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1.  Different susceptibility of medial temporal lobe and basal ganglia atrophy rates to vascular risk factors 
Neurobiology of aging  2013;35(1):72-78.
Atrophy of medial temporal lobe (MTL) and basal ganglia (BG) are characteristic of various neurodegenerative diseases in older people. In search of potentially modifiable factors that lead to atrophy in these structures, we studied the association of vascular risk factors to atrophy of MTL and BG in 368 non-demented men and women [b. 1907–1935] who participated in the Age, Gene/Environment, Susceptibility - Reykjavik Study. A fully automated segmentation pipeline estimated volumes of MTL and BG from whole brain MRI performed at baseline and 2.4 years later. Linear regression models showed higher systolic and diastolic blood pressures and the presence of Apo E ε4 were independently associated with increased atrophy of MTL but no association of vascular risk factors with atrophy of BG. The different susceptibility of MTL and BG atrophy to the presence of vascular risk factors suggests the relatively preserved perfusion of BG when vascular risk factors are present.
doi:10.1016/j.neurobiolaging.2013.07.009
PMCID: PMC3802531  PMID: 23992618
Medial temporal lobe; hippocampus; basal ganglia; thalamus; atrophy; aging; vascular risk factors
2.  Hierarchical multivariate covariance analysis of metabolic connectivity 
Conventional brain connectivity analysis is typically based on the assessment of interregional correlations. Given that correlation coefficients are derived from both covariance and variance, group differences in covariance may be obscured by differences in the variance terms. To facilitate a comprehensive assessment of connectivity, we propose a unified statistical framework that interrogates the individual terms of the correlation coefficient. We have evaluated the utility of this method for metabolic connectivity analysis using [18F]2-fluoro-2-deoxyglucose (FDG) positron emission tomography (PET) data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) study. As an illustrative example of the utility of this approach, we examined metabolic connectivity in angular gyrus and precuneus seed regions of mild cognitive impairment (MCI) subjects with low and high β-amyloid burdens. This new multivariate method allowed us to identify alterations in the metabolic connectome, which would not have been detected using classic seed-based correlation analysis. Ultimately, this novel approach should be extensible to brain network analysis and broadly applicable to other imaging modalities, such as functional magnetic resonance imaging (MRI).
doi:10.1038/jcbfm.2014.165
PMCID: PMC4269748  PMID: 25294129
Alzheimer's disease; β-amyloid; covariance analysis; FDG PET; florbetapir PET; metabolic connectivity; mild cognitive impairment
3.  Developmental Changes in Organization of Structural Brain Networks 
Khundrakpam, Budhachandra S. | Reid, Andrew | Brauer, Jens | Carbonell, Felix | Lewis, John | Ameis, Stephanie | Karama, Sherif | Lee, Junki | Chen, Zhang | Das, Samir | Evans, Alan C. | Ball, William S. | Byars, Anna Weber | Schapiro, Mark | Bommer, Wendy | Carr, April | German, April | Dunn, Scott | Rivkin, Michael J. | Waber, Deborah | Mulkern, Robert | Vajapeyam, Sridhar | Chiverton, Abigail | Davis, Peter | Koo, Julie | Marmor, Jacki | Mrakotsky, Christine | Robertson, Richard | McAnulty, Gloria | Brandt, Michael E. | Fletcher, Jack M. | Kramer, Larry A. | Yang, Grace | McCormack, Cara | Hebert, Kathleen M. | Volero, Hilda | Botteron, Kelly | McKinstry, Robert C. | Warren, William | Nishino, Tomoyuki | Robert Almli, C. | Todd, Richard | Constantino, John | McCracken, James T. | Levitt, Jennifer | Alger, Jeffrey | O'Neil, Joseph | Toga, Arthur | Asarnow, Robert | Fadale, David | Heinichen, Laura | Ireland, Cedric | Wang, Dah-Jyuu | Moss, Edward | Zimmerman, Robert A. | Bintliff, Brooke | Bradford, Ruth | Newman, Janice | Evans, Alan C. | Arnaoutelis, Rozalia | Bruce Pike, G. | Louis Collins, D. | Leonard, Gabriel | Paus, Tomas | Zijdenbos, Alex | Das, Samir | Fonov, Vladimir | Fu, Luke | Harlap, Jonathan | Leppert, Ilana | Milovan, Denise | Vins, Dario | Zeffiro, Thomas | Van Meter, John | Lange, Nicholas | Froimowitz, Michael P. | Botteron, Kelly | Robert Almli, C. | Rainey, Cheryl | Henderson, Stan | Nishino, Tomoyuki | Warren, William | Edwards, Jennifer L. | Dubois, Diane | Smith, Karla | Singer, Tish | Wilber, Aaron A. | Pierpaoli, Carlo | Basser, Peter J. | Chang, Lin-Ching | Koay, Chen Guan | Walker, Lindsay | Freund, Lisa | Rumsey, Judith | Baskir, Lauren | Stanford, Laurence | Sirocco, Karen | Gwinn-Hardy, Katrina | Spinella, Giovanna | McCracken, James T. | Alger, Jeffry R. | Levitt, Jennifer | O'Neill, Joseph
Cerebral Cortex (New York, NY)  2012;23(9):2072-2085.
