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AFNI: Software for analysis and visualization of functional magnetic resonance neuroimages. (1996)

by R W Cox
Venue:Computers and Biomedical Research,
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FMRI visualization of brain activity during a monetary incentive delay task

by Brian Knutson, Andrew Westdorp, Erica Kaiser, Daniel Hommer - NEUROIMAGE 12 , 2010
"... Comparative studies have implicated striatal and mesial forebrain circuitry in the generation of autonomic, endocrine, and behavioral responses for incentives. Using blood oxygen level-dependent functional magnetic resonance imaging, we sought to visualize functional activation of these regions in 1 ..."
Abstract - Cited by 178 (18 self) - Add to MetaCart
Comparative studies have implicated striatal and mesial forebrain circuitry in the generation of autonomic, endocrine, and behavioral responses for incentives. Using blood oxygen level-dependent functional magnetic resonance imaging, we sought to visualize functional activation of these regions in 12 normal volunteers as they anticipated and responded for monetary incentives. Both individual and group analyses of time-series data revealed significant activation of striatal and mesial forebrain structures (including insula, caudate, putamen, and mesial prefrontal cortex) during trials involving both monetary rewards and punishments. In addition to these areas, during trials involving punishment, group analysis revealed activation foci in the anterior cingulate and thalamus. These

Dissociable executive functions in the dynamic control of behavior: inhibition, error detection, and correction

by H. Garavan, T. J. Ross, K. Murphy, R. A. P. Roche, E. A. Stein - Neuroimage , 2002
"... The present study employed event-related fMRI and EEG to investigate the biological basis of the cognitive control of behavior. Using a GO/NOGO task optimized to produce response inhibitions, frequent commission errors, and the opportunity for subsequent behavioral correction, we identified distinct ..."
Abstract - Cited by 159 (4 self) - Add to MetaCart
The present study employed event-related fMRI and EEG to investigate the biological basis of the cognitive control of behavior. Using a GO/NOGO task optimized to produce response inhibitions, frequent commission errors, and the opportunity for subsequent behavioral correction, we identified distinct cortical areas associated with each of these specific executive processes. Two cortical systems, one involving right prefrontal and parietal areas and the second regions of the cingulate, underlay inhibitory control. The involvement of these two systems was predicated upon the difficulty or urgency of the inhibition and each was employed to different extents by high- and low-absentminded subjects. Errors were associated with medial activation incorporating the anterior cingulate and pre-SMA while behavioral alteration subsequent to errors was associated with both the anterior cingulate and the left prefrontal cortex. Furthermore, the EEG data demonstrated that successful response inhibition depended upon the timely activation of cortical areas as predicted by race models of response selection. The results highlight how higher cognitive functions responsible for behavioral control can result from the dynamic interplay of distinct cortical systems. © 2002 Elsevier Science (USA)
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...ojected onto a screen at the subject’s feet and were viewed with the aid of prism glasses attached to the inside of the radiofrequency head coil. All analyses were conducted using AFNI v2.2 software (=-=Cox, 1996-=-). Following image reconstruction, the time-series data were motion corrected using 3D volume registration (least-squares alignment of three translational and three rotational parameters) and differen...

Puzzlingly high correlations in fMRI studies of emotion, personality, and social cognition. Perspect Psychol Sci

by Edward Vul, Christine Harris, Piotr Winkielman, Harold Pashler , 2009
"... ABSTRACT—Functional magnetic resonance imaging (fMRI) studies of emotion, personality, and social cognition have drawn much attention in recent years, with high-profile studies frequently reporting extremely high (e.g.,>.8) cor-relations between brain activation andpersonalitymeasures. We show th ..."
Abstract - Cited by 148 (0 self) - Add to MetaCart
ABSTRACT—Functional magnetic resonance imaging (fMRI) studies of emotion, personality, and social cognition have drawn much attention in recent years, with high-profile studies frequently reporting extremely high (e.g.,>.8) cor-relations between brain activation andpersonalitymeasures. We show that these correlations are higher than should be expected given the (evidently limited) reliability of both fMRI and personality measures. The high correlations are all the more puzzling because method sections rarely contain much detail about how the correlationswere obtained.We surveyed authors of 55 articles that reported findings of this kind to determine a few details on how these correlations were computed. More than half acknowledged using a strategy that computes separate correlations for individual voxels and reports means of only those voxels exceeding chosen thresh-
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...ompute the probability of falsely detecting a cluster of voxels (Type I error). This probability may be estimated using the AlphaSim tool from the AFNI (Analysis for Functional NeuroImaging) program (=-=Cox, 1996-=-).17 We12Although it is possible for voxels registered to the ‘‘average brain’’ to be functionally matched across subjects, the variability in anatomical location of well-studied regions in early visu...

