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Automated quality control for within and between studies diffusion MRI data using a non-parametric framework for movement and distortion correction.

Bastiani M, Cottaar M, Fitzgibbon SP, Suri S, Alfaro-Almagro F, Sotiropoulos SN, Jbabdi S, Andersson JLR.

Neuroimage. 2019 Jan 1;184:801-812. doi: 10.1016/j.neuroimage.2018.09.073. Epub 2018 Sep 26.


Extending the Human Connectome Project across ages: Imaging protocols for the Lifespan Development and Aging projects.

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.

Neuroimage. 2018 Dec;183:972-984. doi: 10.1016/j.neuroimage.2018.09.060. Epub 2018 Sep 24.


Connectivity Fingerprints: From Areal Descriptions to Abstract Spaces.

Mars RB, Passingham RE, Jbabdi S.

Trends Cogn Sci. 2018 Nov;22(11):1026-1037. doi: 10.1016/j.tics.2018.08.009. Epub 2018 Sep 18. Review.


Feasibility of Diffusion Tensor and Morphologic Imaging of Peripheral Nerves at Ultra-High Field Strength.

Schmid AB, Campbell J, Hurley SA, Jbabdi S, Andersson JL, Jenkinson M, Bangerter NK, Bennett DL, Tracey I, Frost R, Clare S.

Invest Radiol. 2018 Dec;53(12):705-713. doi: 10.1097/RLI.0000000000000492.


What is special about the human arcuate fasciculus? Lateralization, projections, and expansion.

Eichert N, Verhagen L, Folloni D, Jbabdi S, Khrapitchev AA, Sibson NR, Mantini D, Sallet J, Mars RB.

Cortex. 2018 May 12. pii: S0010-9452(18)30151-5. doi: 10.1016/j.cortex.2018.05.005. [Epub ahead of print]


An empirical, 21st century evaluation of phrenology.

Parker Jones O, Alfaro-Almagro F, Jbabdi S.

Cortex. 2018 Sep;106:26-35. doi: 10.1016/j.cortex.2018.04.011. Epub 2018 May 9.


Automated processing pipeline for neonatal diffusion MRI in the developing Human Connectome Project.

Bastiani M, Andersson JLR, Cordero-Grande L, Murgasova M, Hutter J, Price AN, Makropoulos A, Fitzgibbon SP, Hughes E, Rueckert D, Victor S, Rutherford M, Edwards AD, Smith SM, Tournier JD, Hajnal JV, Jbabdi S, Sotiropoulos SN.

Neuroimage. 2018 May 28. pii: S1053-8119(18)30488-9. doi: 10.1016/j.neuroimage.2018.05.064. [Epub ahead of print]


Whole brain comparative anatomy using connectivity blueprints.

Mars RB, Sotiropoulos SN, Passingham RE, Sallet J, Verhagen L, Khrapitchev AA, Sibson N, Jbabdi S.

Elife. 2018 May 11;7. pii: e35237. doi: 10.7554/eLife.35237.


A gyral coordinate system predictive of fibre orientations.

Cottaar M, Bastiani M, Chen C, Dikranian K, Van Essen D, Behrens TE, Sotiropoulos SN, Jbabdi S.

Neuroimage. 2018 Aug 1;176:417-430. doi: 10.1016/j.neuroimage.2018.04.040. Epub 2018 Apr 21.


Dissecting the pathobiology of altered MRI signal in amyotrophic lateral sclerosis: A post mortem whole brain sampling strategy for the integration of ultra-high-field MRI and quantitative neuropathology.

Pallebage-Gamarallage M, Foxley S, Menke RAL, Huszar IN, Jenkinson M, Tendler BC, Wang C, Jbabdi S, Turner MR, Miller KL, Ansorge O.

BMC Neurosci. 2018 Mar 13;19(1):11. doi: 10.1186/s12868-018-0416-1.


Bayesian Optimisation of Large-Scale Biophysical Networks.

Hadida J, Sotiropoulos SN, Abeysuriya RG, Woolrich MW, Jbabdi S.

Neuroimage. 2018 Jul 1;174:219-236. doi: 10.1016/j.neuroimage.2018.02.063. Epub 2018 Mar 6.


