PDE-based spatial smoothing: a practical demonstration of impacts on MRI brain extraction, tissue segmentation and registration

Xing, Xiu-Xia; Zhou, You; Adelstein, Jonathan S.; Zuo, Xi‐Nian

doi:10.1016/j.mri.2011.02.007

Cited by 37 publications

(26 citation statements)

References 15 publications

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“…Firstly, MR image noise was removed by using a spatially adaptive non-local means filter and MR intensity heterogeneity correction (Xing et al, 2011; Zuo and Xing, 2011). Brain was extracted with a hybrid watershed/surface deformation procedure and was segmented into different tissues such as the cerebrospinal fluid (CSF), white matter (WM), and deep gray matter (GM) volumetric structures.…”

Section: Methodsmentioning

confidence: 99%

Mind-Body Practice Changes Fractional Amplitude of Low Frequency Fluctuations in Intrinsic Control Networks

et al. 2017

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Cognitive control impairment is a typical symptom largely reported in populations with neurological disorders. Previous studies have provided evidence about the changes in cognitive control induced by mind-body training. However, the neural correlates underlying the effect of extensive mind-body practice on cognitive control remain largely unknown. Using resting-state functional magnetic resonance imaging, we characterized dynamic fluctuations in large-scale intrinsic connectivity networks associated with mind-body practice, and examined their differences between healthy controls and Tai Chi Chuan (TCC) practitioners. Compared with a control group, the TCC group revealed significantly decreased fractional Amplitude of Low Frequency Fluctuations (fALFF) in the bilateral frontoparietal network, default mode network and dorsal prefrontal-angular gyri network. Furthermore, we detected a significant association between mind-body practice experience and fALFF in the default mode network, as well as an association between cognitive control performance and fALFF of the frontoparietal network. This provides the first evidence of large-scale functional connectivity in brain networks associated with mind-body practice, shedding light on the neural network changes that accompany intensive mind-body training. It also highlights the functionally plastic role of the frontoparietal network in the context of the “immune system” of mental health recently developed in relation to flexible hub theory.

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Section: Methodsmentioning

confidence: 99%

Mind-Body Practice Changes Fractional Amplitude of Low Frequency Fluctuations in Intrinsic Control Networks

et al. 2017

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“…The data preprocessing was composed of anatomical and functional processing steps. The structural preprocessing steps included: 1) removal of MR image noise using a spatially adaptive non-local means filter [36,37]; 2) brain extraction using a hybrid watershed/surface deformation procedure; 3) automated segmentation of cerebrospinal fluid (CSF), white matter (WM) and deep gray matter (GM) volumetric structures as well as surface reconstruction; and 4) spatial normalization of individual anatomical images to MNI152 standard brain template. The functional preprocessing steps included: 1) removing the first 5 volumes from each scan to allow for signal equilibration; 2) despiking and slice timing correction; 3) motion correction; 4) 4D grand mean intensity normalization; 5) aligning individual functional images to individual anatomical image using the grey-white matter boundary-based registration (BBR) algorithm [38]; 6) registering individual functional images to MNI152 standard template; 7) regressing out the Friston-24 motion time series and mean signals of WM and CSF to reduce the effects of these confounding factors [39, 40]; 8) removing linear and quadratic trends; and 9) spatial smoothing with Gaussian Kernel (FWHM = 6 mm).…”

Section: Methodsmentioning

confidence: 99%

Amplitude of low-frequency fluctuations in first-episode, drug-naïve depressive patients: A 5-year retrospective study

et al. 2017

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Despite different treatments and courses of illness, depressive symptoms appear similar in bipolar disorder (BD) and major depressive disorder (MDD), causing BD with an onset of depressive episode being frequently misdiagnosed as MDD, and leading to inappropriate treatment and poor clinical outcomes. Therefore, there is an urgent need to explore underlying neural basis to distinguish BD from MDD. The medical records of 80 first-episode, drug-naïve depressive patients with an initial diagnosis of MDD and illness duration of at least 5 years were reviewed retrospectively for this study. Fourteen bipolar depressed patients with a diagnosis conversion from MDD to BD, 14 patients with diagnosis of MDD, and 14 healthy subjects demographically matched with the BD group, were selected to participate in the study. Firstly, we examined whether there were differences among the three groups in whole brain fALFF during resting state. Secondly, clusters showing group differences in fALFF in any two groups were chosen as regions of interest (ROI) and then correlation between clinical features and fALFF values of ROIs were calculated. The BD group showed increased fALFF in bilateral putamen relative to both the MDD group and controls, while the MDD group exhibited decreased fALFF in left superior frontal gyrus (SFG) relative to both the BD group and controls (p < 0.05, corrected). Positive correlations between abnormality in the putamen and symptom severity were observed (significant for the MDD group, p = 0.043; marginally significant for the BD group, p = 0.060/0.076). These results implicate that abnormalities of key regions in the striatum and prefrontal areas may be trait markers for BD and MDD.

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“…Specifically, the anatomical steps were implemented in Freesurfer and FSL: (1) removal of image noise using a spatially adaptive non-local means filter [50,51] , (2) removal of non-brain tissue using a hybrid watershed/surface deformation procedure [52] , (3) automated segmentation of the white matter and deep gray matter volumetric structures (hippocampus, amygdala, caudate, putamen, and ventricles) [53,54] , and (4) a two-step registration of the high-resolution anatomical image to a common stereotaxic space (the Montreal Neurological Institute 152-brain template, MNI152) [55] .…”

Section: Data Preprocessingmentioning

confidence: 99%

Ventral medial prefrontal functional connectivity and emotion regulation in chronic schizophrenia: A pilot study

et al. 2013

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People with schizophrenia exhibit impaired social cognitive functions, particularly emotion regulation. Abnormal activations of the ventral medial prefrontal cortex (vMPFC) during emotional tasks have been demonstrated in schizophrenia, suggesting its important role in emotion processing in patients. We used the resting-state functional connectivity approach, setting a functionally relevant region, the vMPFC, as a seed region to examine the intrinsic functional interactions and communication between the vMPFC and other brain regions in schizophrenic patients. We found hypo-connectivity between the vMPFC and the medial frontal cortex, right middle temporal lobe (MTL), right hippocampus, parahippocampal cortex (PHC) and amygdala. Further, there was a decreased strength of the negative connectivity (or anticorrelation) between the vMPFC and the bilateral dorsal lateral prefrontal cortex (DLPFC) and pre-supplementary motor areas. Among these connectivity alterations, reduced vMPFC-DLPFC connectivity was positively correlated with positive symptoms on the Positive and Negative Syndrome Scale, while vMPFC-right MTL/PHC/amygdala functional connectivity was positively correlated with the performance of emotional regulation in patients. These findings imply that communication and coordination throughout the brain networks are disrupted in schizophrenia. The emotional correlates of vMPFC connectivity suggest a role of the hypo-connectivity between these regions in the neuropathology of abnormal social cognition in chronic schizophrenia.

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PDE-based spatial smoothing: a practical demonstration of impacts on MRI brain extraction, tissue segmentation and registration

Cited by 37 publications

References 15 publications

Mind-Body Practice Changes Fractional Amplitude of Low Frequency Fluctuations in Intrinsic Control Networks

Mind-Body Practice Changes Fractional Amplitude of Low Frequency Fluctuations in Intrinsic Control Networks

Amplitude of low-frequency fluctuations in first-episode, drug-naïve depressive patients: A 5-year retrospective study

Ventral medial prefrontal functional connectivity and emotion regulation in chronic schizophrenia: A pilot study

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