Recent findings from developmental neuroimaging studies suggest that the enhancement of cognitive processes during development may be the result of a fine-tuning of the structural and functional organization of brain with maturation. However, the details regarding the developmental trajectory of large-scale structural brain networks are not yet understood. Here, we used graph theory to examine developmental changes in the organization of structural brain networks in 203 normally growing children and adolescents. Structural brain networks were constructed using interregional correlations in cortical thickness for 4 age groups (early childhood: 4.8–8.4 year; late childhood: 8.5–11.3 year; early adolescence: 11.4–14.7 year; late adolescence: 14.8–18.3 year). Late childhood showed prominent changes in topological properties, specifically a significant reduction in local efficiency, modularity, and increased global efficiency, suggesting a shift of topological organization toward a more random configuration. An increase in number and span of distribution of connector hubs was found in this age group. Finally, inter-regional connectivity analysis and graph-theoretic measures indicated early maturation of primary sensorimotor regions and protracted development of higher order association and paralimbic regions. Our finding reveals a time window of plasticity occurring during late childhood which may accommodate crucial changes during puberty and the new developmental tasks that an adolescent faces.
doi:10.1093/cercor/bhs187
PMCID: PMC3729193  PMID: 22784607
adolescence; connectivity; connector hub; cortical thickness; maturation
4.  β-Amyloid is associated with aberrant metabolic connectivity in subjects with mild cognitive impairment 
Positron emission tomography (PET) studies using [18F]2-fluoro-2-deoxyglucose (FDG) have identified a well-defined pattern of glucose hypometabolism in Alzheimer's disease (AD). The assessment of the metabolic relationship among brain regions has the potential to provide unique information regarding the disease process. Previous studies of metabolic correlation patterns have demonstrated alterations in AD subjects relative to age-matched, healthy control subjects. The objective of this study was to examine the associations between β-amyloid, apolipoprotein E ɛ4 (APOE ɛ4) genotype, and metabolic correlations patterns in subjects diagnosed with mild cognitive impairment (MCI). Mild cognitive impairment subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI) study were categorized into β-amyloid-low and β-amyloid-high groups, based on quantitative analysis of [18F]florbetapir PET scans, and APOE ɛ4 non-carriers and carriers based on genotyping. We generated voxel-wise metabolic correlation strength maps across the entire cerebral cortex for each group, and, subsequently, performed a seed-based analysis. We found that the APOE ɛ4 genotype was closely related to regional glucose hypometabolism, while elevated, fibrillar β-amyloid burden was associated with specific derangements of the metabolic correlation patterns.
doi:10.1038/jcbfm.2014.66
PMCID: PMC4083380  PMID: 24736891
APOE ɛ4; β-amyloid; FDG PET; florbetapir PET; metabolic connectivity; mild cognitive impairment
5.  Common variants at 6q22 and 17q21 are associated with intracranial volume 
Nature genetics  2012;44(5):539-544.
