Data Processing Assistant For Resting-State fMRI Research Articles

Altered resting-state functional connectivity of the brain in children with autism spectrum disorder.

Autism spectrum disorder (ASD) is a group of neurodevelopmental disorders. Brain mapping has shown that functional brain connections are altered in autism. This study investigated the pattern of brain connection changes in autistic people compared to healthy people. This study aimed to analyze functional abnormalities withinthe brain due to ASD, using resting-state functional magnetic resonance imaging (fMRI). Resting-state functional magnetic resonance images of 26 individuals with ASD and 26 healthy controls were obtained from the Autism Brain Imaging Data Exchange (ABIDE) database. The DPARSF (data processing assistant for resting-state fMRI) toolbox was used for resting-state functional image processing, and features related to functional connections were extracted from these images. Then, the extracted features from both groups were compared using an Independent Two-Sample TTest, and the features with significant differences between the two groups were identified. Compared with healthy controls, individuals with ASD showed hyper-connectivity in the frontal lobe, anterior cingulum, parahippocampal, left precuneus, angular, caudate, superior temporal, and left pallidum, as well as hypo-connectivity in the precentral, left superior frontal, left middle orbitofrontal, right amygdala, and left posterior cingulum. Our findings show that abnormal functional connectivity exists in patients with ASD. This study makesan importantadvancement in our understanding ofthe abnormal neurocircuits causing autism.

Functional Reorganizations Outside the Sensorimotor Regions Following Complete Thoracolumbar Spinal Cord Injury.

Studies have shown that loss of sensorimotor function in spinal cord injury (SCI) leads to brain functional reorganization, which may play important roles in motor function recovery. However, the specific functional changes following SCI are still poorly understood. To investigate whether there are functional reorganizations outside the sensorimotor regions after complete thoracolumbar SCI (CTSCI), and how these reorganizations are associated with clinical manifestations. Prospective. Eighteen CTSCI patients (28-67 years of age; 16 men) and 18 age-, gender-matched healthy controls (HCs) (27-64 years of age; 16 men). Resting-state functional magnetic resonance imaging (RS-fMRI) using echo-planar-imaging (EPI) sequence at 3.0 T. Data preprocessing was performed using Data Processing Assistant for Resting-State fMRI (DPARSF). Amplitude of low-frequency fluctuations (ALFF) was used to characterize regional neural function, and seed-based functional connectivity (FC) was used to evaluate the functional integration of the brain network. Two-sample t-tests were used for ALFF and FC measures (the data conform to the normal distribution), partial correlation analysis was used to analyze the correlation between clinical and imaging indicators, and receiver operating characteristic (ROC) analysis was used to search for sensitive imaging indicators. Compared with HCs, CTSCI patients showed decreased ALFF in right lingual gyrus (LG), increased ALFF in right middle frontal gyrus (MFG), and decreased FC between the right LG and Vermis_3 (cluster-level FWE correction with P < 0.05). Subsequent correlation analyses revealed that decreased FC between the right LG and Vermis_3 positively correlated with the visual analog scale (VAS) (P=0.043, r=0.443). Finally, the ROC analysis showed that the area under the curve (AUC) of FC value between right LG and Vermis3 was 0.881. These findings suggest a possible theoretical basis of the mechanism of visual-, emotion-, and cognition-related techniques in rehabilitation training for CTSCI.

Analysis of the differences in brain function response after acupuncture and moxibustion at Zúsānlĭ (足三里ST36) in the patients with functional dyspepsia based on fractional amplitude of low frequency fluctuation of rest functional magnetic resonance imaging

