fMRI paradigm designing and post-processing tools

A Joint Analysis of Multi-Paradigm fMRI Data With Its Application to Cognitive Study

With the development of neuroimaging techniques, a growing amount of multi-modal brain imaging data are collected, facilitating comprehensive study of the brain. In this paper, we jointly analyzed functional magnetic resonance imaging (fMRI) collected under different paradigms in order to understand cognitive behaviors of an individual. To this end, we proposed a novel multi-view learning algorithm called structure-enforced collaborative regression (SCoRe) to extract co-expressed discriminative brain regions under the guidance of anatomical structure of the brain. An advantage of SCoRe over its predecessor collaborative regression (CoRe) lies in its incorporation of group structures in the brain imaging data, which makes the model biologically more meaningful. Results from real data analysis has confirmed that by incorporating prior knowledge of brain structure, SCoRe can deliver better prediction performance and is less sensitive to hyper-parameters than CoRe. After validation with simulation experiments, we applied SCoRe to fMRI data collected from the Philadelphia Neurodevelopmental Cohort and adopted the scores from the wide range achievement test (WRAT) to evaluate an individual's cognitive skills. We located 14 relevant brain regions that can efficiently predict WRAT scores and these brain regions were further confirmed by other independent studies.

Prefiltering based on experimental paradigm for analysis of fMRI complex brain networks

Brain networks offers a new insight about connections between function and anatomical regions of human brain. We present results from brain networks built from functional magnetic resonance images during finger tapping paradigm. Pearson voxel-voxel correlation in time and frequency domains were performed for all subjects. Besides this standard framework we have implemented a new approach consisting in filtering the data with respect to the fMRI paradigm (finger tapping) in order to obtain a better understanding of the network involved in the execution of the task. The main topological graph measures have been compared in both cases: voxel-voxel correlation and voxel-paradigm filtering plus voxel-voxel correlation. With the standard voxel-voxel correlation a clearly free-scale network was obtained. On the other hand, when we prefiltered the paradigm we obtained two different kind of networks: 1) free-scale; 2) random-like. To our best knowledge, this behaviour is reported here for first time for brain networks. We suggest that paradigm signal prefiltering can provide more infomation about the brain networks.

Pediatric Functional Neuroimaging: Practical Tips and Pearls

OBJECTIVE. Functional MRI (fMRI) is clinically used for localization of eloquent cortex before surgical intervention, most commonly motor and language function in patients with tumors or epilepsy. In the pediatric population, special considerations for fMRI relate to limited examination tolerance, small head size, developing anatomy and physiology, and diverse potential abnormalities. In this article, we will highlight pearls and pitfalls of clinical pediatric fMRI including blood oxygenation level-dependent imaging principles, patient preparation, study acquisition, data postprocessing, and examination interpretation. CONCLUSION. Clinical fMRI is indicated for presurgical localization of eloquent cortex in patients with tumors, epilepsy, or other neurologic conditions and requires a solid understanding of technical considerations and data processing. In children, special approaches are needed for patient preparation as well as study design, acquisition, and interpretation. Radiologists should be cognizant of developmental neuroanatomy, causes of neuropathology, and capacity for neuroplasticity in the pediatric population.

Radiomic Texture Analysis Mapping Predicts Areas of True Functional MRI Activity

Individual analysis of functional Magnetic Resonance Imaging (fMRI) scans requires user-adjustment of the statistical threshold in order to maximize true functional activity and eliminate false positives. In this study, we propose a novel technique that uses radiomic texture analysis (TA) features associated with heterogeneity to predict areas of true functional activity. Scans of 15 right-handed healthy volunteers were analyzed using SPM8. The resulting functional maps were thresholded to optimize visualization of language areas, resulting in 116 regions of interests (ROIs). A board-certified neuroradiologist classified different ROIs into Expected (E) and Non-Expected (NE) based on their anatomical locations. TA was performed using the mean Echo-Planner Imaging (EPI) volume, and 20 rotation-invariant texture features were obtained for each ROI. Using forward stepwise logistic regression, we built a predictive model that discriminated between E and NE areas of functional activity, with a cross-validation AUC and success rate of 79.84% and 80.19% respectively (specificity/sensitivity of 78.34%/82.61%). This study found that radiomic TA of fMRI scans may allow for determination of areas of true functional activity, and thus eliminate clinician bias.

The power of using functional fMRI on small rodents to study brain pharmacology and disease

Functional magnetic resonance imaging (fMRI) is an excellent tool to study the effect of pharmacological modulations on brain function in a non-invasive and longitudinal manner. We introduce several blood oxygenation level dependent (BOLD) fMRI techniques, including resting state (rsfMRI), stimulus-evoked (st-fMRI), and pharmacological MRI (phMRI). Respectively, these techniques permit the assessment of functional connectivity during rest as well as brain activation triggered by sensory stimulation and/or a pharmacological challenge. The first part of this review describes the physiological basis of BOLD fMRI and the hemodynamic response on which the MRI contrast is based. Specific emphasis goes to possible effects of anesthesia and the animal’s physiological conditions on neural activity and the hemodynamic response. The second part of this review describes applications of the aforementioned techniques in pharmacologically induced, as well as in traumatic and transgenic disease models and illustrates how multiple fMRI methods can be applied successfully to evaluate different aspects of a specific disorder. For example, fMRI techniques can be used to pinpoint the neural substrate of a disease beyond previously defined hypothesis-driven regions-of-interest. In addition, fMRI techniques allow one to dissect how specific modifications (e.g., treatment, lesion etc.) modulate the functioning of specific brain areas (st-fMRI, phMRI) and how functional connectivity (rsfMRI) between several brain regions is affected, both in acute and extended time frames. Furthermore, fMRI techniques can be used to assess/explore the efficacy of novel treatments in depth, both in fundamental research as well as in preclinical settings. In conclusion, by describing several exemplary studies, we aim to highlight the advantages of functional MRI in exploring the acute and long-term effects of pharmacological substances and/or pathology on brain functioning along with several methodological considerations.

Topographic organization of motor fibre tracts in the human brain: findings in multiple locations using magnetic resonance diffusion tensor tractography

OBJECTIVES

To identify the hand and foot fibre tracts of the corticospinal tract (CST), and to evaluate the relative locations, angles, and distances of two fibre tracts using diffusion tensor tractography (DTT).

METHODS

Twelve healthy subjects were enrolled. The regions of interests (ROIs) were drawn in the functional magnetic resonance imaging (fMRI) activation areas and pons in each subject for fibre tracking. We evaluated fibre tract distributions using distances and angles between two fibre tracts starting from the location of a hand fibre tract in multiple brain regions.

RESULTS

The measured angles and distances were 96.43-150°/2.69-9.93 mm (upper CR), 91.86-180°/1.63-7.42 mm (lower CR), 54.47-75°/0.75-4.45 mm (PLIC), and 3.65-90°/0.11-2.36 mm (pons), respectively. The distributions between CR and other sections, such as PLIC and pons, were statistically significant (p < 0.05). There were no significant differences between the upper and lower CR\ or between the PLIC and pons.

CONCLUSIONS

This study showed that the somatotopic arrangement of the hand fibre tract was located at the anterolateral portion in CR and at the anteromedial portion in PLIC and pons, based on the foot fibre. Our methods and results seem to be helpful in motor control neurological research.

KEY POINTS

• We evaluated somatotopic arrangement of CST at multiple anatomical locations. • Somatotopic arrangements and fibre tract distributions were evaluated based on hand fibre location. • Relative angles, locations, and distances between two fibres vary according to their anatomical locations.