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Mazur-Rosmus W, Krzyżak AT. The effect of elimination of gibbs ringing, noise and systematic errors on the DTI metrics and tractography in a rat brain. Sci Rep 2024; 14:15010. [PMID: 38951163 PMCID: PMC11217413 DOI: 10.1038/s41598-024-66076-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 06/26/2024] [Indexed: 07/03/2024] Open
Abstract
Diffusion tensor imaging (DTI) metrics and tractography can be biased due to low signal-to-noise ratio (SNR) and systematic errors resulting from image artifacts and imperfections in magnetic field gradients. The imperfections include non-uniformity and nonlinearity, effects caused by eddy currents, and the influence of background and imaging gradients. We investigated the impact of systematic errors on DTI metrics of an isotropic phantom and DTI metrics and tractography of a rat brain measured at high resolution. We tested denoising and Gibbs ringing removal methods combined with the B matrix spatial distribution (BSD) method for magnetic field gradient calibration. The results showed that the performance of the BSD method depends on whether Gibbs ringing is removed and the effectiveness of stochastic error removal. Region of interest (ROI)-based analysis of the DTI metrics showed that, depending on the size of the ROI and its location in space, correction methods can remove systematic bias to varying degrees. The preprocessing pipeline proposed and dedicated to this type of data together with the BSD method resulted in an even - 90% decrease in fractional anisotropy (FA) (globally and locally) in the isotropic phantom and - 45% in the rat brain. The largest global changes in the rat brain tractogram compared to the standard method without preprocessing (sDTI) were noticed after denoising. The direction of the first eigenvector obtained from DTI after denoising, Gibbs ringing removal and BSD differed by an average of 56 and 10 degrees in the ROI from sDTI and from sDTI after denoising and Gibbs ringing removal, respectively. The latter can be identified with the amount of improvement in tractography due to the elimination of systematic errors related to imperfect magnetic field gradients. Based on the results, the systematic bias for high resolution data mainly depended on SNR, but the influence of non-uniform gradients could also be seen. After denoising, the BSD method was able to further correct both the metrics and tractography of the diffusion tensor in the rat brain by taking into account the actual distribution of magnetic field gradients independent of the examined object and uniquely dependent on the scanner and sequence. This means that in vivo studies are also subject to this type of errors, which should be taken into account when processing such data.
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Affiliation(s)
| | - Artur T Krzyżak
- AGH University of Krakow, Al. Mickiewicza 30, 30-059, Krakow, Poland.
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2
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Kara D, Koenig K, Lowe M, Nguyen C, Sakaie K. Facilitating diffusion tensor imaging of the brain during continuous gross head motion with first and second order motion compensating diffusion gradients. Magn Reson Med 2024; 91:1556-1566. [PMID: 38073070 PMCID: PMC10872734 DOI: 10.1002/mrm.29924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 01/26/2024]
Abstract
PURPOSE To demonstrate the feasibility of motion compensating diffusion gradient schemes in the acquisition of quality diffusion tensor images (DTI) of the brain during continuous gross head motion. METHODS Five healthy subjects were scanned using a clinical 3 T MRI with and without continuous head motion. For one volunteer, DTI data was acquired using standard (M0) diffusion-weighted (DW) gradients, and first (M1) and second (M2) order gradient schemes that were previously developed for use in cardiac DTI. In four additional volunteers, DTI data was acquired with M0 and M2 gradients. DTI parameters were calculated and compared with established retrospective motion corrections. RESULTS In the absence of motion, DTI parameters calculated from M0, M1, and M2 data were consistent. In the presence of motion, up to 44% of DW images acquired with M0 gradients were corrupted by signal dropout, compared to 0% of the M2 images. In voxelwise comparisons, DTI parameters calculated using motion-M0 data were elevated compared to reference data. Retrospective corrections for extreme motion applied to motion-M0 data did not improve consistency with reference data in cases where motion corrupted >15% of DW images. In contrast, DTI parameters calculated with motion-M2 data were consistent with reference data. CONCLUSION This proof-of-principle study demonstrates that motion compensating diffusion gradients can mitigate artifacts because of continuous motion in DTI of the brain and offers promise for improved DTI accessibility. Further study will be necessary to determine the robustness of the approach in patient populations with high susceptibility to head motion.
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Affiliation(s)
- Danielle Kara
- Cardiovascular Innovation Research Center, Heart, Vascular, and Thoracic Institute, Cleveland Clinic
| | | | - Mark Lowe
- Imaging Sciences, Imaging Institute, Cleveland Clinic
| | - Christopher Nguyen
- Cardiovascular Innovation Research Center, Heart, Vascular, and Thoracic Institute, Cleveland Clinic
- Imaging Sciences, Imaging Institute, Cleveland Clinic
- Biomedical Engineering, Lerner Research Institute, Cleveland Clinic and Case Western Reserve University
| | - Ken Sakaie
- Imaging Sciences, Imaging Institute, Cleveland Clinic
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3
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Donald KA, Hendrikse CJ, Roos A, Wedderburn CJ, Subramoney S, Ringshaw JE, Bradford L, Hoffman N, Burd T, Narr KL, Woods RP, Zar HJ, Joshi SH, Stein DJ. Prenatal alcohol exposure and white matter microstructural changes across the first 6-7 years of life: A longitudinal diffusion tensor imaging study of a South African birth cohort. Neuroimage Clin 2024; 41:103572. [PMID: 38309186 PMCID: PMC10847766 DOI: 10.1016/j.nicl.2024.103572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/05/2024]
Abstract
Prenatal alcohol exposure (PAE) can affect brain development in early life, but few studies have investigated the effects of PAE on trajectories of white matter tract maturation in young children. Here we used diffusion weighted imaging (DWI) repeated over three time points, to measure the effects of PAE on patterns of white matter microstructural development during the pre-school years. Participants were drawn from the Drakenstein Child Health Study (DCHS), an ongoing birth cohort study conducted in a peri-urban community in the Western Cape, South Africa. A total of 342 scans acquired from 237 children as neonates (N = 82 scans: 30 PAE; 52 controls) and at ages 2-3 (N = 121 scans: 27 PAE; 94 controls) and 6-7 years (N = 139 scans: 45 PAE; 94 controls) were included. Maternal alcohol use during pregnancy and other antenatal covariates were collected from 28 to 32 weeks' gestation. Linear mixed effects models with restricted maxium likelihood to accommodate missing data were implemented to investigate the effects of PAE on fractional anisotropy (FA) and mean diffusivity (MD) in specific white matter tracts over time, while adjusting for child sex and maternal education. We found significant PAE-by-time effects on trajectories of FA development in the left superior cerebellar peduncle (SCP-L: p = 0.001; survived FDR correction) and right superior longitudinal fasciculus (SLF-R: p = 0.046), suggesting altered white matter development among children with PAE. Compared with controls, children with PAE demonstrated a more rapid change in FA in these tracts from the neonatal period to 2-3 years of age, followed by a more tapered trajectory for the period from 2-3 to 6-7 years of age, with these trajectories differing from unexposed control children. Given their supporting roles in various aspects of neurocognitive functioning (i.e., motor regulation, learning, memory, language), altered patterns of maturation in the SCP and SLF may contribute to a spectrum of physical, social, emotional, and cognitive difficulties often experienced by children with PAE. This study highlights the value of repeated early imaging in longitudinal studies of PAE, and focus for early childhood as a critical window of potential susceptibility as well as an opportunity for early intervention.
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Affiliation(s)
- K A Donald
- Division of Developmental Paediatrics, Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa; Neuroscience Institute, University of Cape Town, Cape Town, South Africa.
| | - C J Hendrikse
- Division of Developmental Paediatrics, Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa
| | - A Roos
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa; Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa; South African Medical Research Council (SAMRC), Unit on Risk and Resilience in Mental Disorders, University of Cape Town, Cape Town, South Africa
| | - C J Wedderburn
- Division of Developmental Paediatrics, Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa; Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - S Subramoney
- Division of Developmental Paediatrics, Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa
| | - J E Ringshaw
- Division of Developmental Paediatrics, Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa; Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - L Bradford
- Division of Developmental Paediatrics, Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa
| | - N Hoffman
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa; Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - T Burd
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa; South African Medical Research Council (SAMRC), Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - K L Narr
- Ahmanson-Lovelace Brain Mapping Center, Department of Neurology, University of California Los Angeles, Los Angeles, CA, United States; Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA, United States
| | - R P Woods
- Ahmanson-Lovelace Brain Mapping Center, Department of Neurology, University of California Los Angeles, Los Angeles, CA, United States; Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA, United States; The Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, United States; David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - H J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa; South African Medical Research Council (SAMRC), Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - S H Joshi
- Ahmanson-Lovelace Brain Mapping Center, Department of Neurology, University of California Los Angeles, Los Angeles, CA, United States; Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, United States
| | - D J Stein
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa; Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa; South African Medical Research Council (SAMRC), Unit on Risk and Resilience in Mental Disorders, University of Cape Town, Cape Town, South Africa
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Mueller C, Goodman AM, Nenert R, Allendorfer JB, Philip NS, Correia S, Oster RA, LaFrance WC, Szaflarski JP. Repeatability of neurite orientation dispersion and density imaging in patients with traumatic brain injury. J Neuroimaging 2023; 33:802-824. [PMID: 37210714 PMCID: PMC10524628 DOI: 10.1111/jon.13125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 05/05/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023] Open
Abstract
BACKGROUND AND PURPOSE The aim of this study was to assess the repeatability of neurite orientation dispersion and density imaging in healthy controls (HCs) and traumatic brain injury (TBI). METHODS Seventeen HCs and 48 TBI patients were scanned twice over 18 weeks with diffusion imaging. Orientation dispersion (ODI), neurite density (NDI), and the fraction of isotropic diffusion (F-ISO) were quantified in regions of interest (ROIs) from a gray matter, subcortical, and white matter atlas and compared using the coefficient of variation for repeated measures (CVrep ), which quantifies the expected percent change on repeated measurement. We used a modified signed likelihood ratio test (M-SLRT) to compare the CVrep between groups in each ROI while correcting for multiple comparisons. RESULTS NDI exhibited excellent repeatability in both groups; the only group difference was found in the fusiform gyrus, where HCs exhibited better repeatability (M-SLRT = 9.463, p = .0021). ODI also had excellent repeatability in both groups, although repeatability was significantly better in HCs in 16 cortical ROIs (p < .0022) and in the bilateral white matter and bilateral cortex (p < .0027). F-ISO exhibited relatively poor repeatability in both groups, with few group differences. CONCLUSION Overall, the repeatability of the NDI, ODI, and F-ISO metrics over an 18-week period is acceptable for assessing the effects of behavioral or pharmacological interventions, though caution is advised when assessing F-ISO changes over time.
