Abstract:
:Brain extraction, or skull-stripping, is an essential pre-processing step in neuro-imaging that has a direct impact on the quality of all subsequent processing and analyses steps. It is also a key requirement in multi-institutional collaborations to comply with privacy-preserving regulations. Existing automated methods, including Deep Learning (DL) based methods that have obtained state-of-the-art results in recent years, have primarily targeted brain extraction without considering pathologically-affected brains. Accordingly, they perform sub-optimally when applied on magnetic resonance imaging (MRI) brain scans with apparent pathologies such as brain tumors. Furthermore, existing methods focus on using only T1-weighted MRI scans, even though multi-parametric MRI (mpMRI) scans are routinely acquired for patients with suspected brain tumors. In this study, we present a comprehensive performance evaluation of recent deep learning architectures for brain extraction, training models on mpMRI scans of pathologically-affected brains, with a particular focus on seeking a practically-applicable, low computational footprint approach, generalizable across multiple institutions, further facilitating collaborations. We identified a large retrospective multi-institutional dataset of n=3340 mpMRI brain tumor scans, with manually-inspected and approved gold-standard segmentations, acquired during standard clinical practice under varying acquisition protocols, both from private institutional data and public (TCIA) collections. To facilitate optimal utilization of rich mpMRI data, we further introduce and evaluate a novel ''modality-agnostic training'' technique that can be applied using any available modality, without need for model retraining. Our results indicate that the modality-agnostic approach1 obtains accurate results, providing a generic and practical tool for brain extraction on scans with brain tumors.
journal_name
Neuroimagejournal_title
NeuroImageauthors
Thakur S,Doshi J,Pati S,Rathore S,Sako C,Bilello M,Ha SM,Shukla G,Flanders A,Kotrotsou A,Milchenko M,Liem S,Alexander GS,Lombardo J,Palmer JD,LaMontagne P,Nazeri A,Talbar S,Kulkarni U,Marcus D,Colen R,Davatzikosdoi
10.1016/j.neuroimage.2020.117081subject
Has Abstractpub_date
2020-10-15 00:00:00pages
117081eissn
1053-8119issn
1095-9572pii
S1053-8119(20)30567-Xjournal_volume
220pub_type
杂志文章相关文献
NEUROIMAGE文献大全abstract::Classical fear conditioning is an important mechanism to adequately respond and adapt to environmental threats and has been related to the development of fear and anxiety. Both cue and context conditioning have been studied but little is known about their relation to relevant resting state networks. The default mode n...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2017.10.024
更新日期:2018-01-15 00:00:00
abstract::It is well established that the time to name target objects can be influenced by the presence of categorically related versus unrelated distractor items. A variety of paradigms have been developed to determine the level at which this semantic interference effect occurs in the speech production system. In this study, w...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2009.12.067
更新日期:2010-04-01 00:00:00
abstract::Cast shadows can be salient depth cues in three-dimensional (3D) vision. Using a motion illusion in which a ball is perceived to roll in depth on the bottom or to flow in the front plane depending on the slope of the trajectory of its cast shadow, we investigated cortical mechanisms underlying 3D vision based on cast ...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2010.07.075
更新日期:2011-01-01 00:00:00
abstract::The hypothalamus and insular cortex play an essential role in the integration of endocrine and homeostatic signals and their impact on food intake. Resting-state functional connectivity alterations of the hypothalamus, posterior insula (PINS) and anterior insula (AINS) are modulated by metabolic states and caloric int...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2020.116931
更新日期:2020-08-15 00:00:00
abstract:AIM:Voxel-based morphometry analysis of neurological disorders would benefit if it could use data acquired from different scanners, but scanner based contrast variation could interfere with the detection of disease-specific structural abnormalities. In this study we examine MRI data from three different sites to invest...
