TRActs constrained by UnderLying INfant anatomy (TRACULInA): An automated probabilistic tractography tool with anatomical priors for use in the newborn brain

NeuroImage - Tập 199 - Trang 1-17 - 2019
Lilla Zöllei1, Camilo Jaimes2, Elie Saliba3, P. Ellen Grant2, Anastasia Yendiki1
1Massachusetts General Hospital, Boston, United States
2Boston Children's Hospital, Boston, United States
3University of Tours, France

Tài liệu tham khảo

Adams, 2010, Tractography-based quantitation of corticospinal tract development in premature newborns, J. Pediatr., 156, 882, 10.1016/j.jpeds.2009.12.030 Aeby, 2009, Maturation of thalamic radiations between 34 and 41 Weeks' gestation: a combined voxel-based study and probabilistic tractography with diffusion tensor imaging, AJNR, 30, 1780, 10.3174/ajnr.A1660 Agut, 2014, Early identification of brain injury in infants with hypoxic ischemic encephalopathy at high risk for severe impairments: accuracy of MRI performed in the first days of life, BMC Pediatr., 14, 177, 10.1186/1471-2431-14-177 Akazawa, 2016, Probabilistic maps of the white matter tracts with known associated functions on the neonatal brain atlas: application to evaluate longitudinal developmental trajectories in term-born and preterm-born infants, Neuroimage, 128, 167, 10.1016/j.neuroimage.2015.12.026 Alexander, 2017, A new neonatal cortical and subcortical brain atlas: the Melbourne Children's Regional Infant Brain (M-CRIB) atlas, Neuroimage, 147, 841, 10.1016/j.neuroimage.2016.09.068 Anblagan, 2015, Tract shape modeling detects changes associated with preterm birth and neuroprotective treatment effects, Neuroimage Clin., 8, 51, 10.1016/j.nicl.2015.03.021 Ball, 2013, The influence of preterm birth on the developing thalamocortical connectome, Cortex, 49, 1711, 10.1016/j.cortex.2012.07.006 Barkovich, 2000, Concepts of myelin and myelination in neuroradiology, AJNR Am. J. Neuroradiol., 21, 1099 Barkovich, 2005, Magnetic resonance techniques in the assessment of myelin and myelination, J. Inherit. Metab. Dis., 28, 311, 10.1007/s10545-005-5952-z Barkovich, 1988, Normal maturation of the neonatal and infant brain: MR imaging at 1.5 T, Radiology, 166, 173, 10.1148/radiology.166.1.3336675 Bassi, 2008, Probabilistic diffusion tractography of the optic radiations and visual function in preterm infants at term equivalent age, Brain, 131, 573, 10.1093/brain/awm327 Baumann, 2001, Biology of oligodendrocyte and myelin in the mammalian central nervous system, Physiol. Rev., 81, 871, 10.1152/physrev.2001.81.2.871 Beare, 2016, Neonatal brain tissue classification with morphological adaptation and unified segmentation, Front. Neuroinf., 10 Behrens, 2003, Characterization and propagation of uncertainty in diffusion-weighted MR imaging, Magn. Reson. Med., 50, 1077, 10.1002/mrm.10609 Benner, 2011, Diffusion imaging with prospective motion correction and reacquisition, Magn. Reson. Med., 66, 154, 10.1002/mrm.22837 Berman, 2009, Quantitative fiber tracking analysis of the optic radiation correlated with visual performance in premature newborns, AJNR, 30, 10.3174/ajnr.A1304 Braga, 2015, Development of the corticospinal and callosal tracts from extremely premature birth up to 2 Years of age, PLoS One, 10, 10.1371/journal.pone.0125681 Brody, 1987, Sequence of central nervous system myelination in human infancy. I. An autopsy study of myelination, J. Neuropathol. Exp. Neurol., 46, 283, 10.1097/00005072-198705000-00005 de Bruïne, 2011, Tractography of developing white matter of the internal capsule and corpus callosum in very preterm infants, Eur. Radiol., 21, 538, 10.1007/s00330-010-1945-x Catani, 2002, Virtual in vivo interactive dissection of white matter fasciculi in the human brain, Neuroimage, 17, 77, 10.1006/nimg.2002.1136 Ceschin, 2015, Developmental synergy between thalamic structure and interhemispheric connectivity in the visual system of preterm infants, Neuroimage Clin., 