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Affiliation(s)
- Christina Mueller
- Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, 1719 6th Ave S, Birmingham, AL 35233
| | - Adam M. Goodman
- Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, 1719 6th Ave S, Birmingham, AL 35233
| | - Rodolphe Nenert
- Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, 1719 6th Ave S, Birmingham, AL 35233
| | - Jane B. Allendorfer
- Departments of Neurology and Neurobiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Noah S. Philip
- Center for Neurorestoration and Neurotechnology, VA Providence Healthcare System, Providence, RI
| | - Stephen Correia
- Department of Psychiatry, Butler Hospital / Brown University, Providence, RI
| | - Robert A. Oster
- Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - W. Curt LaFrance
- Center for Neurorestoration and Neurotechnology, VA Providence Healthcare System, Providence, RI
- Departments of Psychiatry and Neurology, Rhode Island Hospital / Brown University, Providence, RI
| | - Jerzy P. Szaflarski
- Departments of Neurology, Neurobiology and Neurosurgery, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
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DiPiero M, Rodrigues PG, Gromala A, Dean DC. Applications of advanced diffusion MRI in early brain development: a comprehensive review. Brain Struct Funct 2023; 228:367-392. [PMID: 36585970 PMCID: PMC9974794 DOI: 10.1007/s00429-022-02605-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/21/2022] [Indexed: 01/01/2023]
Abstract
Brain development follows a protracted developmental timeline with foundational processes of neurodevelopment occurring from the third trimester of gestation into the first decade of life. Defining structural maturational patterns of early brain development is a critical step in detecting divergent developmental trajectories associated with neurodevelopmental and psychiatric disorders that arise later in life. While considerable advancements have already been made in diffusion magnetic resonance imaging (dMRI) for pediatric research over the past three decades, the field of neurodevelopment is still in its infancy with remarkable scientific and clinical potential. This comprehensive review evaluates the application, findings, and limitations of advanced dMRI methods beyond diffusion tensor imaging, including diffusion kurtosis imaging (DKI), constrained spherical deconvolution (CSD), neurite orientation dispersion and density imaging (NODDI) and composite hindered and restricted model of diffusion (CHARMED) to quantify the rapid and dynamic changes supporting the underlying microstructural architectural foundations of the brain in early life.
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Affiliation(s)
- Marissa DiPiero
- Department of Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | | | - Alyssa Gromala
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Douglas C Dean
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Department of Medical Physics, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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6
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Plachti A, Baaré WFC, Johansen LB, Thompson WK, Siebner HR, Madsen KS. Stability of associations between neuroticism and microstructural asymmetry of the cingulum during late childhood and adolescence: Insights from a longitudinal study with up to 11 waves. Hum Brain Mapp 2023; 44:1548-1564. [PMID: 36426846 PMCID: PMC9921236 DOI: 10.1002/hbm.26157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/15/2022] [Accepted: 11/09/2022] [Indexed: 11/27/2022] Open
Abstract
Adolescence is characterized by significant brain development and marks a period of the life span with an increased incidence of mood disorders, especially in females. The risk of developing mood disorders is also higher in individuals scoring high on neuroticism, a personality trait characterized by a tendency to experience negative and anxious emotions. We previously found in a cross-sectional study that neuroticism is associated with microstructural left-right asymmetry of the fronto-limbic white matter involved in emotional processing, with opposite effects in female and male adolescents. We now have extended this work collecting longitudinal data in 76 typically developing children and adolescents aged 7-18 years, including repeated MRI sampling up to 11 times. This enabled us, for the first time, to address the critical question, whether the association between neuroticism and frontal-limbic white matter asymmetry changes or remains stable across late childhood and adolescence. Neuroticism was assessed up to four times and showed good intraindividual stability and did not significantly change with age. Conforming our cross-sectional results, females scoring high on neuroticism displayed increased left-right cingulum fractional anisotropy (FA), while males showed decreased left-right cingulum FA asymmetry. Despite ongoing age-related increases in FA in cingulum, the association between neuroticism and cingulum FA asymmetry was already expressed in females in late childhood and remained stable across adolescence. In males, the association appeared to become more prominent during adolescence. Future longitudinal studies need to cover an earlier age span to elucidate the time point at which the relationship between neuroticism and cingulum FA asymmetry arises.
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Affiliation(s)
- Anna Plachti
- Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
| | - William F C Baaré
- Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
| | - Louise Baruël Johansen
- Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
| | - Wesley K Thompson
- Department of Radiology and Division of Biostatistics, Population Neuroscience and Genetics Lab, University of California San Diego, San Diego School of Medicine, La Jolla, California, USA
| | - Hartwig R Siebner
- Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark.,Department of Neurology, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark.,Institute for Clinical Medicine, Faculty of Medical and Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kathrine Skak Madsen
- Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark.,Radiography, Department of Technology, University College Copenhagen, Denmark
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7
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Hiscox LV, Fairchild G, Donald KA, Groenewold NA, Koen N, Roos A, Narr KL, Lawrence M, Hoffman N, Wedderburn CJ, Barnett W, Zar HJ, Stein DJ, Halligan SL. Antenatal maternal intimate partner violence exposure is associated with sex-specific alterations in brain structure among young infants: Evidence from a South African birth cohort. Dev Cogn Neurosci 2023; 60:101210. [PMID: 36764039 PMCID: PMC9929680 DOI: 10.1016/j.dcn.2023.101210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 02/02/2023] [Accepted: 02/04/2023] [Indexed: 02/09/2023] Open
Abstract
Maternal psychological distress during pregnancy has been linked to adverse outcomes in children with evidence of sex-specific effects on brain development. Here, we investigated whether in utero exposure to intimate partner violence (IPV), a particularly severe maternal stressor, is associated with brain structure in young infants from a South African birth cohort. Exposure to IPV during pregnancy was measured in 143 mothers at 28-32 weeks' gestation and infants underwent structural and diffusion magnetic resonance imaging (mean age 3 weeks). Subcortical volumetric estimates were compared between IPV-exposed (n = 63; 52% female) and unexposed infants (n = 80; 48% female), with white matter microstructure also examined in a subsample (IPV-exposed, n = 28, 54% female; unexposed infants, n = 42, 40% female). In confound adjusted analyses, maternal IPV exposure was associated with sexually dimorphic effects in brain volumes: IPV exposure predicted a larger caudate nucleus among males but not females, and smaller amygdala among females but not males. Diffusivity alterations within white matter tracts of interest were evident in males, but not females exposed to IPV. Results were robust to the removal of mother-infant pairs with pregnancy complications. Further research is required to understand how these early alterations are linked to the sex-bias in neuropsychiatric outcomes later observed in IPV-exposed children.
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Affiliation(s)
- Lucy V Hiscox
- Department of Psychology, University of Bath, Bath, UK.
| | | | - Kirsten A Donald
- Department of Pediatrics and Child Health, Red Cross War Memorial Children's Hospital and University of Cape Town, Cape Town, South Africa; The Neuroscience institute, University of Cape Town, Cape Town, South Africa
| | - Nynke A Groenewold
- Department of Pediatrics and Child Health, Red Cross War Memorial Children's Hospital and University of Cape Town, Cape Town, South Africa; The Neuroscience institute, University of Cape Town, Cape Town, South Africa; Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Nastassja Koen
- The Neuroscience institute, University of Cape Town, Cape Town, South Africa; SA MRC Unit on Risk & Resilience in Mental Disorders, Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Annerine Roos
- The Neuroscience institute, University of Cape Town, Cape Town, South Africa; Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Katherine L Narr
- Departments of Neurology, Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Marina Lawrence
- Department of Pediatrics and Child Health, Red Cross War Memorial Children's Hospital and University of Cape Town, Cape Town, South Africa
| | - Nadia Hoffman
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Catherine J Wedderburn
- Department of Pediatrics and Child Health, Red Cross War Memorial Children's Hospital and University of Cape Town, Cape Town, South Africa; The Neuroscience institute, University of Cape Town, Cape Town, South Africa; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Whitney Barnett
- Department of Psychology and Human Development, Vanderbilt University, USA
| | - Heather J Zar
- Department of Pediatrics and Child Health, Red Cross War Memorial Children's Hospital and University of Cape Town, Cape Town, South Africa; SA MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Dan J Stein
- The Neuroscience institute, University of Cape Town, Cape Town, South Africa; SA MRC Unit on Risk & Resilience in Mental Disorders, Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Sarah L Halligan
- Department of Psychology, University of Bath, Bath, UK; Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa; Department of Psychiatry, Stellenbosch University, Stellenbosch, South Africa
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8
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Zhang W, Ille S, Schwendner M, Wiestler B, Meyer B, Krieg SM. Tracking motor and language eloquent white matter pathways with intraoperative fiber tracking versus preoperative tractography adjusted by intraoperative MRI-based elastic fusion. J Neurosurg 2022; 137:1114-1123. [PMID: 35213839 DOI: 10.3171/2021.12.jns212106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/09/2021] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Preoperative fiber tracking (FT) enables visualization of white matter pathways. However, the intraoperative accuracy of preoperative image registration is reduced due to brain shift. Intraoperative FT is currently considered the standard of anatomical accuracy, while intraoperative imaging can also be used to correct and update preoperative data by intraoperative MRI (ioMRI)-based elastic fusion (IBEF). However, the use of intraoperative tractography is restricted due to the need for additional acquisition of diffusion imaging in addition to scanner limitations, quality factors, and setup time. Since IBEF enables compensation for brain shift and updating of preoperative FT, the aim of this study was to compare intraoperative FT with IBEF of preoperative FT. METHODS Preoperative MRI (pMRI) and ioMRI, both including diffusion tensor imaging (DTI) data, were acquired between February and November 2018. Anatomy-based DTI FT of the corticospinal tract (CST) and the arcuate fascicle (AF) was reconstructed at various fractional anisotropy (FA) values on pMRI and ioMRI, respectively. The intraoperative DTI FT, as a baseline tractography, was fused with original preoperative FT and IBEF-compensated FT, processes referred to as rigid fusion (RF) and elastic fusion (EF), respectively. The spatial overlap index (Dice coefficient [DICE]) and distances of surface points (average surface distance [ASD]) of fused FT before and after IBEF were analyzed and compared in operated and nonoperated hemispheres. RESULTS Seventeen patients with supratentorial brain tumors were analyzed. On the operated hemisphere, the overlap index of pre- and intraoperative FT of the CST by DICE significantly increased by 0.09 maximally after IBEF. A significant decrease by 0.5 mm maximally in the fused FT presented by ASD was observed. Similar improvements were found in IBEF-compensated FT, for which AF tractography on the tumor hemispheres increased by 0.03 maximally in DICE and decreased by 1.0 mm in ASD. CONCLUSIONS Preoperative tractography after IBEF is comparable to intraoperative tractography and can be a reliable alternative to intraoperative FT.