The common neural basis of autobiographical memory, prospection, navigation, theory of mind, and the default mode: A quantitative meta-analysis

by R. Nathan Spreng, Raymond A. Mar, Alice S. N. Kim, E. A. Deconstructing - Journal of Cognitive Neuroscience , 2009
"... & A core brain network has been proposed to underlie a number of different processes, including remembering, prospection, navigation, and theory of mind [Buckner, R. L., & Carroll, D. C. Self-projection and the brain. Trends in Cognitive Sciences, 11, 49–57, 2007]. This purported network— me ..."
Abstract - Cited by 129 (8 self) - Add to MetaCart
& A core brain network has been proposed to underlie a number of different processes, including remembering, prospection, navigation, and theory of mind [Buckner, R. L., & Carroll, D. C. Self-projection and the brain. Trends in Cognitive Sciences, 11, 49–57, 2007]. This purported network— medial prefrontal, medial-temporal, and medial and lateral parietal regions—is similar to that observed during defaultmode processing and has been argued to represent selfprojection [Buckner, R. L., & Carroll, D. C. Self-projection and the brain. Trends in Cognitive Sciences, 11, 49–57, 2007] or
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...l., 2005; Turkeltaub et al., 2002; for a discussion of meta-analytic approaches to neuroimaging data, see Wager, Lindquist, & Kaplan, 2007). Conjunction Analysis The ALE maps were imported into AFNI (=-=Cox, 1996-=-), and a conjunction analysis was undertaken to examine the correspondence of consistently activated regions across autobiographical memory, navigation, theory of mind, and default mode. Conjunction w...

A hybrid approach to the skull stripping problem in MRI

by F. Ségonne, A. M. Dale, B E. Busa, B M. Glessner, B D. Salat, B H. K. Hahn, B. Fischl A - NeuroImage , 2004
"... We present a novel skull-stripping algorithm based on a hybrid approach that combines watershed algorithms and deformable surface models. Our method takes advantage of the robustness of the former as well as the surface information available to the latter. The algorithm first localizes a single whit ..."
Abstract - Cited by 127 (11 self) - Add to MetaCart
We present a novel skull-stripping algorithm based on a hybrid approach that combines watershed algorithms and deformable surface models. Our method takes advantage of the robustness of the former as well as the surface information available to the latter. The algorithm first localizes a single white matter voxel in a T1-weighted MRI image, and uses it to create a global minimum in the white matter before applying a watershed algorithm with a preflooding height. The watershed algorithm builds an initial estimate of the brain volume based on the three-dimensional connectivity of the white matter. This first step is robust, and performs well in the presence of intensity nonuniformities and noise, but may erode parts of the cortex that abut bright nonbrain structures such as the eye sockets, or may remove parts of the cerebellum. To correct these inaccuracies, a surface deformation process fits a smooth surface to the masked volume, allowing the incorporation of geometric constraints into the skullstripping procedure. A statistical atlas, generated from a set of accurately segmented brains, is used to validate and potentially correct the segmentation, and the MRI intensity values are locally re-estimated at the boundary of the brain. Finally, a high-resolution surface deformation is performed that accurately matches the outer boundary of the brain, resulting in a robust and automated procedure. Studies by our group and others outperform other publicly available skullstripping tools.
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...hresholding and morphology techniques, combined with an anisotropic diffusion process to localize and segment the brain. Meegama et al. (2001) propose a similar approach. The method proposed by Ward (=-=Cox, 1996-=-; Ward, 1999) generates a segmented brain volume by assembling segmented slices. Morphological operations are used to smooth the brain envelope and refine the final segmentation. Another example can b...

Conceptual processing during the conscious resting state. A functional MRI study

by J. R. Binder, J. A. Frost, T. A. Hammeke, P. S. F. Bellgowan, S. M. Rao, R. W. Cox - J. Cogn. Neurosci , 1999
"... n Localized, task-induced decreases in cerebral blood �ow are a frequent �nding in functional brain imaging research but remain poorly understood. One account of these phenomena postulates processes ongoing during conscious, resting states that are interrupted or inhibited by task performance. Psych ..."
Abstract - Cited by 120 (6 self) - Add to MetaCart
n Localized, task-induced decreases in cerebral blood �ow are a frequent �nding in functional brain imaging research but remain poorly understood. One account of these phenomena postulates processes ongoing during conscious, resting states that are interrupted or inhibited by task performance. Psychological evidence suggests that conscious humans are engaged almost continuously in adaptive processes involving semantic knowledge retrieval, representation in awareness, and directed manipulation of represented knowledge for organization, problem-solving, and planning. If interruption of such “conceptual” processes accounts for task-induced deactivation, tasks that also engage these conceptual processes should not cause deactivation. Furthermore, comparisons between conceptual and nonconceptual tasks should show activation during conceptual tasks of the same brain areas that are “deactivated ” relative to rest.
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...ross subjects. Image Processing and Subtraction Analysis All EPI images were spatially coregistered using an iterative procedure that minimizes variance in voxel intensity differences between images (=-=Cox, 1996-=-b). For each EPI time series, t tests were conducted at each voxel to measure changes in signal intensity between the two alternating comparison conditions. For this analysis, one of the comparison co...

