My Bibliography

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Hoffmann M. Domain-Randomized Deep Learning for Neuroimage Analysis: Selecting Training Strategies, Navigating Challenges, and Maximizing Benefits. IEEE Signal Process Mag. 2025 Jul;42(4):78-90. doi: 10.1109/MSP.2025.3590806. Epub 2025 Nov 24. PubMed PMID: 41306561; PubMed Central PMCID: PMC12646568.

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Tian Q, Ngamsombat C, Lee HH, Berger DR, Wu Y, Fan Q, Bilgic B, Li Z, Novikov DS, Fieremans E, Rosen BR, Lichtman JW, Huang SY. Quantifying axonal features of human superficial white matter from three-dimensional multibeam serial electron microscopy data assisted by deep learning. Neuroimage. 2025 Jun;313:121212. doi: 10.1016/j.neuroimage.2025.121212. Epub 2025 Apr 11. PubMed PMID: 40222502; PubMed Central PMCID: PMC12312701.

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Fu J, Dalca AV, Fischl B, Moreno R, Hoffmann M. LEARNING ACCURATE RIGID REGISTRATION FOR LONGITUDINAL BRAIN MRI FROM SYNTHETIC DATA. Proc IEEE Int Symp Biomed Imaging. 2025 Apr;2025. doi: 10.1109/isbi60581.2025.10980859. Epub 2025 May 12. PubMed PMID: 40630833; PubMed Central PMCID: PMC12237398.

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Lee H, Lee HH, Ma Y, Eskandarian L, Gaudet K, Tian Q, Krijnen EA, Russo AW, Salat DH, Klawiter EC, Huang SY. Age-related alterations in human cortical microstructure across the lifespan: Insights from high-gradient diffusion MRI. Aging Cell. 2024 Nov;23(11):e14267. doi: 10.1111/acel.14267. Epub 2024 Aug 8. PubMed PMID: 39118344; PubMed Central PMCID: PMC11561659.

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Rose PC, Davies C, Cotton MF, Otwombe K, Browne SH, Vaida F, Innes S, Nel ER. Longitudinal controlled attenuation parameter and liver stiffness in children with and without perinatal HIV infection in South Africa. AIDS. 2024 Sep 1;38(11):1638-1647. doi: 10.1097/QAD.0000000000003964. Epub 2024 Jun 20. PubMed PMID: 38905492; PubMed Central PMCID: PMC11317452.

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Fan J, Woods KJ, Jacobson JL, Taylor PA, Toich JTF, Molteno CD, Jacobson SW, Meintjes EM. Lower resting state functional connectivity partially mediates adverse effects of prenatal alcohol exposure on arithmetic performance in children. Alcohol Clin Exp Res (Hoboken). 2024 Jun;48(6):1050-1062. doi: 10.1111/acer.15332. Epub 2024 May 2. PubMed PMID: 38697927; PubMed Central PMCID: PMC11998671.

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Kelley W, Ngo N, Dalca AV, Fischl B, Zöllei L, Hoffmann M. BOOSTING SKULL-STRIPPING PERFORMANCE FOR PEDIATRIC BRAIN IMAGES. Proc IEEE Int Symp Biomed Imaging. 2024 May;2024. doi: 10.1109/isbi56570.2024.10635307. Epub 2024 Aug 22. PubMed PMID: 39371473; PubMed Central PMCID: PMC11451993.

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Madzime J, Jankiewicz M, Meintjes EM, Torre P 3rd, Laughton B, van der Kouwe AJW, Holmes M. Reduced white matter maturation in the central auditory system of children living with HIV. Front Neuroimaging. 2024;3:1341607. doi: 10.3389/fnimg.2024.1341607. eCollection 2024. PubMed PMID: 38510428; PubMed Central PMCID: PMC10951401.

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Mudra Rakshasa-Loots A, Naidoo S, Hamana T, Fanqa B, van Wyhe KS, Lindani F, van der Kouwe AJW, Glashoff R, Kruger S, Robertson F, Cox SR, Meintjes EM, Laughton B. Multi-modal analysis of inflammation as a potential mediator of depressive symptoms in young people with HIV: The GOLD depression study. PLoS One. 2024;19(2):e0298787. doi: 10.1371/journal.pone.0298787. eCollection 2024. PubMed PMID: 38386679; PubMed Central PMCID: PMC10883559.