A biophysical model of dynamic balancing of excitation and inhibition in fast oscillatory large-scale networks.

Abeysuriya RG, Hadida J, Sotiropoulos SN, Jbabdi S, Becker R, Hunt BAE, Brookes MJ, Woolrich MW.

PLoS Comput Biol. 2018 Feb 23;14(2):e1006007. doi: 10.1371/journal.pcbi.1006007. eCollection 2018 Feb.


Functional Segmentation of the Anterior Limb of the Internal Capsule: Linking White Matter Abnormalities to Specific Connections.

Safadi Z, Grisot G, Jbabdi S, Behrens TE, Heilbronner SR, McLaughlin NCR, Mandeville J, Versace A, Phillips ML, Lehman JF, Yendiki A, Haber SN.

J Neurosci. 2018 Feb 21;38(8):2106-2117. doi: 10.1523/JNEUROSCI.2335-17.2017. Epub 2018 Jan 22.


Neuroimage special issue on brain segmentation and parcellation - Editorial.

Craddock RC, Bellec P, Jbabdi S.

Neuroimage. 2018 Apr 15;170:1-4. doi: 10.1016/j.neuroimage.2017.11.063. Epub 2017 Dec 2. No abstract available.


Image processing and Quality Control for the first 10,000 brain imaging datasets from UK Biobank.

Alfaro-Almagro F, Jenkinson M, Bangerter NK, Andersson JLR, Griffanti L, Douaud G, Sotiropoulos SN, Jbabdi S, Hernandez-Fernandez M, Vallee E, Vidaurre D, Webster M, McCarthy P, Rorden C, Daducci A, Alexander DC, Zhang H, Dragonu I, Matthews PM, Miller KL, Smith SM.

Neuroimage. 2018 Feb 1;166:400-424. doi: 10.1016/j.neuroimage.2017.10.034. Epub 2017 Oct 24.


Subthalamic deep brain stimulation sweet spots and hyperdirect cortical connectivity in Parkinson's disease.

Akram H, Sotiropoulos SN, Jbabdi S, Georgiev D, Mahlknecht P, Hyam J, Foltynie T, Limousin P, De Vita E, Jahanshahi M, Hariz M, Ashburner J, Behrens T, Zrinzo L.

Neuroimage. 2017 Sep;158:332-345. doi: 10.1016/j.neuroimage.2017.07.012. Epub 2017 Jul 12.


Improved tractography using asymmetric fibre orientation distributions.

Bastiani M, Cottaar M, Dikranian K, Ghosh A, Zhang H, Alexander DC, Behrens TE, Jbabdi S, Sotiropoulos SN.

Neuroimage. 2017 Sep;158:205-218. doi: 10.1016/j.neuroimage.2017.06.050. Epub 2017 Jun 29.


Investigation of Slow-wave Activity Saturation during Surgical Anesthesia Reveals a Signature of Neural Inertia in Humans.

Warnaby CE, Sleigh JW, Hight D, Jbabdi S, Tracey I.

Anesthesiology. 2017 Oct;127(4):645-657. doi: 10.1097/ALN.0000000000001759.


Evaluating fibre orientation dispersion in white matter: Comparison of diffusion MRI, histology and polarized light imaging.

Mollink J, Kleinnijenhuis M, Cappellen van Walsum AV, Sotiropoulos SN, Cottaar M, Mirfin C, Heinrich MP, Jenkinson M, Pallebage-Gamarallage M, Ansorge O, Jbabdi S, Miller KL.

Neuroimage. 2017 Aug 15;157:561-574. doi: 10.1016/j.neuroimage.2017.06.001. Epub 2017 Jun 8.


Time-efficient and flexible design of optimized multishell HARDI diffusion.

Hutter J, Tournier JD, Price AN, Cordero-Grande L, Hughes EJ, Malik S, Steinweg J, Bastiani M, Sotiropoulos SN, Jbabdi S, Andersson J, Edwards AD, Hajnal JV.

Magn Reson Med. 2018 Mar;79(3):1276-1292. doi: 10.1002/mrm.26765. Epub 2017 May 30.