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Affiliation(s)
| | | | | | - Benedikt Wiestler
- 2Diagnostic and Interventional Neuroradiology, Technical University of Munich School of Medicine, Munich, Germany
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Prenatal depression exposure alters white matter integrity and neurodevelopment in early childhood. Brain Imaging Behav 2022; 16:1324-1336. [PMID: 35000066 PMCID: PMC9107412 DOI: 10.1007/s11682-021-00616-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2021] [Indexed: 11/02/2022]
Abstract
Prenatal exposure to maternal depression increases the risk for onset of emotional and behavioral disorders in children. We investigated the effects of exposure to prenatal depression on white matter microstructural integrity at birth and at 2-3 years, and associated neurodevelopment. Diffusion-weighted images were acquired for children of the Drakenstein Child Health Study at 2-4 weeks postpartum (n=70, 47% boys) and at 2-3 years of age (n=60, 58% boys). Tract-Based Spatial Statistics was used to compare, using an ROI based approach, diffusion tensor metrics across groups defined by presence (>19 on Beck's Depression Inventory and/or >12 on the Edinburgh Postnatal Depression Scale) or absence (below depression thresholds) of depression, and associations with neurodevelopmental measures at age 2-3 years were determined. We did not detect group differences in white matter integrity at neonatal age, but at 2-3 years, children in the exposed group demonstrated higher fractional anisotropy, and lower mean and radial diffusivity in association tracts compared to controls. This was notable in the sagittal stratum (radial diffusivity: p<0.01). Altered white matter integrity metrics were also observed in projection tracts, including the corona radiata, which associated with cognitive and motor outcomes in exposed 2-3-year-olds (p<0.05). Our findings of widespread white matter alterations in 2-3-year-old children with prenatal exposure to depression are consistent with previous findings, as well as with neuroimaging findings in adults with major depression. Further, we identified novel associations of altered white matter integrity with cognitive development in depression-exposed children, suggesting that these neuroimaging findings may have early functional impact.
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10
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What's New and What's Next in Diffusion MRI Preprocessing. Neuroimage 2021; 249:118830. [PMID: 34965454 PMCID: PMC9379864 DOI: 10.1016/j.neuroimage.2021.118830] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 10/26/2021] [Accepted: 12/15/2021] [Indexed: 02/07/2023] Open
Abstract
Diffusion MRI (dMRI) provides invaluable information for the study of tissue microstructure and brain connectivity, but suffers from a range of imaging artifacts that greatly challenge the analysis of results and their interpretability if not appropriately accounted for. This review will cover dMRI artifacts and preprocessing steps, some of which have not typically been considered in existing pipelines or reviews, or have only gained attention in recent years: brain/skull extraction, B-matrix incompatibilities w.r.t the imaging data, signal drift, Gibbs ringing, noise distribution bias, denoising, between- and within-volumes motion, eddy currents, outliers, susceptibility distortions, EPI Nyquist ghosts, gradient deviations, B1 bias fields, and spatial normalization. The focus will be on “what’s new” since the notable advances prior to and brought by the Human Connectome Project (HCP), as presented in the predecessing issue on “Mapping the Connectome” in 2013. In addition to the development of novel strategies for dMRI preprocessing, exciting progress has been made in the availability of open source tools and reproducible pipelines, databases and simulation tools for the evaluation of preprocessing steps, and automated quality control frameworks, amongst others. Finally, this review will consider practical considerations and our view on “what’s next” in dMRI preprocessing.
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11
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Rojoa D, Raheman F, Rassam J, Wade RG. Meta-analysis of the normal diffusion tensor imaging values of the median nerve and how they change in carpal tunnel syndrome. Sci Rep 2021; 11:20935. [PMID: 34686721 PMCID: PMC8536657 DOI: 10.1038/s41598-021-00353-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/05/2021] [Indexed: 02/07/2023] Open
Abstract
Carpal tunnel syndrome (CTS) leads to distortion of axonal architecture, demyelination and fibrosis within the median nerve. Diffusion tensor imaging (DTI) characterises tissue microstructure and generates reproducible proxy measures of nerve 'health' which are sensitive to myelination, axon diameter, fiber density and organisation. This meta-analysis summarises the normal DTI values of the median nerve, and how they change in CTS. This systematic review included studies reporting DTI of the median nerve at the level of the wrist in adults. The primary outcome was to determine the normal fractional anisotropy (FA) and mean diffusivity (MD) of the median nerve. Secondarily, we show how the FA and MD differ between asymptomatic adults and patients with CTS, and how these differences are independent of the acquisition methods. We included 32 studies of 2643 wrists, belonging to 1575 asymptomatic adults and 1068 patients with CTS. The normal FA was 0.58 (95% CI 0.56, 0.59) and the normal MD was 1.138 × 10-3 mm2/s (95% CI 1.101, 1.174). Patients with CTS had a significantly lower FA than controls (mean difference 0.12 [95% CI 0.09, 0.16]). Similarly, the median nerve of patients with CTS had a significantly higher mean diffusivity (mean difference 0.16 × 10-3 mm2/s [95% CI 0.05, 0.27]). The differences were independent of experimental factors. We provide summary estimates of the normal FA and MD of the median nerve in asymptomatic adults. Furthermore, we show that diffusion throughout the length of the median nerve becomes more isotropic in patients with CTS.
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Affiliation(s)
- Djamila Rojoa
- grid.419248.20000 0004 0400 6485Department of Plastic and Reconstructive Surgery, Leicester Royal Infirmary, Leicester, UK
| | - Firas Raheman
- grid.419248.20000 0004 0400 6485Department of Plastic and Reconstructive Surgery, Leicester Royal Infirmary, Leicester, UK
| | - Joseph Rassam
- grid.419248.20000 0004 0400 6485Department of Plastic and Reconstructive Surgery, Leicester Royal Infirmary, Leicester, UK
| | - Ryckie G. Wade
- grid.415967.80000 0000 9965 1030Department of Plastic and Reconstructive Surgery, Leeds Teaching Hospitals Trust, Leeds, UK ,grid.9909.90000 0004 1936 8403Leeds Institute for Medical Research, Advanced Imaging Centre, University of Leeds, Leeds, LS1 3EX UK
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12
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White matter tracts in Bipolar Disorder patients: A comparative study based on diffusion kurtosis and tensor imaging. J Affect Disord 2021; 292:45-55. [PMID: 34098469 DOI: 10.1016/j.jad.2021.05.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 05/12/2021] [Accepted: 05/20/2021] [Indexed: 11/23/2022]
Abstract
BACKGROUND Diffusion kurtosis imaging (DKI), an extension of diffusion tensor imaging (DTI), is a powerful tool for studying human brain.The purpose is to investigate differences between DKI and DTI by comparing parameters in same analysis methods with bipolar disorder (BD) patients. METHODS In this study, we attained in 47 BD patients and 49 age-, sex-, and education-matched healthy controls, complimented DTI and DKI scanning and got Fractional Anisotropy (FA), Mean Diffusion (MD) and Mean Kurtosis (MK). Voxel-wise statistical analysis was performed by the tract-based spatial statistics (TBSS) analysis and atlas-based regional data analysis. RESULTS TBSS analysis showed more widespread regions and higher fidelity in DKI parameters than DTI parameters with the same p-value threshold, and DKI parameters showed significant alterations after Family-Wise Error correction. The DKI-FA value in the corpus callosum, bilateral cingulum (cingulate gyrus), bilateral superior corona radiata, left anterior corona radiata and left posterior corona radiata of BD patients was negatively correlated with the duration of illness. In the atlas-based regional data analysis, the effect size of DTI-FA, DTI-MD, DKI-FA and DKI-MD were quantified using Cohen's d value. DKI-FA and DKI-MD demonstrated more between-group different regions and the higher (p < 0.001) absolute Cohen's d value than DTI-FA. LIMITATIONS This study did not consider the difference between sub-types of BD. CONCLUSIONS Compared to DTI parameters, DKI parameters were more sensitive and stable to probe the local microstructure, and particularly powerful to exploit cerebral alterations in BD patients.
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13
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Schlichting ML, Gumus M, Zhu T, Mack ML. The structure of hippocampal circuitry relates to rapid category learning in humans. Hippocampus 2021; 31:1179-1190. [PMID: 34379847 DOI: 10.1002/hipo.23382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 07/17/2021] [Accepted: 07/24/2021] [Indexed: 11/06/2022]
Abstract
Prior work suggests that complementary white matter pathways within the hippocampus (HPC) differentially support the learning of specific versus general information. In particular, while the trisynaptic pathway (TSP) rapidly forms memories for specific experiences, the monosynaptic pathway (MSP) slowly learns generalities. However, despite the theorized significance of such circuitry, characterizing how information flows within the HPC to support learning in humans remains a challenge. We leveraged diffusion-weighted imaging as a proxy for individual differences in white matter structure linking key regions along with TSP (HPC subfields CA3 and CA1 ) and MSP (entorhinal cortex and CA1 ) and related these differences in hippocampal structure to category learning ability. We hypothesized that learning to categorize the "exception" items that deviated from category rules would benefit from TSP-supported mnemonic specificity. Participant-level estimates of TSP- and MSP-related integrity were constructed from HPC subfield connectomes of white matter streamline density. Consistent with theories of TSP-supported learning mechanisms, we found a specific association between the integrity of CA3 -CA1 white matter connections and exception learning. These results highlight the significant role of HPC circuitry in complex human learning.
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Affiliation(s)
| | - Melisa Gumus
- Department of Psychology, University of Toronto, Toronto, Canada.,Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Teresa Zhu
- Department of Psychology, University of Toronto, Toronto, Canada
| | - Michael L Mack
- Department of Psychology, University of Toronto, Toronto, Canada
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14
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Roos A, Wedderburn CJ, Fouche JP, Subramoney S, Joshi SH, Woods RP, Zar HJ, Narr KL, Stein DJ, Donald KA. Central white matter integrity alterations in 2-3-year-old children following prenatal alcohol exposure. Drug Alcohol Depend 2021; 225:108826. [PMID: 34182371 PMCID: PMC8299546 DOI: 10.1016/j.drugalcdep.2021.108826] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Prenatal alcohol exposure (PAE) remains a potentially preventable, but pervasive risk factor to neurodevelopment. Yet, evidence is lacking on the impact of alcohol on brain development in toddlers. This study aimed to investigate the impact of PAE on brain white matter integrity in 2-3-year-old children. METHODS Children (n = 83, 30-37 months old) of the Drakenstein Child Health Study birth cohort, underwent diffusion MRI on a 3 T Siemens scanner during natural sleep. Parameters were extracted in children with PAE (n = 25, 56 % boys) and unexposed controls (n = 58, 62 % boys) using Tract-based Spatial Statistics, and compared by group. The contribution of maternal tobacco smoking to white matter differences was also explored. RESULTS Children with PAE had altered fractional anisotropy, radial diffusivity and axial diffusivity in brain stem, limbic and association tracts compared to unexposed controls. Notably lower fractional anisotropy was found in the uncinate fasciculus, and lower mean and radial diffusivity were found in the fornix stria terminalis and corticospinal tract (FDR corrected p < 0.05). There was a significant interaction effect of PAE and prenatal tobacco exposure which lowered mean, radial and axial diffusivity in the corticospinal tract significantly in the PAE group but not controls. CONCLUSION Widespread altered white matter microstructural integrity at 2-3 years of age is consistent with findings in neonates in the same and other cohorts, indicating persistence of effects of PAE through early life. Findings also highlight that prenatal tobacco exposure impacts the association of PAE on white matter alterations, amplifying effects in tracts underlying motor function.