Activation of cortical and cerebellar motor areas during executed and imagined hand movements: An fMRI study

by Martin Lotze, Pedro Montoya, Michael Erb, Ernst Hülsmann, Herta Flor, Uwe Klose, Niels Birbaumer, Wolfgang Grodd - Journal of Cognitive Neuroscience , 1999
"... Brain activation during executed (EM) and imagined move-ments (IM) of the right and left hand was studied in 10 healthy right-handed subjects using functional magnetic resonance imagining (fMRI). Low electromyographic (EMG) activity of the musculi ºexor digitorum superªcialis and high vividness of ..."
Abstract - Cited by 108 (2 self) - Add to MetaCart
Brain activation during executed (EM) and imagined move-ments (IM) of the right and left hand was studied in 10 healthy right-handed subjects using functional magnetic resonance imagining (fMRI). Low electromyographic (EMG) activity of the musculi ºexor digitorum superªcialis and high vividness of the imagined movements were trained prior to image acquisition. Regional cerebral activation was measured by fMRI during EM and IM and compared to resting conditions. Anatomically se-lected regions of interest (ROIs) were marked interactively over the entire brain. In each ROI activated pixels above a t value of 2.45 (p < 0.01) were counted and analyzed. In all subjects the supplementary motor area (SMA), the premotor cortex (PMC), and the primary motor cortex (M1) showed signiªcant activation during both EM and IM; the somatosen-sory cortex (S1) was signiªcantly activated only during EM. Ipsilateral cerebellar activation was decreased during IM com-pared to EM. In the cerebellum, IM and EM differed in their foci of maximal activation: Highest ipsilateral activation of the cerebellum was observed in the anterior lobe (Larsell lobule H IV) during EM, whereas a lower maximum was found about 2-cm dorsolateral (Larsell lobule H VII) during IM. The prefron-tal and parietal regions revealed no signiªcant changes during both conditions. The results of cortical activity support the hypothesis that motor imagery and motor performance possess similar neural substrates. The differential activation in the cere-bellum during EM and IM is in accordance with the assumption that the posterior cerebellum is involved in the inhibition of movement execution during imagination.
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...arameter maps was performed (Figure 2). The matching of the cortical data was performed with a Talairach alignment of the 3-D anatomical and functional dataset (see Figure 5A) using the AFNI program (=-=Cox, 1996-=-). For the cerebellum (Figure 4), a linear transformation algorithm was used with reference points at the fourth ventricle and the cranial, caudal, anterior, posterior, and the lateral boarders of the...

A parametric manipulation of factors affecting task-induced deactivation in functional neuroimaging

by Kristen A. Mckiernan, Jacqueline N. Kaufman, Jane Kucera-thompson, Jeffrey R. Binder - Journal of Cognitive Neuroscience , 2003
"... & Task-induced deactivation (TID) refers to a regional decrease in blood flow during an active task relative to a ‘‘resting’ ’ or ‘‘passive’ ’ baseline. We tested the hypothesis that TID results from a reallocation of processing resources by parametrically manipulating task difficulty within thr ..."
Abstract - Cited by 102 (5 self) - Add to MetaCart
& Task-induced deactivation (TID) refers to a regional decrease in blood flow during an active task relative to a ‘‘resting’ ’ or ‘‘passive’ ’ baseline. We tested the hypothesis that TID results from a reallocation of processing resources by parametrically manipulating task difficulty within three factors: target discriminability, stimulus presentation rate, and short-term memory load. Subjects performed an auditory target detection task during functional magnetic resonance imaging (fMRI), responding to a single target tone or, in the short-term memory load conditions, to target sequences. Seven task conditions (a common version and two additional levels for each of the three factors) were each alternated with ‘‘rest’ ’ in a block design. Analysis of covariance identified brain regions in which TID occurred. Analyses of variance identified seven regions (left anterior cingulate/superior frontal gyrus, left middle frontal gyrus, right anterior cingulate gyrus, left and right posterior cingulate gyrus, left posterior parieto-occipital cortex, and right precuneus) in which TID magnitude varied across task levels within a factor. Follow-up tests indicated that for each of the three factors, TID magnitude increased with task difficulty. These results suggest that TID represents reallocation of processing resources from areas in which TID occurs to areas involved in task performance. Short-term memory load and stimulus rate also predict suppression of spontaneous thought, and many of the brain areas showing TID have been linked with semantic processing, supporting claims that TID may be due in part to suspension of spontaneous semantic processes that occur during ‘‘rest’’ (Binder et al., 1999). The concept that the typical ‘‘resting state’ ’ is actually a condition characterized by rich cognitive activity has important implications for the design and analysis of neuroimaging studies. &
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...f 124 contiguous sagittal slices (1.2 mm thick) using a 3-D spoiled gradient-echo sequence (SPGR, GE Medical Systems). Image Analyses All image analysis was completed using the AFNI software package (=-=Cox, 1996-=-a). Subject data were volumetrically registered using an iterative procedure that minimizes variance in voxel intensity differences between images (Cox, 1996b). Both time series for each condition wer...

