Aggarwal M, Jones MV, Calabresi PA, Mori S, Zhang JY (2012) Probing mouse brain microstructure using oscillating gradient diffusion MRI. Magn Reson Med 67(1):98–109. https://doi.org/10.1002/mrm.22981
Article
PubMed
Google Scholar
Alexander DC, Hubbard PL, Hall MG, Moore EA, Ptito M, Parker GJ, Dyrby TB (2010) Orientationally invariant indices of axon diameter and density from diffusion MRI. Neuroimage 52(4):1374–1389. https://doi.org/10.1016/j.neuroimage.2010.05.043
Article
PubMed
Google Scholar
Alomair OI, Brereton IM, Smith MT, Galloway GJ, Kurniawan ND (2015) In vivo high angular resolution diffusion-weighted imaging of mouse brain at 16.4 Tesla. PLoS One 10(6):e0130133. https://doi.org/10.1371/journal.pone.0130133
CAS
Article
PubMed
PubMed Central
Google Scholar
Anderson C, Gerding WM, Fraenz C, Schluter C, Friedrich P, Raane M, Arning L, Epplen JT, Gunturkun O, Beste C, Genc E, Ocklenburg S (2018) PLP1 and CNTN1 gene variation modulates the microstructure of human white matter in the corpus callosum. Brain Struct Funct 223(8):3875–3887. https://doi.org/10.1007/s00429-018-1729-7
CAS
Article
PubMed
Google Scholar
Assaf Y (2018) Imaging laminar structures in the gray matter with diffusion MRI. Neuroimage 17:31120–31125. https://doi.org/10.1016/j.neuroimage.2017.12.096
Article
Google Scholar
Barazany D, Basser PJ, Assaf Y (2009) In vivo measurement of axon diameter distribution in the corpus callosum of rat brain. Brain 132(Pt 5):1210–1220. https://doi.org/10.1093/brain/awp042
Article
PubMed
PubMed Central
Google Scholar
Barth M, Breuer F, Koopmans PJ, Norris DG, Poser BA (2016) Simultaneous multislice (SMS) imaging techniques. Magn Reson Med 75(1):63–81. https://doi.org/10.1002/mrm.25897
Article
PubMed
Google Scholar
Basser PJ, Mattiello J, LeBihan D (1994) MR diffusion tensor spectroscopy and imaging. Biophys J 66(1):259–267. https://doi.org/10.1016/S0006-3495(94)80775-1
CAS
Article
PubMed
PubMed Central
Google Scholar
Beaujoin J, Palomero-Gallagher N, Boumezbeur F, Axer M, Bernard J, Poupon F, Schmitz D, Mangin JF, Poupon C (2018) Post-mortem inference of the human hippocampal connectivity and microstructure using ultra-high field diffusion MRI at 11.7 T. Brain Struct Funct 223(5):2157–2179. https://doi.org/10.1007/s00429-018-1617-1
Article
PubMed
PubMed Central
Google Scholar
Calabrese E, Badea A, Cofer G, Qi Y, Johnson GA (2015) A diffusion MRI tractography connectome of the mouse brain and comparison with neuronal tracer data. Cereb Cortex 25(11):4628–4637. https://doi.org/10.1093/cercor/bhv121
Article
PubMed
PubMed Central
Google Scholar
Colgan N, Siow B, O’Callaghan JM, Harrison IF, Wells JA, Holmes HE, Ismail O, Richardson S, Alexander DC, Collins EC, Fisher EM, Johnson R, Schwarz AJ, Ahmed Z, O’Neill MJ, Murray TK, Zhang H, Lythgoe MF (2016) Application of neurite orientation dispersion and density imaging (NODDI) to a tau pathology model of Alzheimer’s disease. Neuroimage 125:739–744. https://doi.org/10.1016/j.neuroimage.2015.10.043
CAS
Article
PubMed
Google Scholar
