@article {818, title = {Reduction of motion-related artifacts in resting state fMRI using aCompCor.}, journal = {Neuroimage}, volume = {96}, year = {2014}, month = {2014 Aug 1}, pages = {22-35}, abstract = {

Recent studies have illustrated that motion-related artifacts remain in resting-state fMRI (rs-fMRI) data even after common corrective processing procedures have been applied, but the extent to which head motion distorts the data may be modulated by the corrective approach taken. We compare two different methods for estimating nuisance signals from tissues not expected to exhibit BOLD fMRI signals of neuronal origin: 1) the more commonly used mean signal method and 2) the principal components analysis approach (aCompCor: Behzadi et al., 2007). Further, we investigate the added benefit of "scrubbing" (Power et al., 2012) following both methods. We demonstrate that the use of aCompCor removes motion artifacts more effectively than tissue-mean signal regression. In addition, inclusion of more components from anatomically defined regions of no interest better mitigates motion-related artifacts and improves the specificity of functional connectivity estimates. While scrubbing further attenuates motion-related artifacts when mean signals are used, scrubbing provides no additional benefit in terms of motion artifact reduction or connectivity specificity when using aCompCor.

}, issn = {1095-9572}, doi = {10.1016/j.neuroimage.2014.03.028}, author = {Muschelli, John and Nebel, Mary Beth and Caffo, Brian S and Barber, Anita D and Pekar, James J and Mostofsky, Stewart H} } @article {811, title = {Relationships between retinal axonal and neuronal measures and global central nervous system pathology in multiple sclerosis.}, journal = {JAMA Neurol}, volume = {70}, year = {2013}, month = {2013 Jan}, pages = {34-43}, abstract = {

OBJECTIVE: To determine the relationships between conventional and segmentation-derived optical coherence tomography (OCT) retinal layer thickness measures with intracranial volume (a surrogate of head size) and brain substructure volumes in multiple sclerosis (MS).

DESIGN: Cross-sectional study.

SETTING: Johns Hopkins University, Baltimore, Maryland.

PARTICIPANTS: A total of 84 patients with MS and 24 healthy control subjects.

MAIN OUTCOME MEASURES: High-definition spectral-domain OCT conventional and automated segmentation-derived discrete retinal layer thicknesses and 3-T magnetic resonance imaging brain substructure volumes.

RESULTS: Peripapillary retinal nerve fiber layer as well as composite ganglion cell layer+inner plexiform layer thicknesses in the eyes of patients with MS without a history of optic neuritis were associated with cortical gray matter (P=.01 and P=.04, respectively) and caudate (P=.04 and P=.03, respectively) volumes. Inner nuclear layer thickness, also in eyes without a history of optic neuritis, was associated with fluid-attenuated inversion recovery lesion volume (P=.007) and inversely associated with normal-appearing white matter volume (P=.005) in relapsing-remitting MS. As intracranial volume was found to be related with several of the OCT measures in patients with MS and healthy control subjects and is already known to be associated with brain substructure volumes, all OCT-brain substructure relationships were adjusted for intracranial volume. CONCLUSIONS Retinal measures reflect global central nervous system pathology in multiple sclerosis, with thicknesses of discrete retinal layers each appearing to be associated with distinct central nervous system processes. Moreover, OCT measures appear to correlate with intracranial volume in patients with MS and healthy control subjects, an important unexpected factor unaccounted for in prior studies examining the relationships between peripapillary retinal nerve fiber layer thickness and brain substructure volumes.

}, keywords = {Adult, Axons, Caudate Nucleus, Central Nervous System, Cerebral Cortex, Cross-Sectional Studies, Female, Humans, Magnetic Resonance Imaging, Male, Middle Aged, Multiple Sclerosis, Retina, Retinal Neurons, Tomography, Optical Coherence}, issn = {2168-6157}, doi = {10.1001/jamaneurol.2013.573}, author = {Saidha, Shiv and Sotirchos, Elias S and Oh, Jiwon and Syc, Stephanie B and Seigo, Michaela A and Shiee, Navid and Eckstein, Chistopher and Durbin, Mary K and Oakley, Jonathan D and Meyer, Scott A and Frohman, Teresa C and Newsome, Scott and Ratchford, John N and Balcer, Laura J and Pham, Dzung L and Crainiceanu, Ciprian M and Frohman, Elliot M and Reich, Daniel S and Calabresi, Peter A} } @article {710, title = {Relationships Between Retinal Axonal and Neuronal Measures and Global Central Nervous System Pathology in Multiple Sclerosis.}, journal = {Arch Neurol}, year = {2012}, month = {2012 Oct 1}, pages = {1-10}, abstract = {

