Automated processing pipeline for neonatal diffusion MRI in the developing Human Connectome Project.
Brain
Connectome
Diffusion MRI
Newborn
Quality control
Tractography
Journal
NeuroImage
ISSN: 1095-9572
Titre abrégé: Neuroimage
Pays: United States
ID NLM: 9215515
Informations de publication
Date de publication:
15 01 2019
15 01 2019
Historique:
received:
12
10
2017
revised:
25
05
2018
accepted:
26
05
2018
pubmed:
1
6
2018
medline:
6
4
2019
entrez:
1
6
2018
Statut:
ppublish
Résumé
The developing Human Connectome Project is set to create and make available to the scientific community a 4-dimensional map of functional and structural cerebral connectivity from 20 to 44 weeks post-menstrual age, to allow exploration of the genetic and environmental influences on brain development, and the relation between connectivity and neurocognitive function. A large set of multi-modal MRI data from fetuses and newborn infants is currently being acquired, along with genetic, clinical and developmental information. In this overview, we describe the neonatal diffusion MRI (dMRI) image processing pipeline and the structural connectivity aspect of the project. Neonatal dMRI data poses specific challenges, and standard analysis techniques used for adult data are not directly applicable. We have developed a processing pipeline that deals directly with neonatal-specific issues, such as severe motion and motion-related artefacts, small brain sizes, high brain water content and reduced anisotropy. This pipeline allows automated analysis of in-vivo dMRI data, probes tissue microstructure, reconstructs a number of major white matter tracts, and includes an automated quality control framework that identifies processing issues or inconsistencies. We here describe the pipeline and present an exemplar analysis of data from 140 infants imaged at 38-44 weeks post-menstrual age.
Identifiants
pubmed: 29852283
pii: S1053-8119(18)30488-9
doi: 10.1016/j.neuroimage.2018.05.064
pmc: PMC6299258
mid: EMS81153
pii:
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
750-763Subventions
Organisme : European Research Council
ID : 319456
Pays : International
Organisme : NIMH NIH HHS
ID : U01 MH109589
Pays : United States
Organisme : Wellcome Trust
ID : 098369
Pays : United Kingdom
Organisme : NIA NIH HHS
ID : U01 AG052564
Pays : United States
Organisme : Medical Research Council
ID : MR/L009013/1
Pays : United Kingdom
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 203139
Pays : United Kingdom
Informations de copyright
Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.
Références
AJNR Am J Neuroradiol. 2002 Oct;23(9):1445-56
pubmed: 12372731
Neuroimage. 2002 Oct;17(2):825-41
pubmed: 12377157
NMR Biomed. 2002 Nov-Dec;15(7-8):456-67
pubmed: 12489095
Neuroimage. 2003 Oct;20(2):870-88
pubmed: 14568458
Magn Reson Med. 2003 Nov;50(5):1077-88
pubmed: 14587019
Radiology. 2004 Jan;230(1):77-87
pubmed: 14645885
Neuroimage. 2004;23 Suppl 1:S208-19
pubmed: 15501092
Neuroimage. 2004 Nov;23(3):1176-85
pubmed: 15528117
Magn Reson Med. 2005 Jun;53(6):1432-40
pubmed: 15906300
Eur J Radiol. 2006 Feb;57(2):187-98
pubmed: 16439088
Neurosci Biobehav Rev. 2006;30(6):762-74
pubmed: 16890990
Med Image Anal. 2006 Oct;10(5):764-85
pubmed: 16899392
Neuroimage. 2006 Oct 15;33(1):27-38
pubmed: 16905335
Semin Fetal Neonatal Med. 2006 Dec;11(6):489-97
pubmed: 16962837
Neuroimage. 2007 Jan 1;34(1):144-55
pubmed: 17070705
Hum Brain Mapp. 2008 Jan;29(1):14-27
pubmed: 17318834
Cortex. 2008 Sep;44(8):1105-32
