Introduction: Graph theoretical analysis of functional Magnetic Resonance Imaging (fMRI) data has provided new measures of mapping human brain in vivo. Of all methods to measure the functional connectivity between regions, Linear Correlation (LC) calculation of activity time series of the brain regions as a linear measure is considered the most ubiquitous one. The strength of the dependence obligatory for graph construction and analysis is consistently underestimated by LC, because not all the bivariate distributions, but only the marginals are Gaussian. In a number of studies, Mutual Information (MI) has been employed, as a similarity measure between each two time series of the brain regions, a pure nonlinear measure. Owing to the complex fractal organization of the brain indicating self-similarity, more information on the brain can be revealed by fMRI Fractal Dimension (FD) analysis.
Methods: In the present paper, Box-Counting Fractal Dimension (BCFD) is introduced for graph theoretical analysis of fMRI data in 17 methamphetamine drug users and 18 normal controls. Then, BCFD performance was evaluated compared to those of LC and MI methods. Moreover, the global topological graph properties of the brain networks inclusive of global efficiency, clustering coefficient and characteristic path length in addict subjects were investigated too.
Results: Compared to normal subjects by using statistical tests (P<0.05), topological graph properties were postulated to be disrupted significantly during the resting-state fMRI. 
Conclusion: Based on the results, analyzing the graph topological properties (representing the brain networks) based on BCFD is a more reliable method than LC and MI.

Introduction: In recent years, brain functional connectivity studies are extended using the advanced statistical methods. Functional connectivity is identified by synchronous activation in a spatially distinct region of the brain in resting-state functional Magnetic Resonance Imaging (MRI) data. For this purpose there are several methods such as seed-based correlation analysis based on temporal correlation between different Regions of Interests (ROIs) or between brain’s voxels of prior seed.
Methods: In the current study, test-retest Resting State functional MRI (rs-fMRI) data of 21 healthy subjects were analyzed to predict second replication connectivity map using first replication data. A potential estimator is “raw estimator” that uses the first replication data from each subject to predict the second replication connectivity map of the same subject. The second estimator, “mean estimator” uses the average of all sample subjects' connectivity to estimate the correlation map. Shrinkage estimator is made by shrinking raw estimator towards the average connectivity map of all subjects' first replicate. Prediction performance of the second replication correlation map is evaluated by Mean Squared Error (MSE) criteria.
Results: By the employment of seed-based correlation analysis and choosing precentral gyrus as the ROI over 21 subjects in the study, on average MSE for raw, mean and shrinkage estimator were 0.2169, 0.1118, and 0.1103, respectively. Also, percent reduction of MSE for shrinkage and mean estimator in comparison with raw estimator is 49.14 and 48.45, respectively.
Conclusion: Shrinkage approach has the positive effect on the prediction of functional connectivity. When data has a large between session variability, prediction of connectivity map can be improved by shrinking towards population mean. 

Introduction: Tinnitus is a common disorder with a considerable amount of distress that affects the patient`s daily life. No objective tools were approved for measuring tinnitus distress. It can be estimated only by subjective scales and questionnaires, albeit, the Electroencephalography (EEG) studies have reported some alterations regarding tinnitus distress network. This study aimed to investigate the correlation between Tinnitus Handicap Inventory (THI) and the recorded EEG data. 
Methods: A total of 33 chronic tinnitus cases (9 females) with the mean age of 42.67 years were recruited. Their THI scores were collected, and a 3-minute EEG recorded with eye closed at resting-state. The correlation analysis was performed on THI scores and the current density in the selected Region of Interests (ROIs) concerning the distress network for the eight frequency bands. The patients grouped depending on the THI cutoff point of 56 into low and high THI groups, and then the groups were compared for source analysis and functional connectivity between ROIs using standardized low-resolution brain electromagnetic tomography.
Results: A significant positive correlation was seen between THI scores and the electrical activity in the Anterior Cingulate Cortex (ACC), the prefrontal cortex, and the parahippocampus for an alpha band (P<0.05) and in the ACC for beta (P<0.01). Source analysis showed significant differences with increased activity in the high THI group for alpha, beta and gamma bands. Functional connectivity was also elevated in the high THI group between the ROIs in alpha and beta bands.
Conclusion: THI can be a useful tool for measuring tinnitus distress, and it has a high correlation with EEG data.

Introduction: Gait impairment is one of the consequences of cerebral palsy (CP) as a permanent neurological disorder. The therapy-induced neuroplasticity should be accompanied by functional improvement to have a persistent treatment effect. In this regard, we aimed to determine the correlation between brain functional activity changes and walking capacity improvement following treatments in children with hemiplegic CP (HCP).
Methods: Twenty-one spastic HCP children (7-12 years old) were randomly divided into 3 groups. Occupational therapy (OT) was performed for the first group. The second group received repetitive transcranial magnetic stimulation (rTMS) treatment, and the third group underwent anti-gravity treadmill (AlterG system) training. AlterG training and OT were provided for 45 minutes, and rTMS was applied for 20 minutes per session, 3 times per week for 8 weeks. Brain functional activity while executing passive tasks involving knee flexion/extension and ankle plantarflexion/dorsiflexion over the range of motion was quantified using functional magnetic resonance imaging (fMRI). Walking capacity was indexed by clinical measures. Clinical and fMRI evaluations were performed pre- and post-training.
Results: Our results indicate that intensive OT, rTMS, and AlterG training enhance brain functional activity and walking capacity in pediatrics with CP. Also, our results reveal a robust correlation between the corpus callosum (CC) functional activity changes and walking capacity improvement.
Conclusion: Regardless of the type of treatment, the improvement in gait function in children with CP may reflect an increase in brain functional activity in callosal neurons, which may reveal an increase in interhemispheric coupling.