Pathology of callosal damage in ALS: An ex-vivo, 7 T diffusion tensor MRI study.

Cardenas AM, Sarlls JE, Kwan JY, Bageac D, Gala ZS, Danielian LE, Ray-Chaudhury A, Wang HW, Miller KL, Foxley S, Jbabdi S, Welsh RC, Floeter MK.

Neuroimage Clin. 2017 Apr 30;15:200-208. doi: 10.1016/j.nicl.2017.04.024. eCollection 2017.


Concurrent white matter bundles and grey matter networks using independent component analysis.

O'Muircheartaigh J, Jbabdi S.

Neuroimage. 2018 Apr 15;170:296-306. doi: 10.1016/j.neuroimage.2017.05.012. Epub 2017 May 14. Review.


Choice of reference measurements affects quantification of long diffusion time behaviour using stimulated echoes.

Kleinnijenhuis M, Mollink J, Lam WW, Kinchesh P, Khrapitchev AA, Smart SC, Jbabdi S, Miller KL.

Magn Reson Med. 2018 Feb;79(2):952-959. doi: 10.1002/mrm.26711. Epub 2017 May 3.


Resting connectivity predicts task activation in pre-surgical populations.

Parker Jones O, Voets NL, Adcock JE, Stacey R, Jbabdi S.

Neuroimage Clin. 2016 Dec 24;13:378-385. doi: 10.1016/j.nicl.2016.12.028. eCollection 2017.


Perceptually relevant remapping of human somatotopy in 24 hours.

Kolasinski J, Makin TR, Logan JP, Jbabdi S, Clare S, Stagg CJ, Johansen-Berg H.

Elife. 2016 Dec 30;5. pii: e17280. doi: 10.7554/eLife.17280.


Multimodal population brain imaging in the UK Biobank prospective epidemiological study.

Miller KL, Alfaro-Almagro F, Bangerter NK, Thomas DL, Yacoub E, Xu J, Bartsch AJ, Jbabdi S, Sotiropoulos SN, Andersson JL, Griffanti L, Douaud G, Okell TW, Weale P, Dragonu I, Garratt S, Hudson S, Collins R, Jenkinson M, Matthews PM, Smith SM.

Nat Neurosci. 2016 Nov;19(11):1523-1536. doi: 10.1038/nn.4393. Epub 2016 Sep 19.


Revealing the neural fingerprints of a missing hand.

Kikkert S, Kolasinski J, Jbabdi S, Tracey I, Beckmann CF, Johansen-Berg H, Makin TR.

Elife. 2016 Aug 23;5. pii: e15292. doi: 10.7554/eLife.15292.


Using Diffusion Tractography to Predict Cortical Connection Strength and Distance: A Quantitative Comparison with Tracers in the Monkey.

Donahue CJ, Sotiropoulos SN, Jbabdi S, Hernandez-Fernandez M, Behrens TE, Dyrby TB, Coalson T, Kennedy H, Knoblauch K, Van Essen DC, Glasser MF.

J Neurosci. 2016 Jun 22;36(25):6758-70. doi: 10.1523/JNEUROSCI.0493-16.2016.


Task-free MRI predicts individual differences in brain activity during task performance.

Tavor I, Parker Jones O, Mars RB, Smith SM, Behrens TE, Jbabdi S.

Science. 2016 Apr 8;352(6282):216-20. doi: 10.1126/science.aad8127. Epub 2016 Apr 7.


Fusion in diffusion MRI for improved fibre orientation estimation: An application to the 3T and 7T data of the Human Connectome Project.

Sotiropoulos SN, Hernández-Fernández M, Vu AT, Andersson JL, Moeller S, Yacoub E, Lenglet C, Ugurbil K, Behrens TEJ, Jbabdi S.

Neuroimage. 2016 Jul 1;134:396-409. doi: 10.1016/j.neuroimage.2016.04.014. Epub 2016 Apr 9.


Unmasking Latent Inhibitory Connections in Human Cortex to Reveal Dormant Cortical Memories.