Objectiveto explore the differences in the central response after acupuncture and moxibusbution at Zúsānlĭ (足三里ST36) in treatment of functional dyspepsia (FD) based on the analysis of fractional amplitude of low frequency fluctuation (fALFF) of resting-state functional magnetic resonance imaging (rfMRI). Methodsa total of 60 patients with FD were randomized into an acupuncture group and a moxibustion group, 30 cases in each one. In the acupuncture group, acupuncture was applied to bilateral ST36. In the moxibustion group, moxibustion was exerted at bilateral ST36. The treatment was given once a day, 5 times a week, totally for 4 weeks in each group, including 20 treatments with acupuncture or moxibustion. Separately, before and at the end of treatment, rfMRI scanning was conducted in two groups. Using data processing assistant for resting-state fMRI (DPARSF) software and MATLAB data platform, rfMRI data were collected for preprocessing and fALFF analysis. Resultscompared with the data before treatment, after treated with acupuncture at ST36 in FD patients, fALFF value was reduced in the right superior frontal gyrus, left superior frontal gyrus, left inferior frontal gyrus, right cuneus, left precuneus, right middle occipital gyrus, left middle occipital gyrus, etc., and it was increased in the left parahippocampus, right parahippocampus, left cerebellum, etc (all P < 0.01). After treated with moxibustion, the remarkable increase of fALFF was not discovered in brain areas, but fALFF decreased significantly in the left superior parietal gyrus (P < 0.01). Compared with moxibustion at ST36, after acupuncture at ST36 in FD patients, the increase of fALFF appeared in the right putamen and the decrease of it occurred in the middle occipital gyrus, indicating the statistical significance (both P < 0.05). Conclusionthe differences in central function responses are induced in treamtent with acupuncture and moxibustion, which is probably related to the resting-state default network associated with targeted regulation and ventral attention of brain areas in functional dyspepsia.

Abnormal ventral attention network homogeneity in patients with right temporal lobe epilepsy.

The attention network is the structural basis of cognitive function. As one of the two known attention networks, the ventral attention network (VAN) has a significant impact on the cognitive impairment of patients with epilepsy. Nevertheless, changes in network homogeneity (NH) are rarely reported in the VAN of right temporal lobe epilepsy (rTLE) patients. Therefore, we explored the NH of the VAN in rTLE patients in this study. Seventy rTLE patients and 69 healthy controls were recruited. All participants underwent resting-state functional magnetic resonance imaging (fMRI), which was the primary method of evaluation. The executive control reaction time (ECRT) was examined via the attentional network test. The Data Processing Assistant for Resting-State fMRI (DPARSF) was used to analyze NH. The independent component analysis (ICA) and correlation analysis were used in data analysis. Compared to the control group, patients with right temporal lobe epilepsy showed a lower NH in the right superior temporal gyrus, and a longer ECRT. However, abnormal NH values had no significant association with the clinical measurements. Patients with right temporal lobe epilepsy have abnormal NH values in the VAN, and the executive functions in rTLE patients are also altered. The altered NH values in VAN may help provide new insights into the pathophysiology of cognitive impairment in rTLE.

Quantitative analysis of cerebellar lobule morphology and clinical cognitive correlates in refractory temporal lobe epilepsy patients

PurposeThis study was conducted to explore the cerebellar substructure volumetric alterations in refractory unilateral temporal lobe epilepsy (TLE) patients and the relationship with clinical factors and cognitive scores. MethodsA total of 48 unilateral refractory TLE patients and 48 age- and gender-matched normal controls (NCs) were retrospectively studied. All subjects underwent high-resolution magnetic resonance imaging (MRI) and automatically segmented volumetric brain information was obtained using volBrain and Data Processing Assistant for Resting-State fMRI (DPARSF) separately. Clinical seizure features and cognitive scores were acquired by a structured review of medical records. ResultsThe total volumes (TVs) of bilateral crus I, crus II, and IX were significantly smaller in the refractory unilateral TLE epilepsy patients. The gray matter volumes (GMVs) of cerebellar lobules showed lateralized reduction in ipsilateral III, IX, and contralateral crus II. Contralateral crus II GMV showed significant negative correlation with the duration of epilepsy (r = −0.31, p = 0.035) and positive association with the cognitive scores including long-term memory (LTM) (r = 0.39, p = 0.017), short-term memory (STM) (r = 0.51, p = 0.001) verbal comprehension index (VCI) (r = 0.37, p = 0.024), and perceptual organization index (POI) (r = 0.36, p = 0.030). The voxel-based morphometry (VBM) analysis proved similar results. The contralateral crus I GMV was significantly smaller in the generalized onset group (t = 2.536, p = 0.015). ConclusionsThe lobules of the cerebellar in refractory TLE patients manifest different volumetric change characteristics. Crus II contralateral GMV is negatively correlated with the duration of epilepsy and positively associated with the cognitive scores.