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Lee HH, Tian Q, Sheft M, Coronado-Leija R, Ramos-Llorden G, Abdollahzadeh A, Fieremans E, Novikov DS, Huang SY. The effects of axonal beading and undulation on axonal diameter estimation from diffusion MRI: Insights from simulations in human axons segmented from three-dimensional electron microscopy. NMR Biomed. 2024 Apr;37(4):e5087. doi: 10.1002/nbm.5087. Epub 2024 Jan 2. PubMed PMID: 38168082; PubMed Central PMCID: PMC10942763.

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Levitt J, van der Kouwe A, Jeong H, Lewis LD, Bonmassar G. The MotoNet: A 3 Tesla MRI-Conditional EEG Net with Embedded Motion Sensors. Sensors (Basel). 2023 Mar 28;23(7). doi: 10.3390/s23073539. PubMed PMID: 37050598; PubMed Central PMCID: PMC10098760.

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Nwosu EC, Holmes MJ, Cotton MF, Dobbels E, Little F, Laughton B, van der Kouwe A, Robertson F, Meintjes EM. Similar cortical morphometry trajectories from 5 to 9 years in children with perinatal HIV who started treatment before age 2 years and uninfected controls. BMC Neurosci. 2023 Feb 24;24(1):15. doi: 10.1186/s12868-023-00783-7. PubMed PMID: 36829110; PubMed Central PMCID: PMC9951512.

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Rakshasa-Loots AM, Hamana T, Fanqa B, Lindani F, van Wyhe K, Kruger S, Laughton B. isiXhosa translation of the Patient Health Questionnaire (PHQ-9) shows satisfactory psychometric properties for the measurement of depressive symptoms [Stage 2]. Brain Neurosci Adv. 2023 Jan-Dec;7:23982128231194452. doi: 10.1177/23982128231194452. eCollection 2023 Jan-Dec. PubMed PMID: 37667732; PubMed Central PMCID: PMC10475240.

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Yen YF, Stupic KF, Janicke MT, Greve DN, Mareyam A, Stockmann J, Polimeni JR, van der Kouwe A, Keenan KE. T1 relaxation time of ISMRM/NIST T1 phantom spheres at 7 T. NMR Biomed. 2023 May;36(5):e4873. doi: 10.1002/nbm.4873. Epub 2022 Nov 23. PubMed PMID: 36347826.

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Shiohama T, Stewart N, Nangaku M, van der Kouwe AJW, Takahashi E. Identification of association fibers using ex vivo diffusion tractography in Alexander disease brains. J Neuroimaging. 2022 Sep;32(5):866-874. doi: 10.1111/jon.13040. Epub 2022 Aug 19. PubMed PMID: 35983725; PubMed Central PMCID: PMC9474676.

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Rose PC, Nel ED, Cotton MF, Pitcher RD, Otwombe K, Browne SH, Innes S. Prevalence and Risk Factors for Hepatic Steatosis in Children With Perinatal HIV on Early Antiretroviral Therapy Compared to HIV-Exposed Uninfected and HIV-Unexposed Children. Front Pediatr. 2022;10:893579. doi: 10.3389/fped.2022.893579. eCollection 2022. PubMed PMID: 35757117; PubMed Central PMCID: PMC9218275.

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Bayih SG, Jankiewicz M, Alhamud A, van der Kouwe AJW, Meintjes EM. Self-navigated prospective motion correction for 3D-EPI acquisition. Magn Reson Med. 2022 Jul;88(1):211-223. doi: 10.1002/mrm.29202. Epub 2022 Mar 28. PubMed PMID: 35344618.

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Pollatou A, Filippi CA, Aydin E, Vaughn K, Thompson D, Korom M, Dufford AJ, Howell B, Zöllei L, Martino AD, Graham A, Scheinost D, Spann MN. An ode to fetal, infant, and toddler neuroimaging: Chronicling early clinical to research applications with MRI, and an introduction to an academic society connecting the field. Dev Cogn Neurosci. 2022 Apr;54:101083. doi: 10.1016/j.dcn.2022.101083. Epub 2022 Feb 7. Review. PubMed PMID: 35184026; PubMed Central PMCID: PMC8861425.