Barron HC, Vogels TP, Emir UE, Makin TR, O'Shea J, Clare S, Jbabdi S, Dolan RJ, Behrens TE.

Neuron. 2016 Apr 6;90(1):191-203. doi: 10.1016/j.neuron.2016.02.031. Epub 2016 Mar 17.


Investigating the Stability of Fine-Grain Digit Somatotopy in Individual Human Participants.

Kolasinski J, Makin TR, Jbabdi S, Clare S, Stagg CJ, Johansen-Berg H.

J Neurosci. 2016 Jan 27;36(4):1113-27. doi: 10.1523/JNEUROSCI.1742-15.2016.


Anesthesia-induced Suppression of Human Dorsal Anterior Insula Responsivity at Loss of Volitional Behavioral Response.

Warnaby CE, Seretny M, Ní Mhuircheartaigh R, Rogers R, Jbabdi S, Sleigh J, Tracey I.

Anesthesiology. 2016 Apr;124(4):766-78. doi: 10.1097/ALN.0000000000001027.


The extreme capsule fiber complex in humans and macaque monkeys: a comparative diffusion MRI tractography study.

Mars RB, Foxley S, Verhagen L, Jbabdi S, Sallet J, Noonan MP, Neubert FX, Andersson JL, Croxson PL, Dunbar RI, Khrapitchev AA, Sibson NR, Miller KL, Rushworth MF.

Brain Struct Funct. 2016 Nov;221(8):4059-4071. Epub 2015 Dec 1.


Measuring macroscopic brain connections in vivo.

Jbabdi S, Sotiropoulos SN, Haber SN, Van Essen DC, Behrens TE.

Nat Neurosci. 2015 Nov;18(11):1546-55. doi: 10.1038/nn.4134. Epub 2015 Oct 27. Review.


Dentatorubrothalamic tract localization with postmortem MR diffusion tractography compared to histological 3D reconstruction.

Mollink J, van Baarsen KM, Dederen PJ, Foxley S, Miller KL, Jbabdi S, Slump CH, Grotenhuis JA, Kleinnijenhuis M, van Cappellen van Walsum AM.

Brain Struct Funct. 2016 Sep;221(7):3487-501. doi: 10.1007/s00429-015-1115-7. Epub 2015 Oct 5.


A probabilistic atlas of the cerebellar white matter.

van Baarsen KM, Kleinnijenhuis M, Jbabdi S, Sotiropoulos SN, Grotenhuis JA, van Cappellen van Walsum AM.

Neuroimage. 2016 Jan 1;124(Pt A):724-732. doi: 10.1016/j.neuroimage.2015.09.014. Epub 2015 Sep 15.


Tractography Study of Deep Brain Stimulation of the Anterior Cingulate Cortex in Chronic Pain: Key to Improve the Targeting.

Boccard SG, Fernandes HM, Jbabdi S, Van Hartevelt TJ, Kringelbach ML, Quaghebeur G, Moir L, Mancebo VP, Pereira EA, Fitzgerald JJ, Green AL, Stein J, Aziz TZ.

World Neurosurg. 2016 Feb;86:361-70.e1-3. doi: 10.1016/j.wneu.2015.08.065. Epub 2015 Sep 4.


High resolution whole brain diffusion imaging at 7T for the Human Connectome Project.

Vu AT, Auerbach E, Lenglet C, Moeller S, Sotiropoulos SN, Jbabdi S, Andersson J, Yacoub E, Ugurbil K.

Neuroimage. 2015 Nov 15;122:318-31. doi: 10.1016/j.neuroimage.2015.08.004. Epub 2015 Aug 7.


Diffusion tensor imaging of dolphin brains reveals direct auditory pathway to temporal lobe.

Berns GS, Cook PF, Foxley S, Jbabdi S, Miller KL, Marino L.

Proc Biol Sci. 2015 Jul 22;282(1811). pii: 20151203. doi: 10.1098/rspb.2015.1203.


Connectivity-based segmentation of the periaqueductal gray matter in human with brainstem optimized diffusion MRI.

Ezra M, Faull OK, Jbabdi S, Pattinson KT.

