Abstract:
:Magnetic resonance imaging (MRI) intensities are acquired in arbitrary units, making scans non-comparable across sites and between subjects. Intensity normalization is a first step for the improvement of comparability of the images across subjects. However, we show that unwanted inter-scan variability associated with imaging site, scanner effect, and other technical artifacts is still present after standard intensity normalization in large multi-site neuroimaging studies. We propose RAVEL (Removal of Artificial Voxel Effect by Linear regression), a tool to remove residual technical variability after intensity normalization. As proposed by SVA and RUV [Leek and Storey, 2007, 2008, Gagnon-Bartsch and Speed, 2012], two batch effect correction tools largely used in genomics, we decompose the voxel intensities of images registered to a template into a biological component and an unwanted variation component. The unwanted variation component is estimated from a control region obtained from the cerebrospinal fluid (CSF), where intensities are known to be unassociated with disease status and other clinical covariates. We perform a singular value decomposition (SVD) of the control voxels to estimate factors of unwanted variation. We then estimate the unwanted factors using linear regression for every voxel of the brain and take the residuals as the RAVEL-corrected intensities. We assess the performance of RAVEL using T1-weighted (T1-w) images from more than 900 subjects with Alzheimer's disease (AD) and mild cognitive impairment (MCI), as well as healthy controls from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. We compare RAVEL to two intensity-normalization-only methods: histogram matching and White Stripe. We show that RAVEL performs best at improving the replicability of the brain regions that are empirically found to be most associated with AD, and that these regions are significantly more present in structures impacted by AD (hippocampus, amygdala, parahippocampal gyrus, enthorinal area, and fornix stria terminals). In addition, we show that the RAVEL-corrected intensities have the best performance in distinguishing between MCI subjects and healthy subjects using the mean hippocampal intensity (AUC=67%), a marked improvement compared to results from intensity normalization alone (AUC=63% and 59% for histogram matching and White Stripe, respectively). RAVEL is promising for many other imaging modalities.
journal_name
Neuroimagejournal_title
NeuroImageauthors
Fortin JP,Sweeney EM,Muschelli J,Crainiceanu CM,Shinohara RT,Alzheimer's Disease Neuroimaging Initiative.doi
10.1016/j.neuroimage.2016.02.036subject
Has Abstractpub_date
2016-05-15 00:00:00pages
198-212eissn
1053-8119issn
1095-9572pii
S1053-8119(16)00145-2journal_volume
132pub_type
杂志文章相关文献
NEUROIMAGE文献大全abstract::Diffusion imaging of post mortem brains has great potential both as a reference for brain specimens that undergo sectioning, and as a link between in vivo diffusion studies and "gold standard" histology/dissection. While there is a relatively mature literature on post mortem diffusion imaging of animals, human brains ...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2011.03.070
更新日期:2011-07-01 00:00:00
abstract::As the EEG inverse problem does not have a unique solution, the sources reconstructed from EEG and their connectivity properties depend on forward and inverse modeling parameters such as the choice of an anatomical template and electrical model, prior assumptions on the sources, and further implementational details. I...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2017.02.076
更新日期:2017-05-15 00:00:00
abstract::The publisher regrets due to an error in the publishing process the above articles was accidentally withdrawn and has now been published in (Neuroimage 83C December 2013 https://doi.org/10.1016/j.neuroimage.2013.05.115). The publisher would like to apologize for any inconvenience caused. ...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2013.02.041
更新日期:2013-07-15 00:00:00
abstract::We established a strategy to perform cross-validation of serial optical coherence scanner imaging (SOCS) and diffusion tensor imaging (DTI) on a postmortem human medulla. Following DTI, the sample was serially scanned by SOCS, which integrates a vibratome slicer and a multi-contrast optical coherence tomography rig fo...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2014.06.032
更新日期:2014-10-15 00:00:00
abstract::Learning with discriminative methods is generally based on minimizing the misclassification of training samples, which may be unsuitable for imbalanced datasets where the recognition might be biased in favor of the most numerous class. This problem can be addressed with a generative approach, which typically requires ...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2011.05.011
更新日期:2011-08-01 00:00:00
abstract::In line with the notion of a continuously active and dynamic brain, functional networks identified during rest correspond with those revealed by task-fMRI. Characterizing the dynamic cross-talk between these network nodes is key to understanding the successful implementation of effortful cognitive processing in health...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2015.01.026
更新日期:2015-04-01 00:00:00
abstract::The modulation of repetition effects by the lag between first and second presentations of a visual object during a speeded semantic judgment task was examined using both scalp event-related potentials (ERPs) and event-related functional magnetic resonance imaging (efMRI). Four levels of lag were used within a single s...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2003.12.020
更新日期:2004-04-01 00:00:00
