acquisition and processing approaches.
“structure-function modeling using MRI data suffers from a number of inherent limitations in DWI-tractography that have not been overcome by state-of-the-art acquisition and processing approaches (Calabrese et al., 2015; Donahue et al., 2016; Reveley et al., 2015; Thomas et al., 2014).”
From Development of large-scale functional networks from birth to adulthood: A guide to the neuroimaging literature (2017) · cites this paper as Calabrese et al., 2015
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- Authors
- Calabrese, E., Badea, A., Cofer, G., Qi, Y., & Johnson, G. A.
- Affiliations
- Duke University (US)
- Corresponding author
- Calabrese, Evan
- Venue
- Cerebral Cortex
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-06-05
- Volume
- 25
- Issue
- 11
- Pages
- 4628-4637
- ISSN
- 1047-3211 (ISSN-L)
- 1460-2199
- PMC
- PMC4715247
- OpenAlex
- W2169239134
- Cited by
- 221
- References
- 45
- Citations by year
- 2026: 11 · 2025: 15 · 2024: 13 · 2023: 17 · 2022: 19 · 2021: 24 · 2020: 29 · 2019: 27 · 2018: 32 · 2017: 17 · 2016: 14 · 2015: 3
- FWCI
- 17.81
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by-nc
- Locations
- Cerebral Cortex (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- DukeSpace (Duke University) (submittedVersion, cc-by-nc-nd)
- Funders
- National Institutes of Health (1s10od010683-01)
- National Institute on Aging (K01AG041211)
- National Institute of Biomedical Imaging and Bioengineering (P41EB015897)
- Topics
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Advanced Neuroimaging Techniques and Applications
- Life Sciences › Neuroscience › Cognitive Neuroscience › Functional Brain Connectivity Studies
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Advanced MRI Techniques and Applications
- Keywords
- diffusion MRI tractography, structural brain connectivity, probabilistic tractography, Allen Brain Atlas, ex vivo MRI, exogenous contrast agents
- MeSH terms
- Animals, Brain, Contrast Media, Image Processing, Computer-Assisted, Male, Mice, Inbred C57BL, Models, Neurological, Neural Pathways, Diffusion Magnetic Resonance Imaging, Mice, Connectome
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