Optimization of rs-fMRI parameters in the Seed Correlation Analysis (SCA) in DPARSF toolbox: A preliminary study.

There are a number of various methods of resting-state functional magnetic resonance imaging (rs-fMRI) analysis such as independent component analysis, multivariate autoregressive models, or seed correlation analysis however their results depend on arbitrary choice of parameters. Therefore, the aim of this work was to optimize the parameters in the seed correlation analysis using the Data Processing Assistant for Resting-State fMRI (DPARSF) toolbox for rs-fMRI data received from a Siemens Magnetom Skyra 3-Tesla scanner using a whole-brain, gradient-echo echo planar sequence with a 32-channel head coil. Different ranges of the following parameters: amplitude of low-frequency fluctuation (ALFF), Gaussian kernel at FWHM and radius of spherical ROI for 109 regions were tested for 20 healthy volunteers. The highest values of functional connectivity (FC) correlations were found for ALFF 0.01-0.08, spherical ROIs with the 8-mm radius and Gaussian kernel 8mm at FWHM in all the studied areas that is, Auditory, Sensimotor, Visual, and Default Mode Network. The dominating influence of ALFF and smoothing on values of FC correlations was noted.

Combined resting state functional magnetic resonance imaging and diffusion tensor imaging study in patients with idiopathic restless legs syndrome

ObjectiveRestless legs syndrome (RLS) is a common neurological disorder characterized by an urge to move the legs along with paraesthesia deep within them. In this study, we aimed to use diffusion tensor imaging (DTI) and regional homogeneity (ReHo) to investigate the changes in regional spontaneous brain activity change for RLS patients against age- and gender-matched normal control (NC) subjects. MethodsA total of 35 RLS patients and 27 age- and gender-matched NC subjects were recruited for group comparison research that used DTI and ReHo techniques. DTI was analysed by FSL and tract-based spatial statistics (TBSS) software to measure the values of fractional anisotropy (FA) or mean diffusivity (MD) in brain regions. Statistical Parametric Mapping 8 (SPM8) was used for data preprocessing and Data Processing Assistant for Resting-State fMRI (DPARSF) toolbox was used for ReHo calculation. For multiple comparison correction, the AlphaSim program implemented in AFNI was used to control the false-positive rate (corrected p < 0.05). ResultsThere was no significant difference between the iRLS and NC groups in age or gender. In the one-sample t-test, both the NC and RSL groups showed increased ReHo in the bilateral posterior cingulate/precuneus cortex compared to the groups' global means, indicating that the default mode network was at rest. The RLS group showed a smaller cluster size than the NC group. In the two-sample t-test, the RLS group showed increased ReHo in the bilateral middle frontal gyrus, anterior cingulate cortex, caudate nucleus, insula, thalamus, putamen and left posterior cingulate cortex compared to the NC group. The statistical analysis of DTI images did not show any difference between the two groups. TBSS group comparison did not reveal any difference in FA or mean diffusivity (MD) of any brain region. ConclusionRLS patients showed that greater ReHo within the striatum, thalamus and the limbic system, which implies that the emotional processing, motion control and cognition in the cortico-striatal-thalamic-cortical (CSTC) loop may be the site of dysfunction in RLS patients. This finding may provide imaging evidence to explore the pathophysiology of RLS. On the other hand, we did not see any change in the microstructure in the DTI analysis for RLS patients when compared to the NC group, which suggests a metabolic impairment.