During aging, intracranial volume remains unchanged and represents maximally attained brain size, while various interacting biological phenomena lead to brain volume loss. Consequently, intracranial volume and brain volume in late life reflect different genetic influences. Our genome-wide association study in 8,175 community-dwelling elderly did not reveal any genome-wide significant associations (p<5*10−8) for brain volume. In contrast, intracranial volume was significantly associated with two loci: rs4273712 (p=3.4*10−11), a known height locus on chromosome 6q22, and rs9915547, tagging the inversion on chromosome 17q21 (p=1.5*10−12). We replicated the associations of these loci with intracranial volume in a separate sample of 1,752 older persons (p=1.1*10−3 for 6q22 and p=1.2*10−3 for 17q21). Furthermore, we also found suggestive associations of the 17q21 locus with head circumference in 10,768 children (mean age 14.5 months). Our data identify two loci associated with head size, with the inversion on 17q21 also likely involved in attaining maximal brain size.
doi:10.1038/ng.2245
PMCID: PMC3618290  PMID: 22504418
6.  Brain Gray Matter Deficits at 33-Year Follow-Up in Adults with Attention-Deficit/Hyperactivity Disorder Established in Childhood 
Archives of general psychiatry  2011;68(11):1122-1134.
Context
Volumetric studies have reported relatively decreased cortical thickness and gray matter volumes in adults with Attention-Deficit/Hyperactivity Disorder (ADHD) whose childhood status was retrospectively recalled. We present the first prospective study combining cortical thickness and voxel-based morphometry (VBM) in adults diagnosed with ADHD in childhood.
Objective
In adults who had Combined Type ADHD in childhood, to 1) test whether they exhibit cortical thinning and decreased gray matter in regions hypothesized related to ADHD, and 2) test whether anatomic differences are associated with current ADHD diagnosis, including persistence versus remission.
Design
Cross-sectional analysis embedded in a 33-year prospective follow-up at mean age 41.
Setting
Research outpatient center.
Participants
ADHD probands were from a cohort of 207 6–12 year old Caucasian boys; male comparison subjects (n=178) had been free of ADHD in childhood. We obtained MRI scans in 59 probands and 80 comparisons (28% and 45% of original samples, respectively).
Main Outcome Measure
Whole-brain VBM and vertex-wise cortical thickness analyses.
Results
Cortex was significantly thinner in ADHD probands than comparisons in the dorsal attentional network and limbic areas (FDR<0.05, corrected). Additionally, gray matter was significantly decreased in probands in right caudate, right thalamus and bilateral cerebellar hemispheres. Probands with persistent ADHD (n=17) did not differ significantly from remitters (n=26) at FDR<0.05. At uncorrected p<0.05, remitters had thicker cortex relative to those with persistent ADHD in medial occipital cortex, insula, parahippocampus, and prefrontal regions.
Conclusions
We observed anatomic gray matter reductions in adults with childhood ADHD, regardless of current diagnosis. The most affected regions underpin top-down control of attention and regulation of emotion and motivation. Exploratory analyses suggest that diagnostic remission may result from compensatory maturation of prefrontal, cerebellar, and thalamic circuitry.