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Gagoski B, Xu J, Wighton P, Tisdall MD, Frost R, Lo WC, Golland P, van der Kouwe A, Adalsteinsson E, Grant PE. Automated detection and reacquisition of motion-degraded images in fetal HASTE imaging at 3 T. Magn Reson Med. 2022 Apr;87(4):1914-1922. doi: 10.1002/mrm.29106. Epub 2021 Dec 10. PubMed PMID: 34888942; PubMed Central PMCID: PMC8810713.

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Strasser B, Arango NS, Stockmann JP, Gagoski B, Thapa B, Li X, Bogner W, Moser P, Small J, Cahill DP, Batchelor TT, Dietrich J, van der Kouwe A, White J, Adalsteinsson E, Andronesi OC. Improving D-2-hydroxyglutarate MR spectroscopic imaging in mutant isocitrate dehydrogenase glioma patients with multiplexed RF-receive/B(0) -shim array coils at 3 T. NMR Biomed. 2022 Jan;35(1):e4621. doi: 10.1002/nbm.4621. Epub 2021 Oct 5. PubMed PMID: 34609036; PubMed Central PMCID: PMC8717863.

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Slipsager JM, Glimberg SL, Højgaard L, Paulsen RR, Wighton P, Tisdall MD, Jaimes C, Gagoski BA, Grant PE, van der Kouwe A, Olesen OV, Frost R. Comparison of prospective and retrospective motion correction in 3D-encoded neuroanatomical MRI. Magn Reson Med. 2022 Feb;87(2):629-645. doi: 10.1002/mrm.28991. Epub 2021 Sep 7. PubMed PMID: 34490929; PubMed Central PMCID: PMC8635810.

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Madzime J, Holmes M, Cotton MF, Laughton B, van der Kouwe AJW, Meintjes EM, Jankiewicz M. Altered White Matter Tracts in the Somatosensory, Salience, Motor, and Default Mode Networks in 7-Year-Old Children Living with Human Immunodeficiency Virus: A Tractographic Analysis. Brain Connect. 2022 May;12(4):302-319. doi: 10.1089/brain.2020.0948. Epub 2021 Aug 23. PubMed PMID: 34107770; PubMed Central PMCID: PMC9131360.

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Warton FL, Molteno CD, Warton CMR, Wintermark P, Lindinger NM, Dodge NC, Zöllei L, van der Kouwe AJW, Carter RC, Jacobson JL, Jacobson SW, Meintjes EM. Maternal choline supplementation mitigates alcohol exposure effects on neonatal brain volumes. Alcohol Clin Exp Res. 2021 Sep;45(9):1762-1774. doi: 10.1111/acer.14672. Epub 2021 Aug 18. PubMed PMID: 34342017; PubMed Central PMCID: PMC8526390.

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van Wyhe KS, Laughton B, Cotton MF, Meintjes EM, van der Kouwe AJ, Boivin MJ, Kidd M, Thomas KG. Cognitive outcomes at ages seven and nine years in South African children from the children with HIV early antiretroviral (CHER) trial: a longitudinal investigation. J Int AIDS Soc. 2021 Jul;24(7):e25734. doi: 10.1002/jia2.25734. PubMed PMID: 34259393; PubMed Central PMCID: PMC8278859.

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van Biljon N, Robertson F, Holmes M, Cotton MF, Laughton B, van der Kouwe A, Meintjes E, Little F. Multivariate approach for longitudinal analysis of brain metabolite levels from ages 5-11 years in children with perinatal HIV infection. Neuroimage. 2021 Aug 15;237:118101. doi: 10.1016/j.neuroimage.2021.118101. Epub 2021 May 4. PubMed PMID: 33961998; PubMed Central PMCID: PMC8295244.

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Hoffmann M, Moyer DC, Zhang L, Golland P, Gagoski B, Grant PE, van der Kouwe AJ. Learning-based automatic field-of-view positioning for fetal-brain MRI. Proc Int Soc Magn Reson Med Sci Meet Exhib Int Soc Magn Reson Med Sci Meet Exhib. 2021 May;29. PubMed PMID: 36284600; PubMed Central PMCID: PMC9592155.