Crombe A, Planche V, Raffard G, Bourel J, Dubourdieu N, Panatier A, Fukutomi H, Dousset V, Oliet S, Hiba B, Tourdias T (2018) Deciphering the microstructure of hippocampal subfields with in vivo DTI and NODDI: applications to experimental multiple sclerosis. Neuroimage 172:357–368. https://doi.org/10.1016/j.neuroimage.2018.01.061
Article
PubMed
Google Scholar
Deshmane A, Gulani V, Griswold MA, Seiberlich N (2012) Parallel MR imaging. J Magn Reson Imaging 36(1):55–72. https://doi.org/10.1002/jmri.23639
Article
PubMed
PubMed Central
Google Scholar
Dhital B, Kellner E, Kiselev VG, Reisert M (2018) The absence of restricted water pool in brain white matter. Neuroimage 182:398–406. https://doi.org/10.1016/j.neuroimage.2017.10.051
Article
PubMed
Google Scholar
Doan V, Kleindienst AM, McMahon EJ, Long BR, Matsushima GK, Taylor LC (2013) Abbreviated exposure to cuprizone is sufficient to induce demyelination and oligodendrocyte loss. J Neurosci Res 91(3):363–373. https://doi.org/10.1002/jnr.23174
CAS
Article
PubMed
Google Scholar
Edwards LJ, Pine KJ, Ellerbrock I, Weiskopf N, Mohammadi S (2017) NODDI-DTI: estimating neurite orientation and dispersion parameters from a diffusion tensor in healthy white matter. Front Neurosci 11:720. https://doi.org/10.3389/fnins.2017.00720
Article
PubMed
PubMed Central
Google Scholar
Genc S, Malpas CB, Ball G, Silk TJ, Seal ML (2018) Age, sex, and puberty related development of the corpus callosum: a multi-technique diffusion MRI study. Brain Struct Funct 223(6):2753–2765. https://doi.org/10.1007/s00429-018-1658-5
Article
PubMed
Google Scholar
Glasser MF, Smith SM, Marcus DS, Andersson JL, Auerbach EJ, Behrens TE, Coalson TS, Harms MP, Jenkinson M, Moeller S, Robinson EC, Sotiropoulos SN, Xu J, Yacoub E, Ugurbil K, Van Essen DC (2016) The human connectome project’s neuroimaging approach. Nat Neurosci 19(9):1175–1187. https://doi.org/10.1038/nn.4361
CAS
Article
PubMed
PubMed Central
Google Scholar
Grussu F, Schneider T, Tur C, Yates RL, Tachrount M, Ianus A, Yiannakas MC, Newcombe J, Zhang H, Alexander DC, DeLuca GC, Gandini Wheeler-Kingshott CAM (2017) Neurite dispersion: a new marker of multiple sclerosis spinal cord pathology? Ann Clin Transl Neurol 4(9):663–679. https://doi.org/10.1002/acn3.445
CAS
Article
PubMed
PubMed Central
Google Scholar
Guglielmetti C, Le Blon D, Santermans E, Salas-Perdomo A, Daans J, De Vocht N, Shah D, Hoornaert C, Praet J, Peerlings J, Kara F, Bigot C, Mai ZH, Goossens H, Hens N, Hendrix S, Verhoye M, Planas AM, Berneman Z, van der Linden A, Ponsaerts P (2016a) Interleukin-13 immune gene therapy prevents CNS inflammation and demyelination via alternative activation of microglia and macrophages. Glia 64(12):2181–2200. https://doi.org/10.1002/glia.23053
Article
PubMed
Google Scholar
Guglielmetti C, Veraart J, Roelant E, Mai Z, Daans J, Van Audekerke J, Naeyaert M, Vanhoutte G, Palacios RDY, Praet J, Fieremans E, Ponsaerts P, Sijbers J, Van der Linden A, Verhoye M (2016b) Diffusion kurtosis imaging probes cortical alterations and white matter pathology following cuprizone induced demyelination and spontaneous remyelination. Neuroimage 125:363–377. https://doi.org/10.1016/j.neuroimage.2015.10.052