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Affiliation(s)
- Annerine Roos
- SAMRC Unit on Risk and Resilience in Mental Disorders, Department of Psychiatry, Stellenbosch University, South Africa; Department of Pediatrics and Child Health, University of Cape Town, South Africa; Neuroscience Institute, University of Cape Town, South Africa.
| | - Catherine J. Wedderburn
- Department of Pediatrics and Child Health, University of Cape Town, South Africa,Neuroscience Institute, University of Cape Town, South Africa,Department of Clinical Research, London School of Hygiene & Tropical Medicine, United Kingdom
| | - Jean-Paul Fouche
- Neuroscience Institute, University of Cape Town, South Africa,Department of Psychiatry and Mental Health, University of Cape Town, South Africa
| | - Sivenesi Subramoney
- Department of Pediatrics and Child Health, University of Cape Town, South Africa
| | - Shantanu H. Joshi
- Departments of Neurology and of Bioengineering, University of California, Los Angeles, USA
| | - Roger P. Woods
- Departments of Neurology and of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, USA
| | - Heather J. Zar
- Department of Pediatrics and Child Health, University of Cape Town, South Africa
| | - Katherine L. Narr
- Departments of Neurology and of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, USA
| | - Dan J. Stein
- SAMRC Unit on Risk and Resilience in Mental Disorders, Department of Psychiatry, Stellenbosch University, South Africa,Neuroscience Institute, University of Cape Town, South Africa,Department of Psychiatry and Mental Health, University of Cape Town, South Africa
| | - Kirsten A. Donald
- Department of Pediatrics and Child Health, University of Cape Town, South Africa,Neuroscience Institute, University of Cape Town, South Africa
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15
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Griffiths TT, Flather R, Teh I, Haroon HA, Shelley D, Plein S, Bourke G, Wade RG. Diffusion tensor imaging in cubital tunnel syndrome. Sci Rep 2021; 11:14982. [PMID: 34294771 PMCID: PMC8298404 DOI: 10.1038/s41598-021-94211-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/25/2021] [Indexed: 11/09/2022] Open
Abstract
Cubital tunnel syndrome (CuTS) is the 2nd most common compressive neuropathy. To improve both diagnosis and the selection of patients for surgery, there is a pressing need to develop a reliable and objective test of ulnar nerve 'health'. Diffusion tensor imaging (DTI) characterises tissue microstructure and may identify differences in the normal ulnar from those affected by CuTS. The aim of this study was to compare the DTI metrics from the ulnar nerves of healthy (asymptomatic) adults and patients with CuTS awaiting surgery. DTI was acquired at 3.0 T using single-shot echo-planar imaging (55 axial slices, 3 mm thick, 1.5 mm2 in-plane) with 30 diffusion sensitising gradient directions, a b-value of 800 s/mm2 and 4 signal averages. The sequence was repeated with the phase-encoding direction reversed. Data were combined and corrected using the FMRIB Software Library (FSL) and reconstructed using generalized q-sampling imaging in DSI Studio. Throughout the length of the ulnar nerve, the fractional anisotropy (FA), quantitative anisotropy (QA), mean diffusivity (MD), axial diffusivity (AD) and radial diffusivity (RD) were extracted, then compared using mixed-effects linear regression. Thirteen healthy controls (8 males, 5 females) and 8 patients with CuTS (6 males, 2 females) completed the study. Throughout the length of the ulnar nerve, diffusion was more isotropic in patients with CuTS. Overall, patients with CuTS had a 6% lower FA than controls, with the largest difference observed proximal to the cubital tunnel (mean difference 0.087 [95% CI 0.035, 0.141]). Patients with CuTS also had a higher RD than controls, with the largest disparity observed within the forearm (mean difference 0.252 × 10-4 mm2/s [95% CI 0.085 × 10-4, 0.419 × 10-4]). There were no significant differences between patients and controls in QA, MD or AD. Throughout the length of the ulnar nerve, the fractional anisotropy and radial diffusivity in patients with CuTS are different to healthy controls. These findings suggest that DTI may provide an objective assessment of the ulnar nerve and potentially, improve the management of CuTS.
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Affiliation(s)
- Timothy T Griffiths
- Leeds Institute for Medical Research, University of Leeds, Leeds, UK
- Department of Plastic, Reconstructive and Hand Surgery, Leeds Teaching Hospitals Trust, Leeds, UK
| | - Robert Flather
- Leeds Institute for Medical Research, University of Leeds, Leeds, UK
- Department of Plastic, Reconstructive and Hand Surgery, Leeds Teaching Hospitals Trust, Leeds, UK
| | - Irvin Teh
- Leeds Institute for Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
| | - Hamied A Haroon
- Division of Neuroscience and Experimental Psychology, The University of Manchester, Manchester, UK
| | - David Shelley
- The Advanced Imaging Centre, Leeds Teaching Hospitals Trust, Leeds, UK
| | - Sven Plein
- Leeds Institute for Medical Research, University of Leeds, Leeds, UK
- Leeds Institute for Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
| | - Grainne Bourke
- Leeds Institute for Medical Research, University of Leeds, Leeds, UK
- Department of Plastic, Reconstructive and Hand Surgery, Leeds Teaching Hospitals Trust, Leeds, UK
| | - Ryckie G Wade
- Leeds Institute for Medical Research, University of Leeds, Leeds, UK.
- Department of Plastic, Reconstructive and Hand Surgery, Leeds Teaching Hospitals Trust, Leeds, UK.
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16
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Chang X, Mandl RCW, Pasternak O, Brouwer RM, Cahn W, Collin G. Diffusion MRI derived free-water imaging measures in patients with schizophrenia and their non-psychotic siblings. Prog Neuropsychopharmacol Biol Psychiatry 2021; 109:110238. [PMID: 33400942 DOI: 10.1016/j.pnpbp.2020.110238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/16/2020] [Accepted: 12/30/2020] [Indexed: 10/22/2022]
Abstract
Free-water imaging is a diffusion MRI technique that separately models water diffusion hindered by fiber tissue and water that disperses freely in the extracellular space. Studies using this technique have shown that schizophrenia is characterized by a lower level of fractional anisotropy of the tissue compartment (FAt) and higher free-water fractional volume (FW). It is unknown, however, whether such abnormalities are an expression of pre-existing (genetic) risk for schizophrenia or a manifestation of the illness. To investigate the contribution of familial risk factors to white matter abnormalities, we used the free-water imaging technique to assess FAt and FW in a large cohort of 471 participants including 161 patients with schizophrenia, 182 non-psychotic siblings, and 128 healthy controls. In this sample, patients did not show significant differences in FAt as compared to controls, but did exhibit a higher level of FW relative to both controls and siblings in the left uncinate fasciculus, superior corona radiata and fornix / stria terminalis. This increase in FW was found to be related to, though not solely explained by, ventricular enlargement. Siblings did not show significant FW abnormalities. However, siblings did show a higher level of FAt as compared to controls and patients, in line with results of a previous study on the same data using conventional DTI. Taken together, our findings suggest that extracellular free-water accumulation in patients is likely a manifestation of established disease rather than an expression of familial risk for schizophrenia and that super-normal levels of FAt in unaffected siblings may reflect a compensatory process.
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Affiliation(s)
- Xiao Chang
- Department of Psychiatry, University Medical Center Utrecht (UMCU), UMCU Brain Center, Utrecht, the Netherlands; Social, Genetic and Developmental Psychiatry, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK; Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.
| | - René C W Mandl
- Department of Psychiatry, University Medical Center Utrecht (UMCU), UMCU Brain Center, Utrecht, the Netherlands
| | - Ofer Pasternak
- Department of Psychiatry, Psychiatry Neuroimaging Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, USA; Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Rachel M Brouwer
- Department of Psychiatry, University Medical Center Utrecht (UMCU), UMCU Brain Center, Utrecht, the Netherlands
| | - Wiepke Cahn
- Department of Psychiatry, University Medical Center Utrecht (UMCU), UMCU Brain Center, Utrecht, the Netherlands; Altrecht Institute of Mental Health Care, Utrecht, the Netherlands
| | - Guusje Collin
- Department of Psychiatry, University Medical Center Utrecht (UMCU), UMCU Brain Center, Utrecht, the Netherlands; Department of Psychiatry, Psychiatry Neuroimaging Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Boston, USA
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17
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Lahti K, Parkkola R, Jääsaari P, Haataja L, Saunavaara V. The impact of susceptibility correction on diffusion metrics in adolescents. Pediatr Radiol 2021; 51:1471-1480. [PMID: 33893847 PMCID: PMC8266789 DOI: 10.1007/s00247-021-05000-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/16/2020] [Accepted: 02/03/2021] [Indexed: 11/06/2022]
Abstract
BACKGROUND Diffusion tensor imaging is a widely used imaging method of brain white matter, but it is prone to imaging artifacts. The data corrections can affect the measured values. OBJECTIVE To explore the impact of susceptibility correction on diffusion metrics. MATERIALS AND METHODS A cohort of 27 healthy adolescents (18 boys, 9 girls, mean age 12.7 years) underwent 3-T MRI, and we collected two diffusion data sets (anterior-posterior). The data were processed both with and without susceptibility artifact correction. We derived fractional anisotropy, mean diffusivity and histogram data of fiber length distribution from both the corrected and uncorrected data, which were collected from the corpus callosum, corticospinal tract and cingulum bilaterally. RESULTS Fractional anisotropy and mean diffusivity values significantly differed when comparing the pathways in all measured tracts. The fractional anisotropy values were lower and the mean diffusivity values higher in the susceptibility-corrected data than in the uncorrected data. We found a significant difference in total tract length in the corpus callosum and the corticospinal tract. CONCLUSION This study indicates that susceptibility correction has a significant effect on measured fractional anisotropy, and on mean diffusivity values and tract lengths. To receive reliable and comparable results, the correction should be used systematically.
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Affiliation(s)
- Katri Lahti
- Department of Pediatric Neurology, University of Turku and Turku University Hospital, P.O. Box 52, 20521, Turku, Finland.