doi:10.1001/archgenpsychiatry.2011.117
PMCID: PMC3554238  PMID: 22065528
7.  Common variants at 12q14 and 12q24 are associated with hippocampal volume 
Bis, Joshua C. | DeCarli, Charles | Smith, Albert Vernon | van der Lijn, Fedde | Crivello, Fabrice | Fornage, Myriam | Debette, Stephanie | Shulman, Joshua M. | Schmidt, Helena | Srikanth, Velandai | Schuur, Maaike | Yu, Lei | Choi, Seung-Hoan | Sigurdsson, Sigurdur | Verhaaren, Benjamin F.J. | DeStefano, Anita L. | Lambert, Jean-Charles | Jack, Clifford R. | Struchalin, Maksim | Stankovich, Jim | Ibrahim-Verbaas, Carla A. | Fleischman, Debra | Zijdenbos, Alex | den Heijer, Tom | Mazoyer, Bernard | Coker, Laura H. | Enzinger, Christian | Danoy, Patrick | Amin, Najaf | Arfanakis, Konstantinos | van Buchem, Mark A. | de Bruijn, Renée F.A.G. | Beiser, Alexa | Dufouil, Carole | Huang, Juebin | Cavalieri, Margherita | Thomson, Russell | Niessen, Wiro J. | Chibnik, Lori B. | Gislason, Gauti K. | Hofman, Albert | Pikula, Aleksandra | Amouyel, Philippe | Freeman, Kevin B. | Phan, Thanh G. | Oostra, Ben A. | Stein, Jason L. | Medland, Sarah E. | Vasquez, Alejandro Arias | Hibar, Derrek P. | Wright, Margaret J. | Franke, Barbara | Martin, Nicholas G. | Thompson, Paul M. | Nalls, Michael A. | Uitterlinden, Andre G. | Au, Rhoda | Elbaz, Alexis | Beare, Richard J. | van Swieten, John C. | Lopez, Oscar | Harris, Tamara B. | Chouraki, Vincent | Breteler, Monique M.B. | De Jager, Philip L. | Becker, James T. | Vernooij, Meike W. | Knopman, David | Fazekas, Franz | Wolf, Philip A. | van der Lugt, Aad | Gudnason, Vilmundur | Longstreth, W.T. | Brown, Mathew A. | Bennett, David A. | van Duijn, Cornelia M. | Mosley, Thomas H. | Schmidt, Reinhold | Tzourio, Christophe | Launer, Lenore J. | Ikram, M. Arfan | Seshadri, Sudha
Nature genetics  2012;44(5):545-551.
Aging is associated with reductions in hippocampal volume (HV) that are accelerated by Alzheimer’s disease and vascular risk factors. Our genome-wide association study of dementia-free persons (n=9,232) identified 46 SNPs at four loci with p-values <4.0×10-7. Two additional samples (n=2,318) replicated associations at 12q24 within MSRB3/WIF1 (discovery + replication, rs17178006; p=5.3×10-11) and at 12q14 near HRK/FBXW8 (rs7294919; p=2.9×10-11). Remaining associations included one 2q24 SNP within DPP4 (rs6741949; p=2.9×10-7) and nine 9p33 SNPs within ASTN2 (rs7852872; p=1.0×10-7) that were also associated with HV (p<0.05) in a third younger, more heterogeneous sample (n=7,794). The ASTN2 SNP was also associated with decline in cognition in a largely independent sample (n=1,563). These associations implicate genes related to apoptosis (HRK), development (WIF1), oxidative stress (MSR3B), ubiquitination (FBXW8), enzymes targeted by new diabetes medications (DPP4), and neuronal migration (ASTN2), indicating novel genetic influences that influence hippocampal size and possibly the risk of cognitive decline and dementia.
doi:10.1038/ng.2237
PMCID: PMC3427729  PMID: 22504421
8.  Genome-wide association studies of cerebral white matter lesion burden: the CHARGE Consortium 
Annals of neurology  2011;69(6):928-939.
Objective
White matter hyperintensities (WMH) detectable by magnetic resonance imaging (MRI)are part of the spectrum of vascular injury associated with aging of the brain and are thought to reflect ischemic damage to the small deep cerebral vessels. WMH are associated with an increased risk of cognitive and motor dysfunction, dementia, depression, and stroke. Despite a significant heritability, few genetic loci influencing WMH burden have been identified.
Methods
We performed a meta-analysis of genome-wide association studies (GWAS) for WMH burden in 9,361 stroke-free individuals of European descent from 7 community-based cohorts. Significant findings were tested for replication in 3,024 individuals from 2 additional cohorts.
Results
We identified 6 novel risk-associated single nucleotide polymorphisms (SNPs)in one locus on chromosome 17q25 encompassing 6 known genes including WBP2, TRIM65, TRIM47, MRPL38, FBF1, and ACOX1. The most significant association was for rs3744028 (Pdiscovery= 4.0×10−9; Preplication =1.3×10−7; Pcombined =4.0×10−15). Other SNPs in this region also reaching genome-wide significance are rs9894383 (P=5.3×10−9), rs11869977 (P=5.7×10−9), rs936393 (P=6.8×10−9), rs3744017 (P=7.3×10−9), and rs1055129 (P=4.1×10−8). Variant alleles at these loci conferred a small increase in WMH burden (4–8% of the overall mean WMH burden in the sample).