journal_title:NeuroImage
pub_type: 杂志文章,多中心研究
doi:10.1016/j.neuroimage.2008.05.007
更新日期:2008-08-15 00:00:00
abstract::A central question in the study of the neural basis of written language is whether reading and spelling utilize shared orthographic representations. While recent studies employing fMRI to test this question report that the left inferior frontal gyrus (IFG) and ventral occipitotemporal cortex (vOTC) are active during b...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2016.12.054
更新日期:2017-02-15 00:00:00
abstract::The processing of motion changes throughout the visual hierarchy, from spatially restricted 'local motion' in early visual cortex to more complex large-field 'global motion' at later stages. Here we used functional magnetic resonance imaging (fMRI) to examine spatially selective responses in these areas related to the...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2019.05.068
更新日期:2019-10-01 00:00:00
abstract::Cognitive action control depends on cortical-subcortical circuits, involving notably the subthalamic nucleus (STN), as evidenced by local field potentials recordings (LFPs) studies. The STN consistently shows an increase in theta oscillations power during conflict resolution. Some studies have shown that cognitive act...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2019.04.071
更新日期:2019-08-15 00:00:00
abstract::Averaged single trials (AST) allowed the functional magnetic resonance imaging (fMRI) response to auditory stimuli to be measured at high temporal (1 s) and spatial (0.1 cm3) resolution. Using this paradigm we investigated the transient signal response to 100-ms tone bursts in trains of between 100 ms and 25.5 s in to...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1006/nimg.1998.0322
更新日期:1998-04-01 00:00:00
abstract::The hypothalamus consists of numerous nuclei, and is regarded as the highest center for various autonomic functions. Although each hypothalamic nucleus implements a distinct function, it remains difficult to investigate the human hypothalamus at the nucleus level. In the present high-resolution functional MRI study, w...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2017.08.056
更新日期:2017-11-15 00:00:00
abstract::The ability to regulate temptation and manage appetitive cravings is an important aspect of healthy adolescent development, but the neural systems underlying this process are understudied. In the present study, 60 healthy females evenly distributed from 10 to 23years of age used reappraisal to regulate the desire to c...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2014.12.037
更新日期:2015-03-01 00:00:00
abstract::The development of MRI measures as biomarkers for neurodegenerative disease could prove extremely valuable for the assessment of neuroprotective therapies. Much current research is aimed at developing such biomarkers for use in people who are gene-positive for Huntington's disease yet exhibit few or no clinical sympto...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2010.04.273
更新日期:2011-05-15 00:00:00
abstract::The literature suggests that that semantic and phonological fluency tasks selectively activate left Brodmann's area (BA) 45 and 44, respectively, in Broca's speech region. We used functional MRI to test this hypothesis. Subjects performed a semantic and a phonological fluency task. In addition, a syntactic fluency tas...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2008.01.009
更新日期:2008-04-15 00:00:00
abstract::Hemodynamically based functional neuroimaging techniques, such as BOLD fMRI and PET, provide indirect measures of neuronal activity. The quantitative relationship between neuronal activity and the measured signals is not yet precisely known, with uncertainties remaining about the relative contribution by their metabol...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2010.09.032
更新日期:2011-01-15 00:00:00
abstract::The current paper focuses on a relatively new and promising area of the study of EEG transformations during brain information processing based on the reduction of the signal to the discrete quasi-stationary segment sequences which may reflect individual brain microstates or discrete operations. In this framework, the ...