8, 462, 10.1016/j.nicl.2015.05.014 Clayden, 2009, Reproducibility of tract segmentation between sessions using an unsupervised modelling-based approach, Neuroimage, 45, 377, 10.1016/j.neuroimage.2008.12.010 Cohen, 2016, Development of human white matter fiber pathways: from newborn to adult ages, Int. J. Dev. Neurosci., 50, 26, 10.1016/j.ijdevneu.2016.02.002 Dean, 2018, Investigation of brain structure in the 1-month infant, Brain Struct. Funct., 223, 1953, 10.1007/s00429-017-1600-2 Desikan, 2006, An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest, Neuroimage, 31, 968, 10.1016/j.neuroimage.2006.01.021 Despotovic, 2010, Brain volume segmentation in newborn infants using multi-modal MRI with a low inter-slice resolution, Conf. Proc. IEEE Eng. Med. Biol. Soc., 2010, 5038 Dobbing, 1974, The later growth of the brain and its vulnerability, Pediatrics, 53, 2, 10.1542/peds.53.1.2 Doshi, 2013, Multi-atlas skull-stripping, Acad. Radiol., 20, 1566, 10.1016/j.acra.2013.09.010 Dubois, 2008, Asynchrony of the early maturation of white matter bundles in healthy infants: quantitative landmarks revealed noninvasively by diffusion tensor imaging, Hum. Brain Mapp., 29, 14, 10.1002/hbm.20363 Dubois, 2016, Exploring the early organization and maturation of linguistic pathways in the human infant brain, Cerebr. Cortex, 26, 2283, 10.1093/cercor/bhv082 Dudink, 2007, Fractional anisotropy in white matter tracts of very-low-birth-weight infants, Pediatr. Radiol., 37, 1216, 10.1007/s00247-007-0626-7 Elison, 2012, Frontolimbic neural circuitry at 6 months predicts individual differences in joint attention at 9 months, Dev. Sci., 16, 186, 10.1111/desc.12015 Fair, 2010, Maturing thalamocortical functional connectivity across development, Front. Syst. Neurosci., 4, 1 Fischl, 2002, Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain, Neuron, 33, 341, 10.1016/S0896-6273(02)00569-X Fischl, 2004, Automatically parcellating the human cerebral cortex, Cerebr. Cortex, 14, 11, 10.1093/cercor/bhg087 Geng, 2012, Quantitative tract-based white matter development from birth to age 2years, Neuroimage, 61, 542, 10.1016/j.neuroimage.2012.03.057 Geng, 2012, White matter heritability using diffusion tensor imaging in neonatal brains. Twin research and human genetics, Off. J. Int. Soc. Twin Stud., 15, 336 Ghosh, 2010, Evaluating the validity of volume-based and surface-based brain image registration for developmental cognitive neuroscience studies in children 4 to 11 years of age, Neuroimage, 53, 85, 10.1016/j.neuroimage.2010.05.075 Glass, 2010, Quantitative fiber tracking of the optic radiation is correlated with visual evoked potential amplitude in preterm infants, AJNR, 31, 1424, 10.3174/ajnr.A2110 Glenn, 2003, DTI-based three-dimensional tractography detects differences in the pyramidal tracts of infants and children with congenital hemiparesis, J. Magn. Reson. Imaging, 18, 641, 10.1002/jmri.10420 Gousias, 2013, Magnetic resonance imaging of the newborn brain: automatic segmentation of brain images into 50 anatomical regions, PLoS One, 8, 10.1371/journal.pone.0059990 Guevara, 2012, Automatic fiber bundle segmentation in massive tractography datasets using a multi-subject bundle atlas, Neuroimage, 61, 1083, 10.1016/j.neuroimage.2012.02.071 Gui, 2012, Morphology-driven automatic segmentation of MR images of the neonatal brain, Med. Image Anal., 16, 1565, 10.1016/j.media.2012.07.006 Gupta, 2015, Regional differences in fiber tractography predict neurodevelopmental outcomes in neonates with infantile Krabbe disease, Neuroimage Clin., 7, 792, 10.1016/j.nicl.2014.09.014 Hasegawa, 2011, Development of corpus callosum in preterm infants is affected by the prematurity: in vivo assessment of diffusion tensor imaging at term-equivalent age, Pediatr. Res., 69, 10.1203/PDR.0b013e3182084e54 Howell, 2019, The UNC/UMN Baby Con-nectome Project (BCP): an overview of the study design and protocol