Low-frequency fluctuation amplitude analysis of resting-state fMRI for functional brain response differences between acupuncture and moxibustion at Zusanli (ST 36) in patient with functional dyspepsia

To compare and analyze functional brain response characteristics by applying acupuncture or moxibustion to Zusanli (ST 36) in patients with functional dyspepsia (FD) and investigate the differences of central action mechanism resulting from acupuncture or moxibustion. A total of eligible 24 FD cases were divided into two blood-oxygen-level dependent (BOLD) sequences for functional magnetic resonance imaging (fMRI) scan. The amplitude of low frequency fluctuation (ALFF) analyses were conducted on the data of location phase, structure phase, resting state before acupuncture/moxibustion, working state during acupuncture/moxibustion and resting state after acupuncture/moxibustion using Data Processing Assistant for Resting-State fMRI (DPARSF) software. Acupuncture and moxibustion produced significant differences in functional brain response. The working state during acupuncture/moxibustion mainly decreased ALFF values in the right supramarginal gyrus, right superior parietal lobule, right frontal gyrus, upper right occipital lobe, right precuneus and right cingulate gyrus. At the same time, it increased ALFF values in the left cerebellum, right caudate nucleus, right cerebellum and left inferior gyrus. The differences during the resting state after acupuncture/moxibustion were significantly smaller than the working state in intensity and size. It mainly resulted in decrease in ALFF values in the right postcentral gyrus and right supramarginal gyrus and increase in ALFF values in the left precuneus, orbital part of inferior frontal gyrus and right cerebellar peduncles. Needling and moxibustion at Zusanli (ST 36) can produce significant differences in immediate functional brain response.

PreSurgMapp: a MATLAB Toolbox for Presurgical Mapping of Eloquent Functional Areas Based on Task-Related and Resting-State Functional MRI.

The main goal of brain tumor surgery is to maximize tumor resection while minimizing the risk of irreversible postoperative functional sequelae. Eloquent functional areas should be delineated preoperatively, particularly for patients with tumors near eloquent areas. Functional magnetic resonance imaging (fMRI) is a noninvasive technique that demonstrates great promise for presurgical planning. However, specialized data processing toolkits for presurgical planning remain lacking. Based on several functions in open-source software such as Statistical Parametric Mapping (SPM), Resting-State fMRI Data Analysis Toolkit (REST), Data Processing Assistant for Resting-State fMRI (DPARSF) and Multiple Independent Component Analysis (MICA), here, we introduce an open-source MATLAB toolbox named PreSurgMapp. This toolbox can reveal eloquent areas using comprehensive methods and various complementary fMRI modalities. For example, PreSurgMapp supports both model-based (general linear model, GLM, and seed correlation) and data-driven (independent component analysis, ICA) methods and processes both task-based and resting-state fMRI data. PreSurgMapp is designed for highly automatic and individualized functional mapping with a user-friendly graphical user interface (GUI) for time-saving pipeline processing. For example, sensorimotor and language-related components can be automatically identified without human input interference using an effective, accurate component identification algorithm using discriminability index. All the results generated can be further evaluated and compared by neuro-radiologists or neurosurgeons. This software has substantial value for clinical neuro-radiology and neuro-oncology, including application to patients with low- and high-grade brain tumors and those with epilepsy foci in the dominant language hemisphere who are planning to undergo a temporal lobectomy.

Amplitude of low-frequency fluctuation (ALFF) and fractional ALFF in migraine patients: a resting-state functional MRI study