The neural basis of financial risk taking.

by Camelia M Kuhnen , Brian Knutson - Neuron, , 2005
"... Summary Investors systematically deviate from rationality when making financial decisions, yet the mechanisms responsible for these deviations have not been identified. Using event-related fMRI, we examined whether anticipatory neural activity would predict optimal and suboptimal choices in a finan ..."
Abstract - Cited by 98 (6 self) - Add to MetaCart
Summary Investors systematically deviate from rationality when making financial decisions, yet the mechanisms responsible for these deviations have not been identified. Using event-related fMRI, we examined whether anticipatory neural activity would predict optimal and suboptimal choices in a financial decision-making task. We characterized two types of deviations from the optimal investment strategy of a rational risk-neutral agent as risk-seeking mistakes and risk-aversion mistakes. Nucleus accumbens activation preceded risky choices as well as risk-seeking mistakes, while anterior insula activation preceded riskless choices as well as risk-aversion mistakes. These findings suggest that distinct neural circuits linked to anticipatory affect promote different types of financial choices and indicate that excessive activation of these circuits may lead to investing mistakes. Thus, consideration of anticipatory neural mechanisms may add predictive power to the rational actor model of economic decision making.
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...t (e.g., midbrain, ventral striatum). Functional scans of the whole brain were acquired every 2 s (TR = 2 s) with a T2*-sensitive in-/out- spiral pulse sequence (TE = 40 ms, flip = 90°) designed to minimize signal dropout at the base of the brain (Glover and Law, 2001). High-resolution structural scans were subsequently acquired using a T1- weighted spoiled grass sequence (TR = 100 ms; TE = 7 ms, flip = 90°), facilitating subsequent localization and coregistration of functional data. fMRI Analysis Localization analyses were conducted using Analysis of Functional Neural Images (AFNI) software (Cox, 1996). For preprocessing, voxel time series were sinc interpolated to correct for nonsimultaneous slice acquisition within each volume, concatenated across runs, and corrected for three-dimensional motion. Visual inspection of motion correction estimates confirmed that no subject’s head moved more than 2.0 mm in any dimension from one volume acquisition to the next. Preprocessed time series were submitted to a regression model that included three regressors indexing residual motion and six regressors modeling baseline, linear, and quadratic trends for each of the two runs. Regressors of interest we...

Regional homogeneity approach to fMRI data analysis

by Yufeng Zang, A Tianzi Jiang, Yingli Lu, A Yong He, Lixia Tian A - NeuroImage , 2004
"... Kendall’s coefficient concordance (KCC) can measure the similarity of a number of time series. It has been used for purifying a given cluster in functional MRI (fMRI). In the present study, a new method was developed based on the regional homogeneity (ReHo), in which KCC was used to measure the simi ..."
Abstract - Cited by 88 (9 self) - Add to MetaCart
Kendall’s coefficient concordance (KCC) can measure the similarity of a number of time series. It has been used for purifying a given cluster in functional MRI (fMRI). In the present study, a new method was developed based on the regional homogeneity (ReHo), in which KCC was used to measure the similarity of the time series of a given voxel to those of its nearest neighbors in a voxel-wise way. Six healthy subjects performed left and right finger movement tasks in event-related design; five of them were additionally scanned in a rest condition. KCC was compared among the three conditions (left finger movement, right finger movement, and the rest). Results show that bilateral primary motor cortex (M1) had higher KCC in either left or right finger movement condition than in rest condition. Contrary to prediction and to activation pattern, KCC of ipsilateral M1 is significantly higher than contralateral M1 in unilateral finger movement conditions. These results support the previous electrophysiologic findings of increasing ipsilateral M1 excitation during unilateral movement. ReHo can consider as a complementary method to model-driven method, and it could help reveal the complexity of the human brain function. More work is needed to understand the neural mechanism underlying ReHo.
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...mic response may vary from region to region (Moritz et al., 2000) and even from trial to trial (Duann et al., 2002; Richter et al., 1997). General linear model with deconvolution (GLM-De) method (see =-=Cox, 1996-=-; in section Deconvolution Analysis of fMRI Time Series Data by B. Douglas Ward in AFNI. Version 2.12c) allows HRF to vary from voxel to voxel. However, it also takes variability across trials as nois...

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