Interpretation
This large GWAS of WMH burden in community-based cohorts of individuals of European descent identifies a novel locus on chromosome 17. Further characterization of this locus may provide novel insights into the pathogenesis of cerebral WMH.
doi:10.1002/ana.22403
PMCID: PMC3122147  PMID: 21681796
9.  The pipeline system for Octave and Matlab (PSOM): a lightweight scripting framework and execution engine for scientific workflows 
The analysis of neuroimaging databases typically involves a large number of inter-connected steps called a pipeline. The pipeline system for Octave and Matlab (PSOM) is a flexible framework for the implementation of pipelines in the form of Octave or Matlab scripts. PSOM does not introduce new language constructs to specify the steps and structure of the workflow. All steps of analysis are instead described by a regular Matlab data structure, documenting their associated command and options, as well as their input, output, and cleaned-up files. The PSOM execution engine provides a number of automated services: (1) it executes jobs in parallel on a local computing facility as long as the dependencies between jobs allow for it and sufficient resources are available; (2) it generates a comprehensive record of the pipeline stages and the history of execution, which is detailed enough to fully reproduce the analysis; (3) if an analysis is started multiple times, it executes only the parts of the pipeline that need to be reprocessed. PSOM is distributed under an open-source MIT license and can be used without restriction for academic or commercial projects. The package has no external dependencies besides Matlab or Octave, is straightforward to install and supports of variety of operating systems (Linux, Windows, Mac). We ran several benchmark experiments on a public database including 200 subjects, using a pipeline for the preprocessing of functional magnetic resonance images (fMRI). The benchmark results showed that PSOM is a powerful solution for the analysis of large databases using local or distributed computing resources.
doi:10.3389/fninf.2012.00007
PMCID: PMC3318188  PMID: 22493575
pipeline; workflow; Octave; Matlab; open-source; parallel computing; high-performance computing; neuroimaging
10.  LORIS: a web-based data management system for multi-center studies 
Longitudinal Online Research and Imaging System (LORIS) is a modular and extensible web-based data management system that integrates all aspects of a multi-center study: from heterogeneous data acquisition (imaging, clinical, behavior, and genetics) to storage, processing, and ultimately dissemination. It provides a secure, user-friendly, and streamlined platform to automate the flow of clinical trials and complex multi-center studies. A subject-centric internal organization allows researchers to capture and subsequently extract all information, longitudinal or cross-sectional, from any subset of the study cohort. Extensive error-checking and quality control procedures, security, data management, data querying, and administrative functions provide LORIS with a triple capability (1) continuous project coordination and monitoring of data acquisition (2) data storage/cleaning/querying, (3) interface with arbitrary external data processing “pipelines.” LORIS is a complete solution that has been thoroughly tested through a full 10 year life cycle of a multi-center longitudinal project1 and is now supporting numerous international neurodevelopment and neurodegeneration research projects.
doi:10.3389/fninf.2011.00037
PMCID: PMC3262165  PMID: 22319489
database; neuroimaging; longitudinal; multi-center; MRI; data querying; imaging data; behavioral data
11.  Impaired small-world efficiency in structural cortical networks in multiple sclerosis associated with white matter lesion load 
Brain  2009;132(12):3366-3379.
White matter tracts, which play a crucial role in the coordination of information flow between different regions of grey matter, are particularly vulnerable to multiple sclerosis. Many studies have shown that the white matter lesions in multiple sclerosis are associated with focal abnormalities of grey matter, but little is known about the alterations in the coordinated patterns of cortical morphology among regions in the disease. Here, we used cortical thickness measurements from structural magnetic resonance imaging to investigate the relationship between the white matter lesion load and the topological efficiency of structural cortical networks in multiple sclerosis. Network efficiency was defined using a ‘small-world’ network model that quantifies the effectiveness of information transfer within brain networks. In this study, we first classified patients (n = 330) into six subgroups according to their total white matter lesion loads, and identified structural brain networks for each multiple sclerosis group by thresholding the corresponding inter-regional cortical thickness correlation matrix, followed by a network efficiency analysis with graph theoretical approaches. The structural cortical networks in multiple sclerosis demonstrated efficient small-world architecture regardless of the lesion load, an organization that maximizes the information processing at a relatively low wiring cost. However, we found that the overall small-world network efficiency in multiple sclerosis was significantly disrupted in a manner proportional to the extent of total white matter lesions. Moreover, regional efficiency was also significantly decreased in specific brain regions, including the insula and precentral gyrus as well as regions of prefrontal and temporal association cortices. Finally, we showed that the lesions also altered many cortical thickness correlations in the frontal, temporal and parietal lobes. Our results suggest that the white matter lesions in multiple sclerosis might be associated with aberrant neuronal connectivity among widely distributed brain regions, and provide structural (morphological) evidence for the notion of multiple sclerosis as a disconnection syndrome.