- Department of Adolescent Psychiatry, Turku University Hospital, Turku, Finland.
| | - Riitta Parkkola
- Department of Radiology, University of Turku and Turku University Hospital, Turku, Finland
| | - Päivi Jääsaari
- Department of Oral and Maxillofacial Diseases, Turku University Hospital, Turku, Finland
| | - Leena Haataja
- Children's Hospital, and Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Virva Saunavaara
- Department of Medical Physics, Turku University Hospital, Turku, Finland
- Turku PET Centre, Turku University Hospital, Turku, Finland
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18
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Abstract
Prenatal alcohol exposure leads to alterations in cognition, behavior and underlying brain architecture. However, prior studies have not integrated structural and functional imaging data in children with prenatal alcohol exposure. The aim of this study was to characterize disruptions in both structural and functional brain network organization after prenatal alcohol exposure in very early life. A group of 11 neonates with prenatal alcohol exposure and 14 unexposed controls were investigated using diffusion weighted structural and resting state functional magnetic resonance imaging. Covariance networks were created using graph theoretical analyses for each data set, controlling for age and sex. Group differences in global hub arrangement and regional connectivity were determined using nonparametric permutation tests. Neonates with prenatal alcohol exposure and controls exhibited similar global structural network organization. However, global functional networks of neonates with prenatal alcohol exposure comprised of temporal and limbic hubs, while hubs were more distributed in controls representing an early default mode network. On a regional level, controls showed prominent structural and functional connectivity in parietal and occipital regions. Neonates with prenatal alcohol exposure showed regionally, predominant structural and functional connectivity in several subcortical regions and occipital regions. The findings suggest early functional disruption on a global and regional level after prenatal alcohol exposure and indicate suboptimal organization of functional networks. These differences likely underlie sensory dysregulation and behavioral difficulties in prenatal alcohol exposure.
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19
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Dauleac C, Bannier E, Cotton F, Frindel C. Effect of distortion corrections on the tractography quality in spinal cord diffusion-weighted imaging. Magn Reson Med 2021; 85:3241-3255. [PMID: 33475180 DOI: 10.1002/mrm.28665] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 12/20/2022]
Abstract
PURPOSE To assess the impact of a different distortion correction (DC) method and patient geometry (sagittal balance) on the quality of spinal cord tractography rendering according to different tractography approaches. METHODS Forty-four adults free of spinal cord diseases underwent cervical diffusion-weighted imaging. The phase-encoding direction was head→foot. Sequence with opposed polarities (foot→head) was acquired to perform DC. Eddy-current, motion effects, and susceptibility artifact correction methods were used for DC, and two deterministic and one probabilistic tractography approaches were evaluated using MRtrix and DSI Studio tractography software. Fiber length and number of fibers were extracted to evaluate the quality of the tractography rendering. For each subject, cervical lordosis was measured to assess patient geometry. The angle between the main direction of the spinal cord and the orientation of the acquisition box were computed at each spine level to assess acquisition geometry and define an angle threshold for which a tractography of good quality is no longer possible. RESULTS There was a significant improvement in tractography quality after performing DC with susceptibility artifact correction using a deterministic approach based on tensor. Before DC, the angle threshold was defined at C6 (15.2°) compared with C7 (21.9°) after corrections, demonstrating the importance of spinal cord angulation for DC. CONCLUSION The impact of DC on tractography quality is greatly impacted by acquisition geometry. To obtain a good-quality tractography, we propose as a future perspective to adapt the acquisition geometry to that of the patient by automatically adjusting the acquisition box.
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Affiliation(s)
- Corentin Dauleac
- Department of Neurosurgery, Hôpital neurologique et neurochirurgical Pierre Wertheimer, Hospices Civils de Lyon, Lyon, France.,Université de Lyon, Université Claude Bernard Lyon I, Lyon, France.,Laboratoire CREATIS, CNRS UMR5220, INSA-Lyon, Université de Lyon I, Inserm U1206, Lyon, France
| | - Elise Bannier
- Université de Rennes, Inria, CNRS, Inserm, IRISA UMR 6074, Empenn, France.,Department of Radiology, CHU de Rennes, Rennes, France
| | - François Cotton
- Université de Lyon, Université Claude Bernard Lyon I, Lyon, France.,Laboratoire CREATIS, CNRS UMR5220, INSA-Lyon, Université de Lyon I, Inserm U1206, Lyon, France.,Department of Radiology, Centre Hospitalier de Lyon Sud, Hospices Civils de Lyon, Lyon, France
| | - Carole Frindel
- Université de Lyon, Université Claude Bernard Lyon I, Lyon, France.,Laboratoire CREATIS, CNRS UMR5220, INSA-Lyon, Université de Lyon I, Inserm U1206, Lyon, France
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20
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Messinger A, Sirmpilatze N, Heuer K, Loh KK, Mars RB, Sein J, Xu T, Glen D, Jung B, Seidlitz J, Taylor P, Toro R, Garza-Villarreal EA, Sponheim C, Wang X, Benn RA, Cagna B, Dadarwal R, Evrard HC, Garcia-Saldivar P, Giavasis S, Hartig R, Lepage C, Liu C, Majka P, Merchant H, Milham MP, Rosa MGP, Tasserie J, Uhrig L, Margulies DS, Klink PC. A collaborative resource platform for non-human primate neuroimaging. Neuroimage 2020; 226:117519. [PMID: 33227425 PMCID: PMC9272762 DOI: 10.1016/j.neuroimage.2020.117519] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/15/2020] [Accepted: 10/24/2020] [Indexed: 01/12/2023] Open
Abstract
Neuroimaging non-human primates (NHPs) is a growing, yet highly specialized field of neuroscience. Resources that were primarily developed for human neuroimaging often need to be significantly adapted for use with NHPs or other animals, which has led to an abundance of custom, in-house solutions. In recent years, the global NHP neuroimaging community has made significant efforts to transform the field towards more open and collaborative practices. Here we present the PRIMatE Resource Exchange (PRIME-RE), a new collaborative online platform for NHP neuroimaging. PRIME-RE is a dynamic community-driven hub for the exchange of practical knowledge, specialized analytical tools, and open data repositories, specifically related to NHP neuroimaging. PRIME-RE caters to both researchers and developers who are either new to the field, looking to stay abreast of the latest developments, or seeking to collaboratively advance the field.
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Affiliation(s)
- Adam Messinger
- Laboratory of Brain and Cognition, National Institute of Mental Health, Bethesda, USA
| | - Nikoloz Sirmpilatze
- German Primate Center - Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany; Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Katja Heuer
- Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany; Center for Research and Interdisciplinarity (CRI), INSERM U1284, Université de Paris, Paris, France
| | - Kep Kee Loh
- Institut de Neurosciences de la Timone (INT), Aix-Marseille Université, CNRS, UMR 7289, 13005 Marseille, France; Institute for Language, Communication, and the Brain, Aix-Marseille University, Marseille, France
| | - Rogier B Mars
- Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK; Donders Institute for Brain, Cognition, and Behaviour, Radboud University Nijmegen, Montessorilaan 3, 6525 HR Nijmegen, The Netherlands
| | - Julien Sein
- Institut de Neurosciences de la Timone (INT), Aix-Marseille Université, CNRS, UMR 7289, 13005 Marseille, France
| | - Ting Xu
- Child Mind Institute, 101 E 56th St, New York, NY 10022, USA
| | - Daniel Glen
- Scientific and Statistical Computing Core, National Institute of Mental Health, Bethesda, USA
| | - Benjamin Jung
- Laboratory of Brain and Cognition, National Institute of Mental Health, Bethesda, USA; Department of Neuroscience, Brown University, Providence RI USA
| | - Jakob Seidlitz
- Department of Child and Adolescent Psychiatry and Behavioral Science, Children's Hospital of Philadelphia, Philadelphia PA USA; Department of Psychiatry, University of Pennsylvania, Philadelphia PA USA
| | - Paul Taylor
- Scientific and Statistical Computing Core, National Institute of Mental Health, Bethesda, USA
| | - Roberto Toro
- Center for Research and Interdisciplinarity (CRI), INSERM U1284, Université de Paris, Paris, France; Department of Neuroscience, Institut Pasteur, UMR 3571 CNRS, Université de Paris, Paris, France
| | - Eduardo A Garza-Villarreal
- Instituto de Neurobiologia, Universidad Nacional Autónoma de México campus Juriquilla, Queretaro, Mexico
| | - Caleb Sponheim
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago IL USA
| | - Xindi Wang
- McGill Centre for Integrative Neuroscience, Montreal Neurological Institute (MNI), Quebec, Canada
| | - R Austin Benn
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Bastien Cagna
- Institut de Neurosciences de la Timone (INT), Aix-Marseille Université, CNRS, UMR 7289, 13005 Marseille, France
| | - Rakshit Dadarwal
- German Primate Center - Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany; Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Henry C Evrard
- Centre for Integrative Neurosciences, University of Tübingen, Tübingen, Germany; Max Planck Institute for Biological Cybernetics, Tübingen, Germany; Nathan S. Kline Institute for Psychiatric Research, Orangeburg, New York, USA; International Center for Primate Brain Research, Chinese Academy of Science, Shanghai, PRC
| | - Pamela Garcia-Saldivar
- Instituto de Neurobiologia, Universidad Nacional Autónoma de México campus Juriquilla, Queretaro, Mexico
| | - Steven Giavasis
- Child Mind Institute, 101 E 56th St, New York, NY 10022, USA
| | - Renée Hartig
- Centre for Integrative Neurosciences, University of Tübingen, Tübingen, Germany; Max Planck Institute for Biological Cybernetics, Tübingen, Germany; Focus Program Translational Neurosciences, University Medical Center, Mainz, Germany
| | - Claude Lepage
- McGill Centre for Integrative Neuroscience, Montreal Neurological Institute (MNI), Quebec, Canada
| | - Cirong Liu
- Department of Neurobiology, University of Pittsburgh Brain Institute, Pittsburgh PA, USA
| | - Piotr Majka
- Laboratory of Neuroinformatics, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, 02-093 Warsaw, Poland; Australian Research Council, Centre of Excellence for Integrative Brain Function, Monash University Node, Clayton, VIC 3800, Australia; Biomedicine Discovery Institute and Department of Physiology, Monash University, Clayton, VIC 3800, Australia
| | - Hugo Merchant
- Instituto de Neurobiologia, Universidad Nacional Autónoma de México campus Juriquilla, Queretaro, Mexico
| | - Michael P Milham
- Child Mind Institute, 101 E 56th St, New York, NY 10022, USA; Nathan S. Kline Institute for Psychiatric Research, Orangeburg, New York, USA
| | - Marcello G P Rosa
- Australian Research Council, Centre of Excellence for Integrative Brain Function, Monash University Node, Clayton, VIC 3800, Australia; Biomedicine Discovery Institute and Department of Physiology, Monash University, Clayton, VIC 3800, Australia
| | - Jordy Tasserie
- Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Direction de la Recherche Fondamentale, NeuroSpin Center, Gif-sur-Yvette, France; Cognitive Neuroimaging Unit, Institut National de la Santé et de la Recherche Médicale U992, Gif-sur-Yvette, France; Université Paris-Saclay, France
| | - Lynn Uhrig
- Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Direction de la Recherche Fondamentale, NeuroSpin Center, Gif-sur-Yvette, France; Cognitive Neuroimaging Unit, Institut National de la Santé et de la Recherche Médicale U992, Gif-sur-Yvette, France
| | - Daniel S Margulies
- Integrative Neuroscience and Cognition Center, Centre National de la Recherche Scientifique (CNRS) UMR 8002, Paris, France
| | - P Christiaan Klink
- Department of Vision & Cognition, Netherlands Institute for Neuroscience, Amsterdam, The Netherlands.