CAS
Article
PubMed
Google Scholar
Holdsworth SJ, Skare S, Newbould RD, Guzmann R, Blevins NH, Bammer R (2008) Readout-segmented EPI for rapid high resolution diffusion imaging at 3T. Eur J Radiol 65(1):36–46. https://doi.org/10.1016/j.ejrad.2007.09.016
Article
PubMed
Google Scholar
Hollingsworth KG (2015) Reducing acquisition time in clinical MRI by data undersampling and compressed sensing reconstruction. Phys Med Biol 60(21):R297–R322. https://doi.org/10.1088/0031-9155/60/21/R297
Article
PubMed
Google Scholar
Holz M, Heil SR, Sacco A (2000) Temperature-dependent self-diffusion coefficients of water and six selected molecular liquids for calibration in accurate H-1 NMR PFG measurements. Phys Chem Chem Phys 2(20):4740–4742. https://doi.org/10.1039/b005319h
CAS
Article
Google Scholar
Hutchinson EB, Avram AV, Irfanoglu MO, Koay CG, Barnett AS, Komlosh ME, Ozarslan E, Schwerin SC, Juliano SL, Pierpaoli C (2017) Analysis of the effects of noise, DWI sampling, and value of assumed parameters in diffusion MRI models. Magn Reson Med 78(5):1767–1780. https://doi.org/10.1002/mrm.26575
Article
PubMed
PubMed Central
Google Scholar
Jelescu IO, Veraart J, Adisetiyo V, Milla SS, Novikov DS, Fieremans E (2015) One diffusion acquisition and different white matter models: how does microstructure change in human early development based on WMTI and NODDI? Neuroimage 107:242–256. https://doi.org/10.1016/j.neuroimage.2014.12.009
Article
PubMed
Google Scholar
Jelescu IO, Veraart J, Fieremans E, Novikov DS (2016) Degeneracy in model parameter estimation for multi-compartmental diffusion in neuronal tissue. NMR Biomed 29(1):33–47. https://doi.org/10.1002/nbm.3450
Article
PubMed
Google Scholar
Johnson GA, Calabrese E, Badea A, Paxinos G, Watson C (2012) A multidimensional magnetic resonance histology atlas of the Wistar rat brain. Neuroimage 62(3):1848–1856. https://doi.org/10.1016/j.neuroimage.2012.05.041
Article
PubMed
Google Scholar
Kaden E, Kelm ND, Carson RP, Does MD, Alexander DC (2016) Multi-compartment microscopic diffusion imaging. Neuroimage 139:346–359. https://doi.org/10.1016/j.neuroimage.2016.06.002
Article
PubMed
Google Scholar
Kamagata K, Hatano T, Okuzumi A, Motoi Y, Abe O, Shimoji K, Kamiya K, Suzuki M, Hori M, Kumamaru KK, Hattori N, Aoki S (2016) Neurite orientation dispersion and density imaging in the substantia nigra in idiopathic Parkinson disease. Eur Radiol 26(8):2567–2577. https://doi.org/10.1007/s00330-015-4066-8
Article
PubMed
Google Scholar
Kamagata K, Zalesky A, Hatano T, Ueda R, Di Biase MA, Okuzumi A, Shimoji K, Hori M, Caeyenberghs K, Pantelis C, Hattori N, Aoki S (2017) Gray matter abnormalities in idiopathic parkinson’s disease: evaluation by diffusional kurtosis imaging and neurite orientation dispersion and density imaging. Hum Brain Mapp 38(7):3704–3722. https://doi.org/10.1002/hbm.23628
Article
PubMed
PubMed Central
Google Scholar