OBJECTIVE To determine the relationships between conventional and segmentation-derived optical coherence tomography (OCT) retinal layer thickness measures with intracranial volume (a surrogate of head size) and brain substructure volumes in multiple sclerosis (MS). DESIGN Cross-sectional study. SETTING Johns Hopkins University, Baltimore, Maryland. PARTICIPANTS A total of 84 patients with MS and 24 healthy control subjects. MAIN OUTCOME MEASURES High-definition spectral-domain OCT conventional and automated segmentation-derived discrete retinal layer thicknesses and 3-T magnetic resonance imaging brain substructure volumes. RESULTS Peripapillary retinal nerve fiber layer as well as composite ganglion cell layer\ +\ inner plexiform layer thicknesses in the eyes of patients with MS without a history of optic neuritis were associated with cortical gray matter (P\ =\ .01 and P\ =\ .04, respectively) and caudate (P\ =\ .04 and P\ =\ .03, respectively) volumes. Inner nuclear layer thickness, also in eyes without a history of optic neuritis, was associated with fluid-attenuated inversion recovery lesion volume (P\ =\ .007) and inversely associated with normal-appearing white matter volume (P\ =\ .005) in relapsing-remitting MS. As intracranial volume was found to be related with several of the OCT measures in patients with MS and healthy control subjects and is already known to be associated with brain substructure volumes, all OCT-brain substructure relationships were adjusted for intracranial volume. CONCLUSIONS Retinal measures reflect global central nervous system pathology in multiple sclerosis, with thicknesses of discrete retinal layers each appearing to be associated with distinct central nervous system processes. Moreover, OCT measures appear to correlate with intracranial volume in patients with MS and healthy control subjects, an important unexpected factor unaccounted for in prior studies examining the relationships between peripapillary retinal nerve fiber layer thickness and brain substructure volumes.