pubmed: 18619589
Magn Reson Med. 2009 Jun;61(6):1336-49
pubmed: 19319973
Neuroimage. 2009 Oct 15;48(1):63-72
pubmed: 19573611
Neuroimage. 2011 May 1;56(1):8-20
pubmed: 21276861
Magn Reson Med. 2011 Jul;66(1):92-101
pubmed: 21305603
Annu Rev Biomed Eng. 2011 Aug 15;13:345-68
pubmed: 21568716
Med Image Anal. 2012 Jan;16(1):28-37
pubmed: 21636311
Cereb Cortex. 2012 Feb;22(2):455-64
pubmed: 21670100
Neuroimage. 2012 Feb 1;59(3):2255-65
pubmed: 21985910
Neuroimage. 2012 Aug 15;62(2):1299-310
pubmed: 22245355
Magn Reson Med. 2012 Dec;68(6):1846-55
pubmed: 22334356
PLoS One. 2012;7(2):e31029
pubmed: 22347423
Neuroimage. 2012 Jul 16;61(4):1000-16
pubmed: 22484410
J Magn Reson Imaging. 2012 Oct;36(4):961-71
pubmed: 22689498
Pediatr Radiol. 2012 Oct;42(10):1169-82
pubmed: 22903761
Med Image Anal. 2012 Dec;16(8):1550-64
pubmed: 22939612
Cortex. 2013 Jun;49(6):1711-21
pubmed: 22959979
Neuroimage. 2013 Jan 15;65:433-48
pubmed: 23085109
Cereb Cortex. 2014 Mar;24(3):579-92
pubmed: 23131806
AJNR Am J Neuroradiol. 2013 Aug;34(8):1496-505
pubmed: 23518355
Neuroimage. 2013 Aug 1;76:400-11
pubmed: 23523807
Cereb Cortex. 2014 Sep;24(9):2324-33
pubmed: 23547135
Proc Natl Acad Sci U S A. 2013 Jun 4;110(23):9541-6
pubmed: 23696665
Int J Dev Neurosci. 2013 Nov;31(7):512-24
pubmed: 23796902
Neuroradiology. 2013 Sep;55 Suppl 2:65-95
pubmed: 23942765
Front Hum Neurosci. 2013 Oct 29;7:721
pubmed: 24194711
AJNR Am J Neuroradiol. 2014 Apr;35(4):808-14
pubmed: 24231848
AJR Am J Roentgenol. 2014 Jan;202(1):W26-33
pubmed: 24370162
Neuroscience. 2014 Sep 12;276:48-71
pubmed: 24378955
Neuroimage. 2014 Aug 1;96:288-99
pubmed: 24680870
Inf Process Med Imaging. 2013;23:475-86
pubmed: 24683992
Magn Reson Imaging. 2014 Oct;32(8):981-92
pubmed: 24960369
Neuroimage. 2014 Dec;103:214-224
pubmed: 25261000
Cereb Cortex. 2015 Nov;25(11):4310-8
pubmed: 25596587
Cereb Cortex. 2016 Aug;26(8):3370-3378
pubmed: 26209848
Neuroimage. 2015 Nov 15;122:166-76
pubmed: 26236030
Cereb Cortex. 2016 Oct 17;26(11):4381-4391
pubmed: 26405055
Nat Neurosci. 2015 Nov;18(11):1565-7
pubmed: 26414616
Neuron. 2015 Oct 7;88(1):93-109
pubmed: 26447575
Neuroimage. 2016 Jan 15;125:1063-1078
pubmed: 26481672
Neuroimage. 2016 Jun;133:207-223
pubmed: 26826512
Neuroimage. 2016 Jul 1;134:396-409
pubmed: 27071694
Neuroimage. 2016 Nov 1;141:556-572
pubmed: 27393418
Neuroimage. 2016 Nov 1;141:490-501
pubmed: 27421183
Nature. 2016 Aug 11;536(7615):171-178
pubmed: 27437579
Nat Neurosci. 2016 Nov;19(11):1523-1536
pubmed: 27643430
Magn Reson Med. 2017 Aug;78(2):794-804
pubmed: 27643791
Neuroimage. 2017 Apr 1;149:379-392
pubmed: 28153637
Neuroimage. 2017 May 15;152:450-466
pubmed: 28284799
Neuroimage. 2017 Aug 15;157:675-694
pubmed: 28457976
Magn Reson Med. 2018 Mar;79(3):1276-1292
pubmed: 28557055
Trends Cogn Sci. 2017 Sep;21(9):703-717
pubmed: 28610804
Neuroimage. 2017 Sep;158:205-218
pubmed: 28669902
Neuroimage. 2018 Feb 1;166:400-424
pubmed: 29079522
J Child Psychol Psychiatry. 2018 Apr;59(4):350-371
pubmed: 29105061
Neuroimage. 2018 May 1;171:277-295
pubmed: 29277648
Neuroimage. 2018 Nov 15;182:207-218
pubmed: 29305910
Neuroimage. 2018 Jun;173:88-112
pubmed: 29409960
Neuroimage. 2019 Jan 15;185:891-905
pubmed: 29578031
Neuroimage. 2019 Jan 1;184:801-812
pubmed: 30267859
J Neuropathol Exp Neurol. 1988 May;47(3):217-34
pubmed: 3367155
Magn Reson Med. 1995 Jul;34(1):65-73
pubmed: 7674900
J Magn Reson B. 1996 Jun;111(3):209-19
pubmed: 8661285
Radiology. 1998 Oct;209(1):57-66
pubmed: 9769812
Pediatr Res. 1998 Oct;44(4):584-90
pubmed: 9773850