doi:10.1093/brain/awp089
PMCID: PMC2792366  PMID: 19439423
cortical thickness; connectivity; MRI; multiple sclerosis; small-world networks
12.  The Epigenesis of Planum Temporale Asymmetry in Twins 
Variation in hemispheric asymmetry of the planum temporale (PT) has been related to verbal ability. The degree to which genetic and environmental factors mediate PT asymmetry is not known. This study examined the heritability for planar asymmetry in 12 dizygotic (DZ) and 27 monozygotic (MZ) male twin pairs who were between 6 and 16 years of age. There was weak but positive evidence for heritability of planar asymmetry. Co-twin similarity for planar asymmetry and Sylvian fissure morphology increased when excluding twins discordant for writing hand and when excluding twins exhibiting birth weight differences >20% from the analyses. Birth weight differences were also related to twin differences in total cerebral volume, but not central sulcus asymmetry. These results suggest that exogenous perinatal factors affect the epigenesis of planar asymmetry development.
PMCID: PMC2739006  PMID: 12050086
13.  Voxel based modeling and quantification of the proximal femur using inter-subject registration of quantitative CT images 
Bone  2007;41(5):888-895.
We have developed a general framework which employs quantitative computed tomography (QCT) imaging and inter-subject image registration to model the three-dimensional structure of the hip, with the goal of quantifying changes in the spatial distribution of bone as it is affected by aging, drug treatment or mechanical unloading. We have adapted rigid and non-rigid inter-subject registration techniques to transform groups of hip QCT scans into a common reference space and to construct composite proximal femoral models. We have applied this technique to a longitudinal study of 16 astronauts who on average, incurred high losses of hip bone density during spaceflights of 4–6 months on the International Space Station (ISS). We compared the pre-flight and post-flight composite hip models, and observed the gradients of the bone loss distribution. We performed paired t-tests, on a voxel by voxel basis, corrected for multiple comparisons using false discovery rate (FDR), and observed regions inside the proximal femur that showed the most significant bone loss. To validate our registration algorithm, we selected the 16 pre-flight scans and manually marked 4 landmarks for each scan. After registration, the average distance between the mapped landmarks and the corresponding landmarks in the target scan was 2.56mm. The average error due to manual landmark identification was 1.70 mm.
doi:10.1016/j.bone.2007.07.006
PMCID: PMC2080679  PMID: 17707712
14.  Sexual Dimorphism of Brain Developmental Trajectories during Childhood and Adolescence 
NeuroImage  2007;36(4):1065-1073.
Human total brain size is consistently reported to be ~8-10% larger in males, although consensus on regionally-specific differences is weak. Here, in the largest longitudinal pediatric neuroimaging study reported to date (829 scans from 387 subjects, ages 3 to 27 years), we demonstrate the importance of examining size-by-age trajectories of brain development rather than group averages across broad age ranges when assessing sexual dimorphism. Using magnetic resonance imaging (MRI) we found robust male/female differences in the shapes of trajectories with total cerebral volume peaking at age 10.5 in females and 14.5 in males. White matter increases throughout this 24 year period with males having a steeper rate of increase during adolescence. Both cortical and subcortical gray matter trajectories follow an inverted U shaped path with peak sizes 1 to 2 years earlier in females. These sexually dimorphic trajectories confirm the importance of longitudinal data in studies of brain development and underline the need to consider sex matching in studies of brain development.
doi:10.1016/j.neuroimage.2007.03.053
PMCID: PMC2040300  PMID: 17513132

Results 1-14 (14)