journal_title:NeuroImage
pub_type: 临床试验,杂志文章,随机对照试验
doi:10.1016/j.neuroimage.2004.03.013
更新日期:2004-07-01 00:00:00
abstract::Previous studies have shown that individuals with overweight and obesity may experience attentional biases and reduced inhibition toward food stimuli. However, evidence is scarce as to whether the attentional bias is present even before stimuli are consciously recognized. Moreover, it is not known whether or not diffe...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2021.117725
更新日期:2021-01-20 00:00:00
abstract::Efficient perceptual identification of emotionally-relevant stimuli requires optimized neural coding. Because sleep contributes to neural plasticity mechanisms, we asked whether the perceptual representation of emotionally-relevant stimuli within sensory cortices is modified after a period of sleep. We show combined e...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2014.06.003
更新日期:2014-10-15 00:00:00
abstract::A key objective in neuroscience is to improve our understanding of the relationship between brain function and structure. We investigated this in the posterior visual pathways of healthy volunteers by applying functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI) with tractography. The optic ...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2003.11.022
更新日期:2004-04-01 00:00:00
abstract::As the use of ultra-high field (UHF; ≥7T) magnetic resonance (MR) imaging expands, there is an increasing need to establish high-resolution MR imaging protocols for patients with neurological disease. Magnetization transfer (MT) imaging has been used to provide information about changes in the magnitude of the restric...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2016.09.009
更新日期:2018-03-01 00:00:00
abstract::Many cognitive theories of semantic organization stem from reports of patients with selective, category-specific deficits for particular classes of objects (e.g., fruit). The anatomical assumptions underlying the competing claims can be evaluated with functional neuroimaging but the findings to date have been inconsis...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1006/nimg.2001.1002
更新日期:2002-03-01 00:00:00
abstract::Activity of the prefrontal cortex (PFC) has been observed in previous block-design brain imaging studies of self-initiated movements. However, the meaning of these activations remained unclear. A functional MRI experiment was carried out, which utilized an epoch and an event-related analysis approach to the data. We h...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2005.06.044
更新日期:2005-11-15 00:00:00
abstract::Beta+-sensitive probes are useful tools for the measurement of radiotracer kinetics in small animals. They allow the cost-effective development of new PET tracers and offer the possibility to investigate a variety of cerebral processes. The study's main aim was the in vivo evaluation of a probe system for cerebral sur...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2009.06.077
更新日期:2009-11-01 00:00:00
abstract::Neural networks that span the medial temporal lobe (MTL), prefrontal cortex, and posterior cortical regions are essential to episodic memory function in humans. Encoding and retrieval are supported by the engagement of both distinct neural pathways across the cortex and common structures within the medial temporal lob...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2017.03.042
更新日期:2017-07-15 00:00:00
abstract::Theta-burst stimulation (TBS), a novel repetitive transcranial magnetic stimulation (TMS) protocol, is capable of suppressing the amplitude of contralateral motor-evoked potentials (MEP) for several minutes after the end of a conditioning train over the motor cortex. It remains unknown whether TBS leads to effects on ...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2007.11.037
更新日期:2008-03-01 00:00:00
abstract::Increasing evidence suggests that sleep spindles are involved in memory consolidation, but few studies have investigated the effects of learning on brain responses associated with spindles in humans. Here we used simultaneous electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) during sleep to...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2019.03.051
更新日期:2019-07-15 00:00:00
abstract:BACKGROUND:Previous work using quantified EEG has suggested that brain activity in individuals with chronic fatigue syndrome (CFS) and normal persons differs. Our objective was to investigate if specific frequency band-pass regions and spatial locations are associated with CFS using low-resolution electromagnetic brain...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2006.11.007
更新日期:2007-02-15 00:00:00
abstract::Fetal magnetoencephalography (fMEG) is used to study neurological functions of the developing fetus by measuring magnetic signals generated by electrical sources within the fetal brain. For this aim either auditory or visual stimuli are presented and evoked brain activity or spontaneous activity is measured at the sen...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2009.09.025
更新日期:2010-01-15 00:00:00
abstract::The ε4 allele of apolipoprotein E (apoE, protein; APOE, gene) is the most important genetic risk factor for the development of Alzheimer's disease (AD). Cortical structures in the medial temporal lobe (MTL) are important for memory function and are affected early in AD. Both gray matter (GM) and white matter (WM) stru...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2012.06.072
更新日期:2012-10-15 00:00:00
abstract::Alzheimer's disease (AD) is known to cause a variety of disturbances of higher visual functions that are closely related to the neuropathological changes. Visual association areas are more affected than primary visual cortex. Additionally, there is evidence from neuropsychological and imaging studies during rest or pa...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1006/nimg.2002.1271
更新日期:2002-11-01 00:00:00
abstract::Volitional swallowing in humans involves the coordination of both brainstem and cerebral swallowing control regions. Peripheral sensory inputs are necessary for safe and efficient swallowing, and their importance to the patterned components of swallowing has been demonstrated. However, the role of sensory inputs to th...
journal_title:NeuroImage
pub_type: 杂志文章
doi:10.1016/j.neuroimage.2008.04.234
更新日期:2008-08-01 00:00:00