abstract::A lack of consensus exists as to whether there are sex differences in the fMRI BOLD signal correlates of language processing in the human brain. Here, whole-brain fMRI was used to examine the neural activity of 46 adults performing one of two sets of language tasks. Conservative quantitative and qualitative criteria i...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2008.12.034
更新日期:2009-04-15 00:00:00
abstract::Resting-state functional connectivity, manifested as spontaneous synchronous activity in the brain, has been detected by functional MRI (fMRI) across species such as humans, monkeys, and rats. Yet, most networks, especially the classical bilateral connectivity between hemispheres, have not been reliably found in the m...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2013.10.025
更新日期:2014-02-01 00:00:00
abstract::Natural speech builds on contextual relations that can prompt predictions of upcoming utterances. To study the neural underpinnings of such predictive processing we asked 10 healthy adults to listen to a 1-h-long audiobook while their magnetoencephalographic (MEG) brain activity was recorded. We correlated the MEG sig...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2020.116936
更新日期:2020-10-01 00:00:00
abstract::Inhibitory control of actions is one important aspect in daily life to warrant adequate context related behavior. Alpha activity (oscillatory brain activity around 10Hz) has been suggested to play a major role for the implementation of inhibitory control. In the present study electrophysiological correlates of volunta...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2012.09.048
更新日期:2013-01-15 00:00:00
abstract::Diffusion MRI offers great potential in studying the human brain microstructure and connectivity. However, diffusion images are marred by technical problems, such as image distortions and spurious signal loss. Correcting for these problems is non-trivial and relies on having a mechanism that predicts what to expect. I...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2015.07.067
更新日期:2015-11-15 00:00:00
abstract::The extent to which the generation of mental images draws on the neuronal representations involved in visual perception has been the subject of much debate. To investigate this overlap, we assessed whether adaptation to visual stimuli affects the ability to generate visual mental images; such cross-adaptation would in...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2011.10.022
更新日期:2012-02-01 00:00:00
abstract::Perception, motion, and cognition involve the formation of cooperative neuronal assemblies distributed over the cerebral cortex. It remains to explore what characterizes the assemblies, their location, and the structural substrate of assembly formation. In this EEG/fMRI study, we describe the response of the visual ar...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2005.07.045
更新日期:2006-01-15 00:00:00
abstract::We used fMRI to investigate neural activation in reading aloud in bilinguals differing in age of acquisition. Three groups were compared: French-English bilinguals who acquired two languages from birth (simultaneous), French-English bilinguals who learned their L2 after the age of 5 years (sequential), and English-spe...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2015.03.016
更新日期:2015-05-15 00:00:00
abstract::Keeping time is fundamental for our everyday existence. Various isochronous activities, such as locomotion, require us to use internal timekeeping. This phenomenon comes into play also in other human pursuits such as dance and music. When listening to music, we spontaneously perceive and predict its beat. The process ...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2019.116191
更新日期:2020-08-01 00:00:00
abstract::Auditory information communicated through vocalizations, music, or sounds in the environment is commonly used to orient and direct attention to different locations in extrapersonal space. The neural networks subserving attention to auditory space remain poorly understood in comparison to our knowledge about attention ...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2005.10.050
更新日期:2006-04-15 00:00:00
abstract::Activity of cortical local neuronal populations fluctuates continuously, and a large proportion of these fluctuations are shared across populations of neurons. Here we seek organizational rules that link these two phenomena. Using neuronal activity, as identified by functional MRI (fMRI) and for a given voxel or brain...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2013.01.072
更新日期:2013-06-01 00:00:00
abstract::To be able to interact with our environment, we need to transform incoming sensory information into goal-directed motor outputs. Whereas our ability to plan an appropriate movement based on sensory information appears effortless and simple, the underlying brain dynamics are still largely unknown. Here we used magnetoe...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2016.05.027
更新日期:2016-08-01 00:00:00
abstract::Examining the brain at rest is a powerful approach used to understand the intrinsic properties of typical and disordered human brain function, yet task-free paradigms are associated with greater head motion, particularly in young and/or clinical populations such as autism spectrum disorder (ASD) and attention-deficit/...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2020.117524
更新日期:2021-01-15 00:00:00
abstract::This paper presents an open, multi-vendor, multi-field strength magnetic resonance (MR) T1-weighted volumetric brain imaging dataset, named Calgary-Campinas-359 (CC-359). The dataset is composed of images of older healthy adults (29-80 years) acquired on scanners from three vendors (Siemens, Philips and General Electr...