Kleinnijenhuis M, Zerbi V, Kusters B, Slump CH, Barth M, van Cappellen van Walsum AM (2013a) Layer-specific diffusion weighted imaging in human primary visual cortex in vitro. Cortex 49(9):2569–2582. https://doi.org/10.1016/j.cortex.2012.11.015
Article
PubMed
Google Scholar
Kleinnijenhuis M, Zhang H, Wiedermann D, Kusters B, Norris D, van Cappellen van Walsum AM (2013b) Detailed laminar characteristics of the human neocortex revealed by NODDI and histology. In: Proceedings 19th Annual Meeting of the OHBM, pp 3815
Koay CG, Ozarslan E, Johnson KM, Meyerand ME (2012) Sparse and optimal acquisition design for diffusion MRI and beyond. Med Phys 39(5):2499–2511. https://doi.org/10.1118/1.3700166
Article
PubMed
PubMed Central
Google Scholar
Lampinen B, Szczepankiewicz F, Martensson J, van Westen D, Sundgren PC, Nilsson M (2017) Neurite density imaging versus imaging of microscopic anisotropy in diffusion MRI: a model comparison using spherical tensor encoding. Neuroimage 147:517–531. https://doi.org/10.1016/j.neuroimage.2016.11.053
Article
PubMed
Google Scholar
Larkman DJ, Nunes RG (2007) Parallel magnetic resonance imaging. Phys Med Biol 52(7):R15–R55. https://doi.org/10.1088/0031-9155/52/7/R01
Article
PubMed
Google Scholar
Le Bihan D, Mangin JF, Poupon C, Clark CA, Pappata S, Molko N, Chabriat H (2001) Diffusion tensor imaging: concepts and applications. J Magn Reson Imaging 13(4):534–546
Article
PubMed
Google Scholar
Lin TH, Chiang CW, Perez-Torres CJ, Sun P, Wallendorf M, Schmidt RE, Cross AH, Song SK (2017) Diffusion MRI quantifies early axonal loss in the presence of nerve swelling. J Neuroinflammation 14:78. https://doi.org/10.1186/s12974-017-0852-3
Article
PubMed
PubMed Central
Google Scholar
Lustig M, Donoho D, Pauly JM (2007) Sparse MRI: the application of compressed sensing for rapid MR imaging. Magn Reson Med 58(6):1182–1195. https://doi.org/10.1002/mrm.21391
Article
PubMed
Google Scholar
Matsushima GK, Morell P (2001) The neurotoxicant, cuprizone, as a model to study demyelination and remyelination in the central nervous system. Brain Pathol 11(1):107–116
CAS
Article
PubMed
Google Scholar
Nikic I, Merkler D, Sorbara C, Brinkoetter M, Kreutzfeldt M, Bareyre FM, Bruck W, Bishop D, Misgeld T, Kerschensteiner M (2011) A reversible form of axon damage in experimental autoimmune encephalomyelitis and multiple sclerosis. Nat Med 17(4):495. https://doi.org/10.1038/nm.2324
CAS
Article
PubMed
Google Scholar
Petiet AE, Kaufman MH, Goddeeris MM, Brandenburg J, Elmore SA, Johnson GA (2008) High-resolution magnetic resonance histology of the embryonic and neonatal mouse: a 4D atlas and morphologic database. Proc Natl Acad Sci USA 105(34):12331–12336. https://doi.org/10.1073/pnas.0805747105
Article
PubMed
PubMed Central
Google Scholar
Rane S, Duong TQ (2011) Comparison of in vivo and ex vivo diffusion tensor imaging in rhesus macaques at short and long diffusion times. Open Neuroimag J 5:172–178. https://doi.org/10.2174/1874440001105010172
Article
PubMed
PubMed Central
Google Scholar
Sato K, Kerever A, Kamagata K, Tsuruta K, Irie R, Tagawa K, Okazawa H, Arikawa-Hirasawa E, Nitta N, Aoki I, Aoki S (2017) Understanding microstructure of the brain by comparison of neurite orientation dispersion and density imaging (NODDI) with transparent mouse brain. Acta Radiol Open 6(4):2058460117703816. https://doi.org/10.1177/2058460117703816