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Hoffmann M, Turk EA, Gagoski B, Morgan L, Wighton P, Tisdall MD, Reuter M, Adalsteinsson E, Grant PE, Wald LL, van der Kouwe AJW. Rapid head-pose detection for automated slice prescription of fetal-brain MRI. Int J Imaging Syst Technol. 2021 Sep;31(3):1136-1154. doi: 10.1002/ima.22563. Epub 2021 Mar 1. PubMed PMID: 34421216; PubMed Central PMCID: PMC8372849.

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Graham AS, Holmes MJ, Little F, Dobbels E, Cotton MF, Laughton B, van der Kouwe A, Meintjes EM, Robertson FC. MRS suggests multi-regional inflammation and white matter axonal damage at 11 years following perinatal HIV infection. Neuroimage Clin. 2020;28:102505. doi: 10.1016/j.nicl.2020.102505. Epub 2020 Nov 19. PubMed PMID: 33395994; PubMed Central PMCID: PMC7721646.

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Warton FL, Taylor PA, Warton CMR, Molteno CD, Wintermark P, Zöllei L, van der Kouwe AJ, Jacobson JL, Jacobson SW, Meintjes EM. Reduced fractional anisotropy in projection, association, and commissural fiber networks in neonates with prenatal methamphetamine exposure. Dev Neurobiol. 2020 Nov;80(11-12):381-398. doi: 10.1002/dneu.22784. Epub 2020 Oct 27. PubMed PMID: 33010114; PubMed Central PMCID: PMC7855045.

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Esmaeili M, Stockmann J, Strasser B, Arango N, Thapa B, Wang Z, van der Kouwe A, Dietrich J, Cahill DP, Batchelor TT, White J, Adalsteinsson E, Wald L, Andronesi OC. An integrated RF-receive/B(0)-shim array coil boosts performance of whole-brain MR spectroscopic imaging at 7 T. Sci Rep. 2020 Sep 14;10(1):15029. doi: 10.1038/s41598-020-71623-5. PubMed PMID: 32929121; PubMed Central PMCID: PMC7490394.

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Hoffmann M, Frost R, Salat D, Tisdall MD, Polimeni J, van der Kouwe A. Real-time brain masking algorithm improves motion tracking accuracy in scans with volumetric navigators (vNavs). Proc Int Soc Magn Reson Med Sci Meet Exhib Int Soc Magn Reson Med Sci Meet Exhib. 2020 Aug;2020. PubMed PMID: 37576741; PubMed Central PMCID: PMC10416756.

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Cheng J, Dalca AV, Fischl B, Zöllei L. Cortical surface registration using unsupervised learning. Neuroimage. 2020 Nov 1;221:117161. doi: 10.1016/j.neuroimage.2020.117161. Epub 2020 Jul 20. PubMed PMID: 32702486; PubMed Central PMCID: PMC7784120.

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Andronesi OC, Bhattacharyya PK, Bogner W, Choi IY, Hess AT, Lee P, Meintjes EM, Tisdall MD, Zaitzev M, van der Kouwe A. Motion correction methods for MRS: experts' consensus recommendations. NMR Biomed. 2021 May;34(5):e4364. doi: 10.1002/nbm.4364. Epub 2020 Jul 20. PubMed PMID: 33089547; PubMed Central PMCID: PMC7855523.

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Zöllei L, Iglesias JE, Ou Y, Grant PE, Fischl B. Infant FreeSurfer: An automated segmentation and surface extraction pipeline for T1-weighted neuroimaging data of infants 0-2 years. Neuroimage. 2020 Sep;218:116946. doi: 10.1016/j.neuroimage.2020.116946. Epub 2020 May 20. PubMed PMID: 32442637; PubMed Central PMCID: PMC7415702.

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Ter Telgte A, Scherlek AA, Reijmer YD, van der Kouwe AJ, van Harten T, Duering M, Bacskai BJ, de Leeuw FE, Frosch MP, Greenberg SM, van Veluw SJ. Histopathology of diffusion-weighted imaging-positive lesions in cerebral amyloid angiopathy. Acta Neuropathol. 2020 May;139(5):799-812. doi: 10.1007/s00401-020-02140-y. Epub 2020 Feb 27. PubMed PMID: 32108259; PubMed Central PMCID: PMC7185568.