To evaluate the amplitude of low-frequency oscillations (LFOs) of the brain in migraine patients using amplitude of low-frequency fluctuation (ALFF) and fractional ALFF in the interictal period, in comparison to healthy controls (HCs). A total of 54 subjects, including 30 migraineurs and 24 gender- and age-matched HCs completed the fMRI. All the data and ALFF, fALFF analyses were preprocessed with the Data Processing Assistant for Resting-State fMRI (DPARSF). All of the statistical analyses were performed using the REST software to explore the differences in ALFF and fALFF between migraine patients and HCs. In contrast to HCs, migraine patients showed significant ALFF increase in the left medulla and pons, the bilateral cerebellum posterior lobe and right insula. The regions showing decreased ALFF in migraine patients included the bilateral cerebellum posterior lobe, left cerebellum anterior lobe, bilateral orbital cortex, right middle frontal gyrus, bilateral occipital lobe, right fusiform gyrus, and bilateral postcentral gyrus. The fALFFs in migraine patients were significantly increased in the bilateral insular and left orbital cortex, but were decreased in the left occipital lobe and bilateral cerebellum posterior lobe. These ALFF and fALFF alterations in the brain regions of migraineurs are in keeping with the domains associated with pain and cognition. Such brain functional alteration may contribute to further understanding of migraine-related network imbalances demonstrated in previous studies.

Abnormal Intrinsic Brain Activity Patterns in Patients with Subcortical Ischemic Vascular Dementia

ObjectivesTo investigate the amplitude of low-frequency fluctuations (ALFF) alteration of whole brain in patients with subcortical ischemic vascular dementia (SIVD).Materials and MethodsThirty patients with SIVD and 35 control subjects were included in this study. All of them underwent structural MRI and rs-fMRI scan. The structural data were processed using the voxel-based morphometry 8 toolbox (VBM8). The rs-fMRI data were processed using Statistical Parametric Mapping (SPM8) and Data Processing Assistant for Resting-State fMRI (DPARSF) software. Within-group analysis was performed with a one-sample Student's t-test to identify brain regions with ALFF value larger than the mean. Intergroup analysis was performed with a two-sample Student's t-test to identify ALFF differences of whole brain between SIVD and control subjects. Partial correlations between ALFF values and Montreal Cognitive Assessment (MoCA) and Mini-Mental State Examination (MMSE) scores were analyzed in the SIVD group across the parameters of age, gender, years of education, and GM volume.ResultsWithin-group analysis showed that the bilateral anterior cingulate cortex (ACC), posterior cingulate cortex, medial prefrontal cortex (MPFC), inferior parietal lobe (IPL), occipital lobe, and adjacent precuneus had significantly higher standardized ALFF values than the global mean ALFF value in both groups. Compared to the controls, patients with SIVD presented lower ALFF values in the bilateral precuneus and higher ALFF values in the bilateral ACC, left insula and hippocampus. Including GM volume as an extra covariate, the ALFF inter-group difference exhibited highly similar spatial patterns to those without GM volume correcting. Close negative correlations were found between the ALFF values of left insula and the MoCA and MMSE scores of SIVD patients.ConclusionSIVD is associated with a unique spontaneous aberrant activity of rs-fMRI signals, and measurement of ALFF in the precuneus, ACC, insula, and hippocampus may aid in the detection of SIVD.

DPARSF: a MATLAB toolbox for “pipeline” data analysis of resting-state fMRI

Resting-state functional magnetic resonance imaging (fMRI) has attracted more and more attention because of its effectiveness, simplicity and non-invasiveness in exploration of the intrinsic functional architecture of the human brain. However, user-friendly toolbox for “pipeline” data analysis of resting-state fMRI is still lacking. Based on some functions in Statistical Parametric Mapping (SPM) and Resting-State fMRI Data Analysis Toolkit (REST), we have developed a MATLAB toolbox called Data Processing Assistant for Resting-State fMRI (DPARSF) for “pipeline” data analysis of resting-state fMRI. After the user arranges the Digital Imaging and Communications in Medicine (DICOM) files and click a few buttons to set parameters, DPARSF will then give all the preprocessed (slice timing, realign, normalize, smooth) data and results for functional connectivity, regional homogeneity, amplitude of low-frequency fluctuation (ALFF), and fractional ALFF. DPARSF can also create a report for excluding subjects with excessive head motion and generate a set of pictures for easily checking the effect of normalization. In addition, users can also use DPARSF to extract time courses from regions of interest.