Article
PubMed
PubMed Central
Google Scholar
Schneider T, Brownlee W, Zhang H, Ciccarelli O, Miller DH, Wheeler-Kingshott CG (2017) Sensitivity of multi-shell NODDI to multiple sclerosis white matter changes: a pilot study. Funct Neurol 32(2):97–101
Article
PubMed
PubMed Central
Google Scholar
Sepehrband F, Clark KA, Ullmann JF, Kurniawan ND, Leanage G, Reutens DC, Yang Z (2015) Brain tissue compartment density estimated using diffusion-weighted MRI yields tissue parameters consistent with histology. Hum Brain Mapp 36(9):3687–3702. https://doi.org/10.1002/hbm.22872
Article
PubMed
PubMed Central
Google Scholar
Sepehrband F, Alexander DC, Kurniawan ND, Reutens DC, Yang Z (2016) Towards higher sensitivity and stability of axon diameter estimation with diffusion-weighted MRI. NMR Biomed 29(3):293–308. https://doi.org/10.1002/nbm.3462
Article
PubMed
PubMed Central
Google Scholar
Sepehrband F, O’Brien K, Barth M (2017) A time-efficient acquisition protocol for multipurpose diffusion-weighted microstructural imaging at 7 Tesla. Magn Reson Med 78(6):2170–2184. https://doi.org/10.1002/mrm.26608
CAS
Article
PubMed
Google Scholar
Simons M, Misgeld T, Kerschensteiner M (2014) A unified cell biological perspective on axon-myelin injury. J Cell Biol 206(3):335–345. https://doi.org/10.1083/jcb.201404154
CAS
Article
PubMed
PubMed Central
Google Scholar
Skripuletz T, Lindner M, Kotsiari A, Garde N, Fokuhl J, Linsmeier F, Trebst C, Stangel M (2008) Cortical demyelination is prominent in the murine cuprizone model and is strain-dependent. Am J Pathol 172(4):1053–1061. https://doi.org/10.2353/ajpath.2008.070850
Article
PubMed
PubMed Central
Google Scholar
Stejskal EO, Tanner JE (1965) Spin diffusion measurements: spin echoes in the presence of a time-dependent field gradient. J Chem Phys 42(1):288–292. https://doi.org/10.1063/1.1695690
CAS
Article
Google Scholar
Sun SW, Liang HF, Trinkaus K, Cross AH, Armstrong RC, Song SK (2006) Noninvasive detection of cuprizone induced axonal damage and demyelination in the mouse corpus callosum. Magn Reson Med 55(2):302–308. https://doi.org/10.1002/mrm.20774
Article
PubMed
Google Scholar
Tagge I, O’Connor A, Chaudhary P, Pollaro J, Berlow Y, Chalupsky M, Bourdette D, Woltjer R, Johnson M, Rooney W (2016) Spatio-temporal patterns of demyelination and remyelination in the cuprizone mouse model. PLoS One 11(4):e0152480. https://doi.org/10.1371/journal.pone.0152480
CAS
Article
PubMed
PubMed Central
Google Scholar
Tariq M, Schneider T, Alexander DC, Gandini Wheeler-Kingshott CA, Zhang H (2016) Bingham-NODDI: mapping anisotropic orientation dispersion of neurites using diffusion MRI. Neuroimage 133:207–223. https://doi.org/10.1016/j.neuroimage.2016.01.046
Article
PubMed
Google Scholar
Thiessen JD, Zhang Y, Zhang H, Wang L, Buist R, Del Bigio MR, Kong J, Li XM, Martin M (2013) Quantitative MRI and ultrastructural examination of the cuprizone mouse model of demyelination. NMR Biomed 26(11):1562–1581. https://doi.org/10.1002/nbm.2992