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Simegn GL, Alhamud A, van der Kouwe AJW, Meintjes E, Robertson F. Repeatability and reproducibility of prospective motion- and shim corrected 2D glycoCEST MRI. Quant Imaging Med Surg. 2019 Oct;9(10):1674-1685. doi: 10.21037/qims.2019.09.15. PubMed PMID: 31728311; PubMed Central PMCID: PMC6828578.

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van Veluw SJ, Scherlek AA, Freeze WM, Ter Telgte A, van der Kouwe AJ, Bacskai BJ, Frosch MP, Greenberg SM. Different microvascular alterations underlie microbleeds and microinfarcts. Ann Neurol. 2019 Aug;86(2):279-292. doi: 10.1002/ana.25512. Epub 2019 Jun 14. PubMed PMID: 31152566; PubMed Central PMCID: PMC8722100.

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van Niekerk A, van der Kouwe A, Meintjes E. Toward "plug and play" prospective motion correction for MRI by combining observations of the time varying gradient and static vector fields. Magn Reson Med. 2019 Sep;82(3):1214-1228. doi: 10.1002/mrm.27790. Epub 2019 May 7. PubMed PMID: 31066109; PubMed Central PMCID: PMC7266630.

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Frost R, Wighton P, Karahanoğlu FI, Robertson RL, Grant PE, Fischl B, Tisdall MD, van der Kouwe A. Markerless high-frequency prospective motion correction for neuroanatomical MRI. Magn Reson Med. 2019 Jul;82(1):126-144. doi: 10.1002/mrm.27705. Epub 2019 Feb 28. PubMed PMID: 30821010; PubMed Central PMCID: PMC6491242.

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van Niekerk A, Meintjes E, van der Kouwe A. A Wireless Radio Frequency Triggered Acquisition Device (WRAD) for Self-Synchronised Measurements of the Rate of Change of the MRI Gradient Vector Field for Motion Tracking. IEEE Trans Med Imaging. 2019 Jul;38(7):1610-1621. doi: 10.1109/TMI.2019.2891774. Epub 2019 Jan 10. PubMed PMID: 30629498; PubMed Central PMCID: PMC7192240.

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Simegn GL, Van der Kouwe AJW, Robertson FC, Meintjes EM, Alhamud A. Real-time simultaneous shim and motion measurement and correction in glycoCEST MRI using double volumetric navigators (DvNavs). Magn Reson Med. 2019 Apr;81(4):2600-2613. doi: 10.1002/mrm.27597. Epub 2018 Dec 2. PubMed PMID: 30506877; PubMed Central PMCID: PMC7251754.

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Bookheimer SY, Salat DH, Terpstra M, Ances BM, Barch DM, Buckner RL, Burgess GC, Curtiss SW, Diaz-Santos M, Elam JS, Fischl B, Greve DN, Hagy HA, Harms MP, Hatch OM, Hedden T, Hodge C, Japardi KC, Kuhn TP, Ly TK, Smith SM, Somerville LH, Uğurbil K, van der Kouwe A, Van Essen D, Woods RP, Yacoub E. The Lifespan Human Connectome Project in Aging: An overview. Neuroimage. 2019 Jan 15;185:335-348. doi: 10.1016/j.neuroimage.2018.10.009. Epub 2018 Oct 15. PubMed PMID: 30332613; PubMed Central PMCID: PMC6649668.

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Harms MP, Somerville LH, Ances BM, Andersson J, Barch DM, Bastiani M, Bookheimer SY, Brown TB, Buckner RL, Burgess GC, Coalson TS, Chappell MA, Dapretto M, Douaud G, Fischl B, Glasser MF, Greve DN, Hodge C, Jamison KW, Jbabdi S, Kandala S, Li X, Mair RW, Mangia S, Marcus D, Mascali D, Moeller S, Nichols TE, Robinson EC, Salat DH, Smith SM, Sotiropoulos SN, Terpstra M, Thomas KM, Tisdall MD, Ugurbil K, van der Kouwe A, Woods RP, Zöllei L, Van Essen DC, Yacoub E. Extending the Human Connectome Project across ages: Imaging protocols for the Lifespan Development and Aging projects. Neuroimage. 2018 Dec;183:972-984. doi: 10.1016/j.neuroimage.2018.09.060. Epub 2018 Sep 24. PubMed PMID: 30261308; PubMed Central PMCID: PMC6484842.