development, Neuroimage, 185, 891, 10.1016/j.neuroimage.2018.03.049 Iglesias, 2012, A generative model for multi-atlas segmentation across modalities, Proc. IEEE Int. Symp. Biomed. Imag., 888 Izbudak, 2011, MR imaging of the term and preterm neonate with diffuse brain injury, Magn. Reson. Imag. Clin. N. Am., 19, 709, 10.1016/j.mric.2011.08.014 Jbabdi, 2007, A Bayesian framework for global tractography, Neuroimage, 37, 116, 10.1016/j.neuroimage.2007.04.039 Jenkinson, 2001, A global optimisation method for robust affine registration of brain images, Med. Image Anal., 5, 143, 10.1016/S1361-8415(01)00036-6 Jenkinson, 2002, Improved optimization for the robust and accurate linear registration and motion correction of brain images, Neuroimage, 17, 825, 10.1006/nimg.2002.1132 Jin, 2014, Automatic clustering of white matter fibers in brain diffusion MRI with an application to genetics, Neuroimage, 100, 75, 10.1016/j.neuroimage.2014.04.048 Jog, 2015, MR image synthesis by contrast learning on neighbor-hood ensembles, Med. Image Anal., 24, 63, 10.1016/j.media.2015.05.002 Johansen-Berg, 2005, Functional–anatomical validation and individual variation of diffusion tractography-based segmentation of the human thalamus, Cerebr. Cortex, 15, 30, 10.1093/cercor/bhh105 Jones, 2003, Determining and visualizing uncertainty in estimates of fiber orientation from diffusion tensor MRI, Magn. Reson. Med., 49, 7, 10.1002/mrm.10331 Kawasaki, 2019, Clinical factors that affect the relationship between head circumference and brain volume in very-low-birth-weight infants, J. Neuroimaging, 29, 104, 10.1111/jon.12558 Kersbergen, 2015, Corticospinal tract injury precedes thalamic volume reduction in preterm infants with cystic periventricular leukomalacia, J. Pediatr., 167, 260, 10.1016/j.jpeds.2015.05.013 Kidowaki, 2017, Longitudinal change in white matter in preterm infants without magnetic resonance imaging abnormalities: assessment of serial diffusion tensor imaging and their relationship to neurodevelopmental outcomes, Brain Dev., 1, 40, 10.1016/j.braindev.2016.07.007 Koenraads, 2016, Prediction of visual field defects in newborn infants with perinatal arterial ischemic stroke using early MRI and DTI-based tractography of the optic radiation, Eur. J. Paediatr. Neurol., 20, 309, 10.1016/j.ejpn.2015.11.010 Koldewyn, 2014, Differences in the right inferior longitudinal fasciculus but no general disruption of white matter tracts in children with ASD, Proc. Natl. Acad. Sci. U.S.A, 111, 1981, 10.1073/pnas.1324037111 van Kooij, 2011, Fiber tracking at term displays gender differences regarding cognitive and motor outcome at 2 Years of age in preterm infants, Pediatr. Res., 70, 10.1203/PDR.0b013e318232a963 Langer, 2017, White matter alterations in infants at risk for developmental dyslexia, Cerebr. Cortex, 27, 1027 Lee, 2015, Quantitative tract-based white matter heritability in twin neonates, Neuroimage, 111, 123, 10.1016/j.neuroimage.2015.02.021 Liu, 2010, Structural asymmetries in motor and language networks in a population of healthy preterm neonates at term equivalent age: a diffusion tensor imaging and probabilistic tractography study, Neuroimage, 51, 783, 10.1016/j.neuroimage.2010.02.066 Liu, 2011, Gender differences in language and motor-related fibers in a population of healthy preterm neonates at term-equivalent age: a diffusion tensor and probabilistic tractography study, AJNR, 32, 2011, 10.3174/ajnr.A2690 Liu, 2012, White matter abnormalities are related to microstructural changes in preterm neonates at term-equivalent age: a diffusion tensor imaging and probabilistic tractography study, AJNR, 33, 839, 10.3174/ajnr.A2872 de Macedo Rodrigues, 2015, A FreeSurfer-compliant consistent manual segmentation of infant brains spanning the 0-2 year age range, Front. Hum. Neurosci., 9, 21, 10.3389/fnhum.2015.00021 Maddah, 2008, A unified framework for clustering and quantitative analysis