CAS
Article
PubMed
Google Scholar
Vu AT, Auerbach E, Lenglet C, Moeller S, Sotiropoulos SN, Jbabdi S, Andersson J, Yacoub E, Ugurbil K (2015) High resolution whole brain diffusion imaging at 7T for the Human Connectome Project. Neuroimage 122:318–331. https://doi.org/10.1016/j.neuroimage.2015.08.004
CAS
Article
PubMed
Google Scholar
Wang N, Anderson RJ, Badea A, Cofer G, Dibb R, Qi Y, Johnson GA (2018a) Whole mouse brain structural connectomics using magnetic resonance histology. Brain Struct Funct 223(9):4323–4335. https://doi.org/10.1007/s00429-018-1750-x
CAS
Article
PubMed
PubMed Central
Google Scholar
Wang N, Badar F, Xia Y (2018b) Compressed sensing in quantitative determination of GAG concentration in cartilage by microscopic MRI. Magn Reson Med 79(6):3163–3171. https://doi.org/10.1002/mrm.26973
Article
PubMed
Google Scholar
Wang N, Mirando AJ, Cofer G, Qi Y, Hilton MJ, Johnson GA (2019) Diffusion tractography of the rat knee at microscopic resolution. Magn Reson Med 81(6):3775–3786. https://doi.org/10.1002/mrm.27652
Article
PubMed
Google Scholar
Xie M, Tobin JE, Budde MD, Chen CI, Trinkaus K, Cross AH, McDaniel DP, Song SK, Armstrong RC (2010) Rostrocaudal analysis of corpus callosum demyelination and axon damage across disease stages refines diffusion tensor imaging correlations with pathological features. J Neuropathol Exp Neurol 69(7):704–716. https://doi.org/10.1097/NEN.0b013e3181e3de90
Article
PubMed
Google Scholar
Yeh FC, Wedeen VJ, Tseng WY (2011) Estimation of fiber orientation and spin density distribution by diffusion deconvolution. Neuroimage 55(3):1054–1062. https://doi.org/10.1016/j.neuroimage.2010.11.087
Article
PubMed
Google Scholar
Yeh FC, Verstynen TD, Wang Y, Fernandez-Miranda JC, Tseng WY (2013) Deterministic diffusion fiber tracking improved by quantitative anisotropy. PLoS One 8(11):e80713. https://doi.org/10.1371/journal.pone.0080713
CAS
Article
PubMed
PubMed Central
Google Scholar
Zhang H, Hubbard PL, Parker GJ, Alexander DC (2011) Axon diameter mapping in the presence of orientation dispersion with diffusion MRI. Neuroimage 56(3):1301–1315. https://doi.org/10.1016/j.neuroimage.2011.01.084
Article
PubMed
Google Scholar
Zhang H, Schneider T, Wheeler-Kingshott CA, Alexander DC (2012a) NODDI: practical in vivo neurite orientation dispersion and density imaging of the human brain. Neuroimage 61(4):1000–1016. https://doi.org/10.1016/j.neuroimage.2012.03.072
Article
PubMed
Google Scholar
Zhang J, Jones MV, McMahon MT, Mori S, Calabresi PA (2012b) In vivo and ex vivo diffusion tensor imaging of cuprizone-induced demyelination in the mouse corpus callosum. Magn Reson Med 67(3):750–759. https://doi.org/10.1002/mrm.23032
Article
PubMed
Google Scholar
Zolal A, Sames M, Burian M, Novakova M, Malucelli A, Hejcl A, Bartos R, Vachata P, Derner M (2012) The effect of a gadolinium-based contrast agent on diffusion tensor imaging. Eur J Radiol 81(8):1877–1882. https://doi.org/10.1016/j.ejrad.2011.04.074
Article
PubMed
Google Scholar