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Moser P, Hingerl L, Strasser B, Považan M, Hangel G, Andronesi OC, van der Kouwe A, Gruber S, Trattnig S, Bogner W. Whole-slice mapping of GABA and GABA(+) at 7T via adiabatic MEGA-editing, real-time instability correction, and concentric circle readout. Neuroimage. 2019 Jan 1;184:475-489. doi: 10.1016/j.neuroimage.2018.09.039. Epub 2018 Sep 19. PubMed PMID: 30243974; PubMed Central PMCID: PMC7212034.

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Iglesias JE, Insausti R, Lerma-Usabiaga G, Bocchetta M, Van Leemput K, Greve DN, van der Kouwe A, Fischl B, Caballero-Gaudes C, Paz-Alonso PM. A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology. Neuroimage. 2018 Dec;183:314-326. doi: 10.1016/j.neuroimage.2018.08.012. Epub 2018 Aug 17. PubMed PMID: 30121337; PubMed Central PMCID: PMC6215335.

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Robertson FC, Holmes MJ, Cotton MF, Dobbels E, Little F, Laughton B, van der Kouwe AJW, Meintjes EM. Perinatal HIV Infection or Exposure Is Associated With Low N-Acetylaspartate and Glutamate in Basal Ganglia at Age 9 but Not 7 Years. Front Hum Neurosci. 2018;12:145. doi: 10.3389/fnhum.2018.00145. eCollection 2018. PubMed PMID: 29867401; PubMed Central PMCID: PMC5949349.

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Edlow BL, Keene CD, Perl DP, Iacono D, Folkerth RD, Stewart W, Mac Donald CL, Augustinack J, Diaz-Arrastia R, Estrada C, Flannery E, Gordon WA, Grabowski TJ, Hansen K, Hoffman J, Kroenke C, Larson EB, Lee P, Mareyam A, McNab JA, McPhee J, Moreau AL, Renz A, Richmire K, Stevens A, Tang CY, Tirrell LS, Trittschuh EH, van der Kouwe A, Varjabedian A, Wald LL, Wu O, Yendiki A, Young L, Zöllei L, Fischl B, Crane PK, Dams-O'Connor K. Multimodal Characterization of the Late Effects of Traumatic Brain Injury: A Methodological Overview of the Late Effects of Traumatic Brain Injury Project. J Neurotrauma. 2018 Jul 15;35(14):1604-1619. doi: 10.1089/neu.2017.5457. Epub 2018 May 3. PubMed PMID: 29421973; PubMed Central PMCID: PMC6016096.

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Toich JTF, Taylor PA, Holmes MJ, Gohel S, Cotton MF, Dobbels E, Laughton B, Little F, van der Kouwe AJW, Biswal B, Meintjes EM. Functional Connectivity Alterations between Networks and Associations with Infant Immune Health within Networks in HIV Infected Children on Early Treatment: A Study at 7 Years. Front Hum Neurosci. 2017;11:635. doi: 10.3389/fnhum.2017.00635. eCollection 2017. PubMed PMID: 29375341; PubMed Central PMCID: PMC5768628.

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Fan J, Taylor PA, Jacobson SW, Molteno CD, Gohel S, Biswal BB, Jacobson JL, Meintjes EM. Localized reductions in resting-state functional connectivity in children with prenatal alcohol exposure. Hum Brain Mapp. 2017 Oct;38(10):5217-5233. doi: 10.1002/hbm.23726. Epub 2017 Jul 22. PubMed PMID: 28734059; PubMed Central PMCID: PMC6377933.

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Saygin ZM, Kliemann D, Iglesias JE, van der Kouwe AJW, Boyd E, Reuter M, Stevens A, Van Leemput K, McKee A, Frosch MP, Fischl B, Augustinack JC. High-resolution magnetic resonance imaging reveals nuclei of the human amygdala: manual segmentation to automatic atlas. Neuroimage. 2017 Jul 15;155:370-382. doi: 10.1016/j.neuroimage.2017.04.046. Epub 2017 May 4. PubMed PMID: 28479476; PubMed Central PMCID: PMC5557007.