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21
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Hong SJ, Hyung B, Paquola C, Bernhardt BC. The Superficial White Matter in Autism and Its Role in Connectivity Anomalies and Symptom Severity. Cereb Cortex 2020; 29:4415-4425. [PMID: 30566613 DOI: 10.1093/cercor/bhy321] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 01/11/2018] [Accepted: 11/26/2018] [Indexed: 12/29/2022] Open
Abstract
In autism spectrum disorders (ASDs), the majority of neuroimaging studies have focused on the analysis of cortical morphology. White matter changes remain less understood, particularly their association to cortical structure and function. Here, we focused on region that has gained only little attention in ASD neuroimaging: the superficial white matter (SWM) immediately beneath the cortical interface, a compartment playing a prominent role in corticogenesis that incorporates long- and short-range fibers implicated in corticocortical connectivity. Studying a multicentric dataset of ASD and neurotypical controls, we harnessed surface-based techniques to aggregate microstructural SWM diffusion features. Multivariate analysis revealed SWM anomalies in ASD compared with controls in medial parietal and temporoparietal regions. Effects were similar in children and adolescents/adults and consistent across sites. Although SWM anomalies were more confined when correcting for cortical thickness and surface area, findings were overall robust. Diffusion anomalies modulated functional connectivity reductions in ASD and related to symptom severity. Furthermore, mediation models indicated a link between SWM changes, functional connectivity, and symptom load. Analyses targeting the SWM offer a novel perspective on the interplay between structural and functional network perturbations in ASD, highlighting a potentially important neurobiological substrate contributing to its diverse behavioral phenotype.
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Affiliation(s)
- Seok-Jun Hong
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada.,Center for the Developing Brain, Child Mind Institute, 101 E 56th St, New York, NY 10022, USA
| | - Brian Hyung
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Casey Paquola
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Boris C Bernhardt
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
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22
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Diffusion tensor imaging of the roots of the brachial plexus: a systematic review and meta-analysis of normative values. Clin Transl Imaging 2020; 8:419-431. [PMID: 33282795 PMCID: PMC7708343 DOI: 10.1007/s40336-020-00393-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 09/25/2020] [Indexed: 02/06/2023]
Abstract
Purpose Diffusion tensor magnetic resonance imaging (DTI) characterises tissue microstructure and provides proxy measures of myelination, axon diameter, fibre density and organisation. This may be valuable in the assessment of the roots of the brachial plexus in health and disease. Therefore, there is a need to define the normal DTI values. Methods The literature was systematically searched for studies of asymptomatic adults who underwent DTI of the brachial plexus. Participant characteristics, scanning protocols, and measurements of the fractional anisotropy (FA) and mean diffusivity (MD) of each spinal root were extracted by two independent review authors. Generalised linear modelling was used to estimate the effect of experimental conditions on the FA and MD. Meta-analysis of root-level estimates was performed using Cohen's method with random effects. Results Nine articles, describing 316 adults (1:1 male:female) of mean age 35 years (SD 6) were included. Increments of ten diffusion sensitising gradient directions reduced the mean FA by 0.01 (95% CI 0.01, 0.03). Each year of life reduced the mean MD by 0.03 × 10-3 mm2/s (95% CI 0.01, 0.04). At 3-T, the pooled mean FA of the roots was 0.36 (95% CI 0.34, 0.38; I 2 98%). The pooled mean MD of the roots was 1.51 × 10-3 mm2/s (95% CI 1.45, 1.56; I 2 99%). Conclusions The FA and MD of the roots of the brachial plexus vary according to experimental conditions and participant factors. We provide summary estimates of the normative values in different conditions which may be valuable to researchers and clinicians alike.
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23
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Tokariev M, Vuontela V, Perkola J, Lönnberg P, Lano A, Andersson S, Metsäranta M, Carlson S. A protocol for the analysis of DTI data collected from young children. MethodsX 2020; 7:100878. [PMID: 32382519 PMCID: PMC7200313 DOI: 10.1016/j.mex.2020.100878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/19/2020] [Indexed: 01/01/2023] Open
Abstract
Software packages were applied to mitigate the effects of artifacts and to produce robust tensor estimation. Opposite phase-encoding directions were used in DTI acquisition to improve correction for EPI distortions. Advanced tensor-based registration of DTI images was obtained using a population-specific template.
Analysis of scalar maps obtained by diffusion tensor imaging (DTI) produce valuable information about the microstructure of the brain white matter. The DTI scanning of child populations, compared with adult groups, requires specifically designed data acquisition protocols that take into consideration the trade-off between the scanning time, diffusion strength, number of diffusion directions, and the applied analysis techniques. Furthermore, inadequate normalization of DTI images and non-robust tensor reconstruction have profound effects on data analyses and may produce biased statistical results. Here, we present an acquisition sequence that was specifically designed for pediatric populations, and describe the analysis steps of the DTI data collected from extremely preterm-born young school-aged children and their age- and gender-matched controls. The protocol utilizes multiple software packages to address the effects of artifacts and to produce robust tensor estimation. The computation of a population-specific template and the nonlinear registration of tensorial images with this template were implemented to improve alignment of brain images from the children.
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Affiliation(s)
- Maksym Tokariev
- Department of Neuroscience and Biomedical Engineering, Aalto University School of Science, Espoo, Finland.,Department of Physiology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Virve Vuontela
- Department of Neuroscience and Biomedical Engineering, Aalto University School of Science, Espoo, Finland.,Department of Physiology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jaana Perkola
- Department of Clinical Neurophysiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Piia Lönnberg
- Department of Child Neurology, Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Aulikki Lano
- Department of Child Neurology, Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Sture Andersson
- Department of Pediatrics, Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Marjo Metsäranta
- Department of Pediatrics, Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Synnöve Carlson
- Department of Neuroscience and Biomedical Engineering, Aalto University School of Science, Espoo, Finland.,Department of Physiology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Advanced Magnetic Imaging Centre, Aalto University School of Science, Espoo, Finland
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24
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Gu X, Eklund A. Evaluation of Six Phase Encoding Based Susceptibility Distortion Correction Methods for Diffusion MRI. Front Neuroinform 2019; 13:76. [PMID: 31866847 PMCID: PMC6906182 DOI: 10.3389/fninf.2019.00076] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/21/2019] [Indexed: 11/23/2022] Open
Abstract
Purpose: Susceptibility distortions impact diffusion MRI data analysis and is typically corrected during preprocessing. Correction strategies involve three classes of methods: registration to a structural image, the use of a fieldmap, or the use of images acquired with opposing phase encoding directions. It has been demonstrated that phase encoding based methods outperform the other two classes, but unfortunately, the choice of which phase encoding based method to use is still an open question due to the absence of any systematic comparisons. Methods: In this paper we quantitatively evaluated six popular phase encoding based methods for correcting susceptibility distortions in diffusion MRI data. We employed a framework that allows for the simulation of realistic diffusion MRI data with susceptibility distortions. We evaluated the ability for methods to correct distortions by comparing the corrected data with the ground truth. Four diffusion tensor metrics (FA, MD, eigenvalues and eigenvectors) were calculated from the corrected data and compared with the ground truth. We also validated two popular indirect metrics using both simulated data and real data. The two indirect metrics are the difference between the corrected LR and AP data, and the FA standard deviation over the corrected LR, RL, AP, and PA data. Results: We found that DR-BUDDI and TOPUP offered the most accurate and robust correction compared to the other four methods using both direct and indirect evaluation metrics. EPIC and HySCO performed well in correcting b0 images but produced poor corrections for diffusion weighted volumes, and also they produced large errors for the four diffusion tensor metrics. We also demonstrate that the indirect metric (the difference between corrected LR and AP data) gives a different ordering of correction quality than the direct metric. Conclusion: We suggest researchers to use DR-BUDDI or TOPUP for susceptibility distortion correction. The two indirect metrics (the difference between corrected LR and AP data, and the FA standard deviation) should be interpreted together as a measure of distortion correction quality. The performance ranking of the various tools inferred from direct and indirect metrics differs slightly. However, across all tools, the results of direct and indirect metrics are highly correlated indicating that the analysis of indirect metrics may provide a good proxy of the performance of a correction tool if assessment using direct metrics is not feasible.
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Affiliation(s)
- Xuan Gu
- Division of Medical Informatics, Department of Biomedical Engineering, Linköping University, Linköping, Sweden.,Center for Medical Image Science and Visualization, Linköping University, Linköping, Sweden
| | - Anders Eklund
- Division of Medical Informatics, Department of Biomedical Engineering, Linköping University, Linköping, Sweden.,Center for Medical Image Science and Visualization, Linköping University, Linköping, Sweden.,Division of Statistics and Machine Learning, Department of Computer and Information Science, Linköping University, Linköping, Sweden
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25
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Maximov II, Alnæs D, Westlye LT. Towards an optimised processing pipeline for diffusion magnetic resonance imaging data: Effects of artefact corrections on diffusion metrics and their age associations in UK Biobank. Hum Brain Mapp 2019; 40:4146-4162. [PMID: 31173439 PMCID: PMC6865652 DOI: 10.1002/hbm.24691] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/14/2019] [Accepted: 05/27/2019] [Indexed: 12/30/2022] Open
Abstract
Increasing interest in the structural and functional organisation of the human brain encourages the acquisition of big data sets comprising multiple neuroimaging modalities, often accompanied by additional information obtained from health records, cognitive tests, biomarkers and genotypes. Diffusion weighted magnetic resonance imaging data enables a range of promising imaging phenotypes probing structural connections as well as macroanatomical and microstructural properties of the brain. The reliability and biological sensitivity and specificity of diffusion data depend on processing pipeline. A state-of-the-art framework for data processing facilitates cross-study harmonisation and reduces pipeline-related variability. Using diffusion magnetic resonance imaging (MRI) data from 218 individuals in the UK Biobank, we evaluate the effects of different processing steps that have been suggested to reduce imaging artefacts and improve reliability of diffusion metrics. In lack of a ground truth, we compared diffusion metric sensitivity to age between pipelines. By comparing distributions and age sensitivity of the resulting diffusion metrics based on different approaches (diffusion tensor imaging, diffusion kurtosis imaging and white matter tract integrity), we evaluate a general pipeline comprising seven postprocessing blocks: noise correction; Gibbs ringing correction; evaluation of field distortions; susceptibility, eddy-current and motion-induced distortion corrections; bias field correction; spatial smoothing and final diffusion metric estimations. Based on this evaluation, we suggest an optimised processing pipeline for diffusion weighted MRI data.