of white matter fiber tracts, Med. Image Anal., 12, 191, 10.1016/j.media.2007.10.003 Makropoulos, 2014, Automatic whole brain MRI segmentation of the developing neonatal brain, IEEE Trans. Med. Imaging, 33, 1818, 10.1109/TMI.2014.2322280 Miller, 2002, Serial quantitative diffusion tensor MRI of the premature brain: development in newborns with and without injury, J. Magn. Reson. Imaging, 2002 Neil, 1998, Normal brain in human newborns: apparent diffusion coefficient and diffusion anisotropy measured by using diffusion tensor MR imaging, Radiology, 209, 57, 10.1148/radiology.209.1.9769812 O'Donnell, 2007, Automatic tractography segmentation using a high-dimensional white matter atlas, IEEE Trans. Med. Imaging, 26, 1562, 10.1109/TMI.2007.906785 Ou, 2011, DRAMMS: deformable registration via attribute matching and mutual-saliency weighting, Med. Image Anal., 15, 622, 10.1016/j.media.2010.07.002 Ou, 2018 Padilla, 2015, Brain growth gains and losses in extremely preterm infants at term, Cerebr. Cortex, 25, 1897, 10.1093/cercor/bht431 Pannek, 2014, Magnetic resonance diffusion tractography of the preterm infant brain: a systematic review, Dev. Med. Child Neurol., 56, 113, 10.1111/dmcn.12250 Partridge, 2005, Tractography-based quantitation of diffusion tensor imaging parameters in white matter tracts of preterm newborns, J. Magn. Reson. Imaging, 22, 467, 10.1002/jmri.20410 Partridge, 2006, Pyramidal tract maturation after brain injury in newborns with heart disease, Ann. Neurol., 59, 640, 10.1002/ana.20772 Pieterman, 2016, Cerebello-cerebral connectivity in the developing brain, Brain Struct. Funct., 1 Poretti, 2013, Neonatal neuroimaging findings in inborn errors of metabolism, J. Magn. Reson. Imaging, 37, 294, 10.1002/jmri.23693 Postelnicu, 2009, Combined volumetric and surface registration, IEEE Trans. Med. Imaging, 28, 508, 10.1109/TMI.2008.2004426 Prastawa, 2005, Automatic segmentation of MR images of the developing newborn brain, Med. Image Anal., 9, 457, 10.1016/j.media.2005.05.007 Prayer, 2001, Visualization of nonstructural changes in early white matter development on diffusion-weighted MR images: evidence supporting premyelination anisotropy, AJNR Am. J. Neuroradiol., 22, 1572 Provenzale, 2010, Correlation of apparent diffusion coefficient and fractional anisotropy values in the developing infant brain, Am. J. Roentgenol., 195, W456, 10.2214/AJR.10.4886 van Pul, 2012, Quantitative fiber tracking in the corpus callosum and internal capsule reveals microstructural abnormalities in preterm infants at term-equivalent age, AJNR, 33, 10.3174/ajnr.A2859 Rasmussen, 2016, A novel maturation index based on neonatal diffusion tensor imaging reflects typical perinatal white matter development in humans, Int. J. Dev. Neurosci. : Off. J. Int. Soc. Develop. Neurosci., 56, 42, 10.1016/j.ijdevneu.2016.12.004 Rasmussen, 2018 Ratnarajah, 2014, Multi-label segmentation of white matter structures: application to neonatal brains, Neuroimage, 102, 913, 10.1016/j.neuroimage.2014.08.001 Reuter, 2010, Highly accurate inverse consistent registration: a robust approach, Neuroimage, 53, 1181, 10.1016/j.neuroimage.2010.07.020 Reuter, 2015, Head motion during MRI acquisition reduces gray matter volume and thickness estimates, Neuroimage, 107, 107, 10.1016/j.neuroimage.2014.12.006 Ros, 2013, Atlas-guided cluster analysis of large tractography datasets, PLoS One, 8, 10.1371/journal.pone.0083847 Roy, 2013, Magnetic resonance image example-based contrast synthesis, IEEE Trans. Med. Imaging, 32, 2348, 10.1109/TMI.2013.2282126 Sadeghi, 2016, Twin-singleton developmental study of brain white matter anatomy, Hum. Brain Mapp., 38, 1009, 10.1002/hbm.23435 Smith, 2002, Fast robust automated brain extraction, Hum. Brain Mapp., 17, 143, 10.1002/hbm.10062 Smith, 2004, Advances in functional and structural MR image analysis and implementation as FSL, Neuroimage, 23, S208, 10.1016/j.neuroimage.2004.07.051 