}, issn = {1538-3687}, doi = {10.1001/archneurol.2013.573}, author = {Saidha, Shiv and Sotirchos, Elias S and Oh, Jiwon and Syc, Stephanie B and Seigo, Michaela A and Shiee, Navid and Eckstein, Chistopher and Durbin, Mary K and Oakley, Jonathan D and Meyer, Scott A and Frohman, Teresa C and Newsome, Scott and Ratchford, John N and Balcer, Laura J and Pham, Dzung L and Crainiceanu, Ciprian M and Frohman, Elliot M and Reich, Daniel S and Calabresi, Peter A} } @article {abikoff2012quantile, title = {Remediating Organizational Functioning in Children with ADHD: Immediate and Long- Term Effects from a Randomized Controlled Trial}, journal = {Journal of Consulting and Clinical Psychology}, year = {2012}, note = {In Press}, author = {Howard Abikoff, Richard Gallagher, Karen C. Wells, Desiree W. Murray, Lei Huang, Feihan Lu, and Petkova, E.} } @article {shee, title = {Revisiting Brain Atrophy and Its Relationship to Disability in Multiple Sclerosis}, journal = {PLoS ONE}, volume = {7}, number = {5}, year = {2012}, month = {05}, pages = {e37049}, publisher = {Public Library of Science}, doi = {10.1371/journal.pone.0037049}, url = {http://dx.doi.org/10.1371\%2Fjournal.pone.0037049}, author = {Shiee, N and Bazin, P and Zackowski, K and Farrell, S and Harrison, D and Newsome, S and Ratchford, J and Caffo, B and Calabresi, P and Pham, D and Reich, D.} } @article {MRM:MRM22818, title = {On the relationship between seed-based and ICA-based measures of functional connectivity}, journal = {Magnetic Resonance in Medicine}, volume = {66}, number = {3}, year = {2011}, pages = {644{\textendash}657}, publisher = {Wiley Subscription Services, Inc., A Wiley Company}, keywords = {between network connectivity, blood oxygenation level dependent fMRI, functional connectivity, ICA, seed-based connectivity, within network connectivity}, issn = {1522-2594}, doi = {10.1002/mrm.22818}, url = {http://dx.doi.org/10.1002/mrm.22818}, author = {Joel, S. and Caffo, B and van Zijl, P and Pekar, J} } @article {reiss2011resampling, title = {Resampling-Based Information Criteria for Best-Subset Regression}, journal = {Annals of the Institute of Statistical Mathematics}, year = {2011}, author = {Reiss, P.T. and Huang, L. and Cavanaugh, J.E. and Krain Roy, A.} } @article {hao, title = {Redefining CpG Islands Using a Hidden Markov Models}, journal = {Biostatistics, PMCID: PMC2883304}, volume = {11}, number = {3}, year = {2010}, pages = {499{\textendash}514}, author = {Wu, H and Caffo, B and Jaffee, H and Feinberg, A and Irizarry, R} } @article {vidwan2010relation, title = {Relation of platelet count to bleeding and vascular complications in patients undergoing coronary angiography}, journal = {The American journal of cardiology}, volume = {105}, number = {9}, year = {2010}, pages = {1219{\textendash}1222}, publisher = {Elsevier}, author = {Vidwan, P. and Lee, S. and Rossi, J.S. and Stouffer, G.A.} } @article {lindquist2008rapid, title = {Rapid three-dimensional functional magnetic resonance imaging}, year = {2008}, author = {Lindquist, Martin A and Zhang, Cun-Hui and Glover, Gary and Shepp, Lawrence} } @article {Crai:Digg:Rowl:rejo:2008, title = {Rejoinder}, journal = {Journal of the American Statistical Association}, volume = {103}, number = {481}, year = {2008}, pages = {43{\textendash}43}, author = {Crainiceanu, C and Diggle, Peter J. and Rowlingson, Barry} } @article {Grev:Crai:Kche:Pete:rest:2008, title = {Restricted Likelihood Ratio Testing for Zero Variance Components in Linear Mixed Models}, journal = {Journal of Computational and Graphical Statistics}, volume = {17}, number = {4}, year = {2008}, pages = {870{\textendash}891}, keywords = {Nonparametric smoothing, nonregular problem, parametric bootstrap, penalized splines}, author = {Greven, S. and Crainiceanu, C and K{\"u}chenhoff, Helmut and Peters, Annette} } @article {pmid17344421, title = {Reduced kidney function as a risk factor for incident heart failure: the atherosclerosis risk in communities (ARIC) study}, journal = {J. Am. Soc. Nephrol.}, volume = {18}, number = {4}, year = {2007}, month = {Apr}, pages = {1307{\textendash}1315}, author = {Kottgen, A. and Russell, S. D. and Loehr, L. R. and Crainiceanu, C and Rosamond, W. D. and Chang, P. P. and Chambless, L. E. and Coresh, J.} } @article {schwartz2007relations, title = {Relations of brain volumes with cognitive function in males 45 years and older with past lead exposure}, journal = {Neuroimage, PMCID: PMC2038986}, volume = {37}, number = {2}, year = {2007}, pages = {633{\textendash}641}, publisher = {Elsevier}, author = {Schwartz, B and Chen, S and Caffo, B and Stewart, W and Bolla, K and Yousem, D and Davatzikos, C.} } @article {Crai:Rupp:rest:2004, title = {Restricted Likelihood Ratio Tests in Nonparametric Longitudinal Models}, journal = {Statistica Sinica}, volume = {14}, number = {3}, year = {2004}, pages = {713{\textendash}729}, keywords = {Bootstrap, linear mixed models, non-standard asymptotics, penalized splines, subject-specific curves, Variance components}, author = {Crainiceanu, C and Ruppert, D.} } @article {agresti2000random, title = {Random-effects modeling of categorical response data}, journal = {Sociological Methodology}, volume = {30}, year = {2000}, pages = {27{\textendash}80}, publisher = {Blackwell Publishers}, author = {Agresti, A and Booth, J and Hobert, J and Caffo, B} }