Hum Brain Mapp. 2015 Sep;36(9):3459-71. doi: 10.1002/hbm.22855. Epub 2015 Jul 2.


Correction: Accelerating Fibre Orientation Estimation from Diffusion Weighted Magnetic Resonance Imaging Using GPUs.

Hernández M, Guerrero GD, Cecilia JM, García JM, Inuggi A, Jbabdi S, Behrens TE, Sotiropoulos SN.

PLoS One. 2015 Jun 12;10(6):e0130915. doi: 10.1371/journal.pone.0130915. eCollection 2015. No abstract available.


Thalamo-Cortical Disruption Contributes to Short-Term Memory Deficits in Patients with Medial Temporal Lobe Damage.

Voets NL, Menke RA, Jbabdi S, Husain M, Stacey R, Carpenter K, Adcock JE.

Cereb Cortex. 2015 Nov;25(11):4584-95. doi: 10.1093/cercor/bhv109. Epub 2015 May 24.


Heritability of fractional anisotropy in human white matter: a comparison of Human Connectome Project and ENIGMA-DTI data.

Kochunov P, Jahanshad N, Marcus D, Winkler A, Sprooten E, Nichols TE, Wright SN, Hong LE, Patel B, Behrens T, Jbabdi S, Andersson J, Lenglet C, Yacoub E, Moeller S, Auerbach E, Ugurbil K, Sotiropoulos SN, Brouwer RM, Landman B, Lemaitre H, den Braber A, Zwiers MP, Ritchie S, van Hulzen K, Almasy L, Curran J, deZubicaray GI, Duggirala R, Fox P, Martin NG, McMahon KL, Mitchell B, Olvera RL, Peterson C, Starr J, Sussmann J, Wardlaw J, Wright M, Boomsma DI, Kahn R, de Geus EJ, Williamson DE, Hariri A, van 't Ent D, Bastin ME, McIntosh A, Deary IJ, Hulshoff Pol HE, Blangero J, Thompson PM, Glahn DC, Van Essen DC.

Neuroimage. 2015 May 1;111:300-11. doi: 10.1016/j.neuroimage.2015.02.050. Epub 2015 Mar 4.


Improving diffusion-weighted imaging of post-mortem human brains: SSFP at 7 T.

Foxley S, Jbabdi S, Clare S, Lam W, Ansorge O, Douaud G, Miller K.

Neuroimage. 2014 Nov 15;102 Pt 2:579-89. doi: 10.1016/j.neuroimage.2014.08.014. Epub 2014 Aug 13.


Differential structural and resting state connectivity between insular subdivisions and other pain-related brain regions.

Wiech K, Jbabdi S, Lin CS, Andersson J, Tracey I.

Pain. 2014 Oct;155(10):2047-55. doi: 10.1016/j.pain.2014.07.009. Epub 2014 Jul 15.


A model for extra-axonal diffusion spectra with frequency-dependent restriction.

Lam WW, Jbabdi S, Miller KL.

Magn Reson Med. 2015 Jun;73(6):2306-20. doi: 10.1002/mrm.25363. Epub 2014 Jul 15.


MSM: a new flexible framework for Multimodal Surface Matching.

Robinson EC, Jbabdi S, Glasser MF, Andersson J, Burgess GC, Harms MP, Smith SM, Van Essen DC, Jenkinson M.

Neuroimage. 2014 Oct 15;100:414-26. doi: 10.1016/j.neuroimage.2014.05.069. Epub 2014 Jun 2.


Motor skill learning induces changes in white matter microstructure and myelination.

Sampaio-Baptista C, Khrapitchev AA, Foxley S, Schlagheck T, Scholz J, Jbabdi S, DeLuca GC, Miller KL, Taylor A, Thomas N, Kleim J, Sibson NR, Bannerman D, Johansen-Berg H.

J Neurosci. 2013 Dec 11;33(50):19499-503. doi: 10.1523/JNEUROSCI.3048-13.2013.


Long-range connectomics.

Jbabdi S, Behrens TE.

Ann N Y Acad Sci. 2013 Dec;1305:83-93. doi: 10.1111/nyas.12271. Epub 2013 Sep 24. Review.

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