Sølsnes, 2016, Limited microstructural and connectivity deficits despite subcortical vol-ume reductions in school-aged children born preterm with very low birth weight, Neuroimage, 130, 24, 10.1016/j.neuroimage.2015.12.029 Swanson, 2015, Splenium development and early spoken language in human infants, Dev. Sci., 20, 10.1111/desc.12360 Swanson, 2018, Development of white matter circuitry in infants with fragile X syndrome, JAMA Psychiatr., 75, 505, 10.1001/jamapsychiatry.2018.0180 Talos, 2006 Terrier, 2014 Terrier, 2015, Tractographie cerebrale : definition de Nouvelles regles anatomiques Thompson, 2011, Characterization of the corpus callosum in very preterm and fullterm infants utilizing MRI, Neuroimage, 55, 479, 10.1016/j.neuroimage.2010.12.025 Thompson, 2012, Corpus callosum alterations in very preterm infants: perinatal correlates and 2 year neurodevelopmental outcomes, Neuroimage, 59, 3571, 10.1016/j.neuroimage.2011.11.057 Thompson, 2014, Regional white matter microstructure in very preterm infants: predictors and 7 year outcomes, Cortex, 52, 60, 10.1016/j.cortex.2013.11.010 Verde, 2014, UNC-Utah NA-MIC framework for DTI fiber tract analysis, Front. Neuroinf., 7 Wakana, 2004, Fiber tract-based atlas of human white matter anatomy, Radiology, 230, 77, 10.1148/radiol.2301021640 Wakana, 2007, Reproducibility of quantitative tractography methods applied to cerebral white matter, Neuroimage, 36, 630, 10.1016/j.neuroimage.2007.02.049 Walsh, 2017, The frequency and severity of MRI abnormalities in infants with mild neonatal encephalopathy, J. Pediatr., 187, 26, 10.1016/j.jpeds.2017.03.065 Wang, 2007, Diffusion toolkit: a software package for diffusion imaging data processing and tractography Wang, 2013, Application of neuroanatomical features to tractography clustering, Hum. Brain Mapp., 34, 2089, 10.1002/hbm.22051 Wang, 2015, LINKS: learning-based multi-source Integration framework for Segmentation of infant brain images, Neuroimage, 108, 160, 10.1016/j.neuroimage.2014.12.042 Weisenfeld, 2009, Automatic segmentation of newborn brain MRI, Neuroimage, 47, 564, 10.1016/j.neuroimage.2009.04.068 Wolff, 2015, Altered corpus callosum morphology associated with autism over the first 2 years of life, Brain : J. Neurol., 138, 2046, 10.1093/brain/awv118 Woolrich, 2009, Bayesian analysis of neuroimaging data in FSL, Neuroimage, 45, S173, 10.1016/j.neuroimage.2008.10.055 Yeatman JD, 2012, Tract profiles of white matter properties: automating fiber-tract quantification, PLoS One, 7, 10.1371/journal.pone.0049790 Yendiki, 2011, Automated probabilistic reconstruction of white-matter pathways in health and disease using an atlas of the underlying anatomy, Front. Neuroinf., 5, 23, 10.3389/fninf.2011.00023 Yendiki, 2014, Spurious group differences due to head motion in a diffu-sion MRI study, Neuroimage, 88, 79, 10.1016/j.neuroimage.2013.11.027 Yendiki, 2016, Joint reconstruction of white-matter pathways from longitudi-nal diffusion MRI data with anatomical priors, Neuroimage, 127, 277, 10.1016/j.neuroimage.2015.12.003 Yoo, 2005, Vivo visualization of white matter fiber tracts of preterm- and term-infant brains with diffusion tensor magnetic resonance imaging, Investig. Radiol., 40, 10.1097/01.rli.0000149491.69201.cb Yoshida, 2013, Diffusion tensor imaging of normal brain development, Pediatr. Radiol., 43, 15, 10.1007/s00247-012-2496-x Zhang, 2008, Automated fiber tracking of human brain white matter us-ing diffusion tensor imaging, Neuroimage, 42, 771, 10.1016/j.neuroimage.2008.04.241 Zöllei, 2010, Improved tractography alignment using combined volumetric and surface registration, Neuroimage, 51, 206, 10.1016/j.neuroimage.2010.01.101 Zöllei, 2017, FreeSurfer image processing pipeline for infant clinical MRI images Zwicker, 2013, SNAP-II predicts corticospinal tract development in premature newborns, Pediatr. Neurol., 48, 123, 10.1016/j.pediatrneurol.2012.10.016