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Affiliation(s)
- Ivan I. Maximov
- Department of PsychologyUniversity of OsloOsloNorway
- Department of Mental Health and AddictionNorwegian Centre for Mental Disorders Research spiepr132 (NORMENT), Oslo University Hospital & Institute of Clinical Medicine, University of OsloOsloNorway
| | - Dag Alnæs
- Department of Mental Health and AddictionNorwegian Centre for Mental Disorders Research spiepr132 (NORMENT), Oslo University Hospital & Institute of Clinical Medicine, University of OsloOsloNorway
| | - Lars T. Westlye
- Department of PsychologyUniversity of OsloOsloNorway
- Department of Mental Health and AddictionNorwegian Centre for Mental Disorders Research spiepr132 (NORMENT), Oslo University Hospital & Institute of Clinical Medicine, University of OsloOsloNorway
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26
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Brun L, Pron A, Sein J, Deruelle C, Coulon O. Diffusion MRI: Assessment of the Impact of Acquisition and Preprocessing Methods Using the BrainVISA-Diffuse Toolbox. Front Neurosci 2019; 13:536. [PMID: 31275091 PMCID: PMC6593278 DOI: 10.3389/fnins.2019.00536] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/08/2019] [Indexed: 12/28/2022] Open
Abstract
Diffusion MR images are prone to severe geometric distortions induced by head movement, eddy-current and inhomogeneity of magnetic susceptibility. Various correction methods have been proposed that depend on the choice of the acquisition settings and potentially provide highly different data quality. However, the impact of this choice has not been evaluated in terms of the ratio between scan time and preprocessed data quality. This study aims at investigating the impact of six well-known preprocessing methods, each associated to specific acquisition settings, on the outcome of diffusion analyses. For this purpose, we developed a comprehensive toolbox called Diffuse which automatically guides the user to the best preprocessing pipeline according to the input data. Using MR images of 20 subjects from the HCP dataset, we compared the six pre-processing pipelines regarding the following criteria: the ability to recover brain’s true geometry, the tensor model estimation and derived indices in the white matter, and finally the spatial dispersion of six well known connectivity pathways. As expected the pipeline associated to the longer acquisition fully repeated with reversed phase-encoding (RPE) yielded the higher data quality and was used as a reference to evaluate the other pipelines. In this way, we highlighted several significant aspects of other pre-processing pipelines. Our results first established that eddy-current correction improves the tensor-fitting performance with a localized impact especially in the corpus callosum. Concerning susceptibility distortions, we showed that the use of a field map is not sufficient and involves additional smoothing, yielding to an artificial decrease of tensor-fitting error. Of most importance, our findings demonstrate that, for an equivalent scan time, the acquisition of a b0 volume with RPE ensures a better brain’s geometry reconstruction and local improvement of tensor quality, without any smoothing of the image. This was found to be the best scan time/data quality compromise. To conclude, this study highlights and attempts to quantify the strong dependence of diffusion metrics on acquisition settings and preprocessing methods.
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Affiliation(s)
- Lucile Brun
- Institut de Neurosciences de La Timone, Aix-Marseille University, CNRS, UMR 7289, Marseille, France
| | - Alexandre Pron
- Institut de Neurosciences de La Timone, Aix-Marseille University, CNRS, UMR 7289, Marseille, France
| | - Julien Sein
- Institut de Neurosciences de La Timone, Aix-Marseille University, CNRS, UMR 7289, Marseille, France
| | - Christine Deruelle
- Institut de Neurosciences de La Timone, Aix-Marseille University, CNRS, UMR 7289, Marseille, France
| | - Olivier Coulon
- Institut de Neurosciences de La Timone, Aix-Marseille University, CNRS, UMR 7289, Marseille, France
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27
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Micro- and Macrostructural White Matter Integrity in Never-Treated and Currently Unmedicated Patients With Schizophrenia and Effects of Short-Term Antipsychotic Treatment. BIOLOGICAL PSYCHIATRY: COGNITIVE NEUROSCIENCE AND NEUROIMAGING 2019; 4:462-471. [PMID: 30852126 DOI: 10.1016/j.bpsc.2019.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/17/2018] [Accepted: 01/08/2019] [Indexed: 01/26/2023]
Abstract
BACKGROUND Schizophrenia is associated with progressive white matter changes, but it is unclear whether antipsychotic medications contribute to these. Our objective was to characterize effects of short-term treatment with risperidone on white matter diffusion indices. METHODS We recruited 42 patients with schizophrenia (30 never treated and 12 currently untreated) and 42 matched healthy control subjects in this prospective case-control neuroimaging study. Patients received a 6-week trial of risperidone. Using diffusion tensor imaging, we assessed microstructural (fractional anisotropy, mean diffusivity, and radial diffusivity) and macrostructural (radial fiber trophy) white matter integrity deficits in unmedicated patients compared with control subjects and change in white matter integrity in patients before and after antipsychotic treatment (mean risperidone dose at end point was 3.73 ± 1.72 mg). RESULTS At baseline, fractional anisotropy was decreased in the left medial temporal white matter (cluster extent: 123 voxels; Montreal Neurological Institute peak coordinates: x = -51, y = -44, z = -7; α < .05), and mean diffusivity was increased in the fusiform/lingual gyrus white matter extending to the hippocampal part of the cingulum (cluster extent: 185 voxels; peak coordinates: x = -27, y = -49, z = 2; α < .04) in patients compared with control subjects. Radial diffusivity and macrostructure were not abnormal. None of the diffusion indices showed a significant change after 6 weeks of treatment with both voxelwise and whole-brain white matter analyses. CONCLUSIONS We demonstrate microstructural white matter integrity abnormalities in the absence of macrostructural impairment in unmedicated patients with primarily early-stage schizophrenia. In our data, we found no significant white matter changes after short-term treatment with risperidone.
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28
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Wilke M, Groeschel S, Lorenzen A, Rona S, Schuhmann MU, Ernemann U, Krägeloh‐Mann I. Clinical application of advanced MR methods in children: points to consider. Ann Clin Transl Neurol 2018; 5:1434-1455. [PMID: 30480038 PMCID: PMC6243383 DOI: 10.1002/acn3.658] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/10/2018] [Accepted: 08/10/2018] [Indexed: 12/11/2022] Open
Abstract
The application of both functional MRI and diffusion MR tractography prior to a neurosurgical operation is well established in adults, but less so in children, for several reasons. For this review, we have identified several aspects (task design, subject preparation, actual scanning session, data processing, interpretation of results, and decision-making) where pediatric peculiarities should be taken into account. Further, we not only systematically identify common issues, but also provide solutions, based on our experience as well as a review of the pertinent literature. The aim is to provide the clinician as well as the imaging scientist with information that helps to plan, conduct, and interpret such a clinically-indicated exam in a way that maximizes benefit for, and minimizes the burden on the individual child.
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Affiliation(s)
- Marko Wilke
- Department of Pediatric Neurology and Developmental MedicineChildren's HospitalTuebingenGermany
- Children's Hospital and Department of NeuroradiologyExperimental Pediatric NeuroimagingTuebingenGermany
| | - Samuel Groeschel
- Department of Pediatric Neurology and Developmental MedicineChildren's HospitalTuebingenGermany
- Children's Hospital and Department of NeuroradiologyExperimental Pediatric NeuroimagingTuebingenGermany
| | - Anna Lorenzen
- Department of Pediatric Neurology and Developmental MedicineChildren's HospitalTuebingenGermany
- Children's Hospital and Department of NeuroradiologyExperimental Pediatric NeuroimagingTuebingenGermany
| | - Sabine Rona
- Department of NeurosurgeryUniversity HospitalTuebingenGermany
| | | | - Ulrike Ernemann
- Department of Diagnostic and Interventional NeuroradiologyUniversity HospitalUniversity of TübingenTuebingenGermany
| | - Ingeborg Krägeloh‐Mann
- Department of Pediatric Neurology and Developmental MedicineChildren's HospitalTuebingenGermany
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29
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Lee DH, Lee DW, Henry D, Park HJ, Han BS, Woo DC. Minimisation of Signal Intensity Differences in Distortion Correction Approaches of Brain Magnetic Resonance Diffusion Tensor Imaging. Eur Radiol 2018; 28:4314-4323. [PMID: 29651768 DOI: 10.1007/s00330-018-5382-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 01/30/2018] [Accepted: 02/12/2018] [Indexed: 11/28/2022]
Abstract
OBJECTIVES To evaluate the effects of signal intensity differences between the b0 image and diffusion tensor imaging (DTI) in the image registration process. METHODS To correct signal intensity differences between the b0 image and DTI data, a simple image intensity compensation (SIMIC) method, which is a b0 image re-calculation process from DTI data, was applied before the image registration. The re-calculated b0 image (b0ext) from each diffusion direction was registered to the b0 image acquired through the MR scanning (b0nd) with two types of cost functions and their transformation matrices were acquired. These transformation matrices were then used to register the DTI data. For quantifications, the dice similarity coefficient (DSC) values, diffusion scalar matrix, and quantified fibre numbers and lengths were calculated. RESULTS The combined SIMIC method with two cost functions showed the highest DSC value (0.802 ± 0.007). Regarding diffusion scalar values and numbers and lengths of fibres from the corpus callosum, superior longitudinal fasciculus, and cortico-spinal tract, only using normalised cross correlation (NCC) showed a specific tendency toward lower values in the brain regions. CONCLUSION Image-based distortion correction with SIMIC for DTI data would help in image analysis by accounting for signal intensity differences as one additional option for DTI analysis. KEY POINTS • We evaluated the effects of signal intensity differences at DTI registration. • The non-diffusion-weighted image re-calculation process from DTI data was applied. • SIMIC can minimise the signal intensity differences at DTI registration.
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Affiliation(s)
- Dong-Hoon Lee
- Faculty of Health Sciences and Brain & Mind Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Do-Wan Lee
- Center for Bioimaging of New Drug Development, and MR Core Lab., Asan Institute for Life Sciences, Asan Medical Center, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 138-736, Republic of Korea
| | - David Henry
- Faculty of Health Sciences and Brain & Mind Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Hae-Jin Park
- Department of Radiation Oncology, Ajou University School of Medicine, Suwon, Gyeonggi, Republic of Korea
| | - Bong-Soo Han
- Department of Radiological Science, College of Health Science, Yonsei University, 1 Yonseidae-gil, Wonju, Gangwon, 220-710, Republic of Korea.
| | - Dong-Cheol Woo
- Center for Bioimaging of New Drug Development, and MR Core Lab., Asan Institute for Life Sciences, Asan Medical Center, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 138-736, Republic of Korea. .,Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
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30
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Wen MC, Heng HSE, Lu Z, Xu Z, Chan LL, Tan EK, Tan LCS. Differential White Matter Regional Alterations in Motor Subtypes of Early Drug-Naive Parkinson's Disease Patients. Neurorehabil Neural Repair 2018; 32:129-141. [PMID: 29347868 DOI: 10.1177/1545968317753075] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Parkinson's disease (PD) can be classified into tremor dominant (TD) and postural instability and gait difficulty (PIGD) subtypes with TD considered as the benign subtype. The neural alterations of the 2 subtypes in the early stages before administration of medications remain elusive. OBJECTIVE This study assessed the subtype-related white matter (WM) microstructural features in newly diagnosed and drug-naive PD patients from the Parkinson's Progression Markers Initiative (PPMI). METHODS Sixty-five early PDs with stable subtypes (52 TD and 13 PIGD patients) and 61 controls underwent diffusion tensor imaging (DTI) scanning and clinical assessment. Tract-based special statistics (TBSS), graph-theoretical and network-based analyses were used to compare WM regional and network features between groups. RESULTS No differences in disease stages and duration were found between the 2 patient groups. TD patients showed increased fractional anisotropy (FA), but decreased radial and axial diffusivities (RD and AD) in several projection, association, and commissural tracts, compared with PIGD patients and controls. Motor severity had mild-to-moderate correlations with FA and RD of the corpus callosum (genu) in TD, but strong correlations with FA and RD of multiple association tracts in PIGD. Conversely, no significant network changes were noted. CONCLUSIONS TD patients showed regionally increased FA but decreased diffusivities, implying neural reorganization to compensate PD pathology in early stages. PIGD patients, despite having similar disease stages and duration, exhibited more WM degradation. These results demonstrate differential WM regional features between the 2 subtypes in early PD and support the notion of TD being a benign subtype.