journal_title:NeuroImage
pub_type: 杂志文章,评审
doi:10.1016/j.neuroimage.2017.08.021
更新日期:2018-04-15 00:00:00
abstract::The aim of this novel technique is to allow researchers, particularly those operating at high static magnetic field strengths on fMRI applications, to tailor the static magnetic field within the brain. The optimum solution for their experimental needs is reached, utilizing the full potential of the active shims at the...
journal_title:NeuroImage
pub_type: 临床试验,杂志文章
doi:
更新日期:2002-10-01 00:00:00
abstract:BACKGROUND:High sensation-seekers (HSS) pursue novelty even at the cost of self-harm. When challenged, HSS are less anxious, show blunted physiological (cortisol, startle) and neurobiological (prefrontal-limbic) responses, and devalue aversive outcomes. Here, we investigate how these features interact under conditions ...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2014.08.038
更新日期:2014-12-01 00:00:00
abstract::Quantitative assessment of the myelin water content in the brain can substantially improve our understanding of white matter diseases such as multiple sclerosis. In this study, in vivo myelin water content was estimated using T(2)* relaxation with multi-slice acquisitions in magnetic resonance imaging (MRI). The main ...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2010.04.023
更新日期:2010-08-01 00:00:00
abstract::The effects of functional magnetic resonance imaging (fMRI) acoustic noise were investigated on the parameters of event-related responses (ERPs) elicited during auditory matching-to-sample location and pitch working memory tasks. Stimuli were tones with varying location (left or right) and frequency (high or low). Sub...
journal_title:NeuroImage
pub_type: 临床试验,杂志文章
doi:10.1016/S1053-8119(03)00390-2
更新日期:2003-10-01 00:00:00
abstract::When a head is placed in an MRI scanner, differences between the magnetic susceptibility of tissue, bone, and air distort the magnetic field. While some of the resulting inhomogeneity can be corrected by the shimming process, much of it cannot, and this causes distortion (sometimes referred to as geometric distortion)...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1006/nimg.2002.1281
更新日期:2003-01-01 00:00:00
abstract::Stereotypes associated with gender, race, ethnicity and religion are powerful forces in human social interactions. Previous neuroimaging and neuropsychological studies point to a role of the prefrontal cortex in controlling stereotypical responses. Here we used transcranial magnetic stimulation (TMS) in combination wi...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2011.02.037
更新日期:2011-06-01 00:00:00
abstract::Despite its importance as the prime method for non-invasive assessment of human brain function, functional MRI (fMRI) was repeatedly challenged with regards to the validity of the fMRI-derived brain activation maps. Amygdala fMRI was particularly targeted, as the amygdala's anatomical position in the ventral brain com...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2020.116585
更新日期:2020-05-01 00:00:00
abstract::Carpal tunnel syndrome (CTS) is a common entrapment neuropathy of the median nerve characterized by paresthesias and pain in the first, second, and third digits. We hypothesize that aberrant afferent input in CTS will lead to cortical plasticity. Functional MRI (fMRI) and neurophysiological testing were performed on C...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2005.12.017
更新日期:2006-06-01 00:00:00
abstract::In fMRI, time courses with similar temporal "activation" patterns may belong to different brain regions (i.e., these regions are functionally connected, coactivated). A group of time courses (TCs) corresponding to a particular type of temporal activation pattern should be maximally self-consistent (homogeneous). We de...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1006/nimg.2000.0729
更新日期:2001-04-01 00:00:00