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Affiliation(s)
| | | | - Zhonghao Lu
- 1 National Neuroscience Institute, Singapore, Singapore
| | - Zheyu Xu
- 1 National Neuroscience Institute, Singapore, Singapore
| | | | - Eng King Tan
- 1 National Neuroscience Institute, Singapore, Singapore.,3 Duke-NUS Medical School, Singapore, Singapore
| | - Louis C S Tan
- 1 National Neuroscience Institute, Singapore, Singapore.,3 Duke-NUS Medical School, Singapore, Singapore
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Dosenbach NUF, Koller JM, Earl EA, Miranda-Dominguez O, Klein RL, Van AN, Snyder AZ, Nagel BJ, Nigg JT, Nguyen AL, Wesevich V, Greene DJ, Fair DA. Real-time motion analytics during brain MRI improve data quality and reduce costs. Neuroimage 2017; 161:80-93. [PMID: 28803940 PMCID: PMC5731481 DOI: 10.1016/j.neuroimage.2017.08.025] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 08/04/2017] [Accepted: 08/07/2017] [Indexed: 11/30/2022] Open
Abstract
Head motion systematically distorts clinical and research MRI data. Motion artifacts have biased findings from many structural and functional brain MRI studies. An effective way to remove motion artifacts is to exclude MRI data frames affected by head motion. However, such post-hoc frame censoring can lead to data loss rates of 50% or more in our pediatric patient cohorts. Hence, many scanner operators collect additional 'buffer data', an expensive practice that, by itself, does not guarantee sufficient high-quality MRI data for a given participant. Therefore, we developed an easy-to-setup, easy-to-use Framewise Integrated Real-time MRI Monitoring (FIRMM) software suite that provides scanner operators with head motion analytics in real-time, allowing them to scan each subject until the desired amount of low-movement data has been collected. Our analyses show that using FIRMM to identify the ideal scan time for each person can reduce total brain MRI scan times and associated costs by 50% or more.
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Affiliation(s)
- Nico U F Dosenbach
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA; Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA; Program in Occupational Therapy, Washington University, St. Louis, MO, USA.
| | - Jonathan M Koller
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Eric A Earl
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
| | - Oscar Miranda-Dominguez
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA
| | - Rachel L Klein
- Department of Psychiatry, Oregon Health & Science University, Portland, OR, USA
| | - Andrew N Van
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Abraham Z Snyder
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA; Department of Radiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Bonnie J Nagel
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA; Department of Psychiatry, Oregon Health & Science University, Portland, OR, USA
| | - Joel T Nigg
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA; Department of Psychiatry, Oregon Health & Science University, Portland, OR, USA
| | - Annie L Nguyen
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA; Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Victoria Wesevich
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Deanna J Greene
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA; Department of Radiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Damien A Fair
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, USA; Department of Psychiatry, Oregon Health & Science University, Portland, OR, USA; Advanced Imaging Research Center, Oregon Health & Science University, Portland, OR, USA.
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Graham MS, Drobnjak I, Jenkinson M, Zhang H. Quantitative assessment of the susceptibility artefact and its interaction with motion in diffusion MRI. PLoS One 2017; 12:e0185647. [PMID: 28968429 PMCID: PMC5624609 DOI: 10.1371/journal.pone.0185647] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 09/16/2017] [Indexed: 01/15/2023] Open
Abstract
In this paper we evaluate the three main methods for correcting the susceptibility-induced artefact in diffusion-weighted magnetic-resonance (DW-MR) data, and assess how correction is affected by the susceptibility field's interaction with motion. The susceptibility artefact adversely impacts analysis performed on the data and is typically corrected in post-processing. Correction strategies involve either registration to a structural image, the application of an acquired field-map or the use of additional images acquired with different phase-encoding. Unfortunately, the choice of which method to use is made difficult by the absence of any systematic comparisons of them. In this work we quantitatively evaluate these methods, by extending and employing a recently proposed framework that allows for the simulation of realistic DW-MR datasets with artefacts. Our analysis separately evaluates the ability for methods to correct for geometric distortions and to recover lost information in regions of signal compression. In terms of geometric distortions, we find that registration-based methods offer the poorest correction. Field-mapping techniques are better, but are influenced by noise and partial volume effects, whilst multiple phase-encode methods performed best. We use our simulations to validate a popular surrogate metric of correction quality, the comparison of corrected data acquired with AP and LR phase-encoding, and apply this surrogate to real datasets. Furthermore, we demonstrate that failing to account for the interaction of the susceptibility field with head movement leads to increased errors when analysing DW-MR data. None of the commonly used post-processing methods account for this interaction, and we suggest this may be a valuable area for future methods development.
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Affiliation(s)
- Mark S. Graham
- Centre for Medical Image Computing & Department of Computer Science, University College London, London, United Kingdom
| | - Ivana Drobnjak
- Centre for Medical Image Computing & Department of Computer Science, University College London, London, United Kingdom
| | - Mark Jenkinson
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Hui Zhang
- Centre for Medical Image Computing & Department of Computer Science, University College London, London, United Kingdom
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Jankiewicz M, Holmes MJ, Taylor PA, Cotton MF, Laughton B, van der Kouwe AJW, Meintjes EM. White Matter Abnormalities in Children with HIV Infection and Exposure. Front Neuroanat 2017; 11:88. [PMID: 29033797 PMCID: PMC5627060 DOI: 10.3389/fnana.2017.00088] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/20/2017] [Indexed: 11/13/2022] Open
Abstract
Background: Due to changes in guidelines and access to treatment, more children start combination antiretroviral therapy (ART) in infancy. With few studies examining the long-term effects of perinatal HIV infection and early ART on neurodevelopment, much is still unknown about brain maturation in the presence of HIV and ART. Follow-up studies of HIV infected (HIV+) children are important for monitoring brain development in the presence of HIV infection and ART. Methods: We use diffusion tensor imaging (DTI) to examine white matter (WM) in 65 HIV+ and 46 control (HIV exposed uninfected (HEU) and HIV unexposed uninfected (HU)) 7-year-old children. This is a follow up of a cohort studied at 5 years, where we previously reported lower fractional anisotropy (FA) in corticospinal tract (CST) and mean diffusivity (MD) increases in inferior/superior longitudinal fasciculi (ILF/SLF), inferior fronto-occipital fasciculus (IFOF) and uncinate fasciculus (UF) in HIV+ children compared to uninfected controls. In addition, we also found a difference in FA related to age at which ART was initiated. Results: At 7 years, we found two regions in the left IFOF and left ILF with lower FA in HIV+ children compared to controls. Higher MD was observed in a similar region in the IFOF, albeit bilaterally, as well as multiple clusters bilaterally in the superior corona radiata (SCR), the anterior thalamic radiation (ATR) and the right forceps minor. Unlike at 5 years, we found no impact on WM of ART initiation. In HEU children, we found a cluster in the right posterior corona radiata with higher FA compared to HU children, while bilateral regions in the CST demonstrated reduced MD. Conclusions: At age 7, despite early ART and viral load (VL) suppression, we continue to observe differences in WM integrity. WM damage observed at age 5 years persists, and new damage is evident. The continued observation of regions with lower FA and higher MD in HIV+ children point to disruptions in ongoing white matter development regardless of early ART. Lastly, in HEU children we find higher FA and lower MD in clusters in the CST tract suggesting that perinatal HIV/ART exposure has a long-term impact on WM development.
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Affiliation(s)
- Marcin Jankiewicz
- Division of Biomedical Engineering, Department of Human Biology, University of Cape Town, Cape Town, South Africa
| | - Martha J Holmes
- Division of Biomedical Engineering, Department of Human Biology, University of Cape Town, Cape Town, South Africa
| | - Paul A Taylor
- Scientific and Statistical Computing Core, National Institutes of Health, Bethesda, MD, United States
| | | | | | - André J W van der Kouwe
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, United States
| | - Ernesta M Meintjes
- Division of Biomedical Engineering, Department of Human Biology, University of Cape Town, Cape Town, South Africa
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Shahim P, Holleran L, Kim JH, Brody DL. Test-retest reliability of high spatial resolution diffusion tensor and diffusion kurtosis imaging. Sci Rep 2017; 7:11141. [PMID: 28894296 PMCID: PMC5593980 DOI: 10.1038/s41598-017-11747-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/30/2017] [Indexed: 02/03/2023] Open
Abstract
We assessed the test-retest reliability of high spatial resolution diffusion tensor imaging (DTI) and diffusion kurtosis imaging (DKI). Diffusion MRI was acquired using a Siemens 3 Tesla Prisma scanner with 80 mT/m gradients and a 32-channel head coil from each of 3 concussive traumatic brain injury (cTBI) patients and 4 controls twice 0 to 24 days apart. Coefficients of variation (CoV) for DTI parameters were calculated in each DTI Studio parcellated white matter tract at 1.25 mm and 1.75 mm isotropic voxel resolution, as well as DKI parameters at 1.75 mm isotropic. Overall, fractional anisotropy had the best reliability, with mean CoV at 5% for 1.25 mm and 3.5% for 1.75 mm isotropic voxels. Mean CoV for the other DTI metrics were <7.0% for both 1.25 and 1.75 mm isotropic voxels. The mean CoV was ≤4.5% across the DKI metrics. In the commonly injured orbitofrontal and temporal pole regions CoV was <3.5% for all parameters. Thus, with appropriate processing, high spatial resolution advanced diffusion MRI has good to excellent test-retest reproducibility in both human cTBI patients and controls. However, further technical improvements will be needed to reliably discern the most subtle diffusion abnormalities, especially at high spatial resolution.
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Affiliation(s)
- Pashtun Shahim
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA. .,Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden. .,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.
| | - Laurena Holleran
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Joong H Kim
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - David L Brody
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA.,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri, USA
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