High spatio-temporal resolution in functional MRI with 3D echo planar imaging using cylindrical excitation and a CAIPIRINHA undersampling pattern

Purpose The combination of 3D echo planar imaging (3D‐EPI) with a 2D‐CAIPIRINHA undersampling scheme provides high flexibility in the optimization for spatial or temporal resolution. This flexibility can be increased further with the addition of a cylindrical excitation pulse, which exclusively excites the brain regions of interest. Here, 3D‐EPI was combined with a 2D radiofrequency pulse to reduce the brain area from which signal is generated, and hence, allowing either reduction of the field of view or reduction of parallel imaging noise amplification. Methods 3D‐EPI with cylindrical excitation and 4 × 3‐fold undersampling in a 2D‐CAIPIRINHA sampling scheme was used to generate functional MRI (fMRI) data with either 2‐mm or 0.9‐mm in‐plane resolution and 1.1‐s temporal resolution over a 5‐cm diameter cylinder placed over both temporal lobes for an auditory fMRI experiment. Results Significant increases in image signal‐to‐noise ratio (SNR) and temporal SNR (tSNR) were found for both 2‐mm isotropic data and the high‐resolution protocol when using the cylindrical excitation pulse. Both protocols yielded highly significant blood oxygenation level–dependent responses for the presentation of natural sounds. Conclusion The higher tSNR of the cylindrical excitation 3D‐EPI data makes this sequence an ideal choice for high spatiotemporal resolution fMRI acquisitions. Magn Reson Med 79:2589–2596, 2018. © 2017 International Society for Magnetic Resonance in Medicine

Altered Resting-State Functional Connectivity of the Frontal-Striatal Reward System in Social Anxiety Disorder

We investigated differences in the intrinsic functional brain organization (functional connectivity) of the human reward system between healthy control participants and patients with social anxiety disorder. Functional connectivity was measured in the resting-state via functional magnetic resonance imaging (fMRI). 53 patients with social anxiety disorder and 33 healthy control participants underwent a 6-minute resting-state fMRI scan. Functional connectivity of the reward system was analyzed by calculating whole-brain temporal correlations with a bilateral nucleus accumbens seed and a ventromedial prefrontal cortex seed. Patients with social anxiety disorder, relative to the control group, had (1) decreased functional connectivity between the nucleus accumbens seed and other regions associated with reward, including ventromedial prefrontal cortex; (2) decreased functional connectivity between the ventromedial prefrontal cortex seed and lateral prefrontal regions, including the anterior and dorsolateral prefrontal cortices; and (3) increased functional connectivity between both the nucleus accumbens seed and the ventromedial prefrontal cortex seed with more posterior brain regions, including anterior cingulate cortex. Social anxiety disorder appears to be associated with widespread differences in the functional connectivity of the reward system, including markedly decreased functional connectivity between reward regions and between reward regions and lateral prefrontal cortices, and markedly increased functional connectivity between reward regions and posterior brain regions.Massachusetts Institute of Technology (Janet and Sheldon Razin Fellowship

Modeling of the hemodynamic responses in block design fMRI studies

The hemodynarnic response function (HRF) describes the local response of brain vasculature to functional activation. Accurate HRF modeling enables the investigation of cerebral blood flow regulation and improves our ability to interpret fMRI results. Block designs have been used extensively as fMRI paradigms because detection power is maximized; however, block designs are not optimal for HRF parameter estimation. Here we assessed the utility of block design fMRI data for HRF modeling. The trueness (relative deviation), precision (relative uncertainty), and identifiability (goodness-of-fit) of different HRF models were examined and test-retest reproducibility of HRF parameter estimates was assessed using computer simulations and fMRI data from 82 healthy young adult twins acquired on two occasions 3 to 4 months apart. The effects of systematically varying attributes of the block design paradigm were also examined. In our comparison of five HRF models, the model comprising the sum of two gamma functions with six free parameters had greatest parameter accuracy and identifiability. Hemodynamic response function height and time to peak were highly reproducible between studies and width was moderately reproducible but the reproducibility of onset time was low. This study established the feasibility and test-retest reliability of estimating HRF parameters using data from block design fMRI studies

Altered functional connectivity in lesional peduncular hallucinosis with REM sleep behavior disorder

Brainstem lesions causing peduncular hallucinosis (PH) produce vivid visual hallucinations occasionally accompanied by sleep disorders. Overlapping brainstem regions modulate visual pathways and REM sleep functions via gating of thalamocortical networks. A 66-year-old man with paroxysmal atrial fibrillation developed abrupt–onset complex visual hallucinations with preserved insight and violent dream enactment behavior. Brain MRI showed restricted diffusion in the left rostrodorsal pons suggestive of an acute ischemic stroke. REM sleep behavior disorder (RBD) was diagnosed on polysomnography. We investigated the integrity of ponto-geniculate-occipital circuits with seed-based resting-state functional connectivity MRI (rs-fcMRI) in this patient compared to 46 controls. Rs-fcMRI revealed significantly reduced functional connectivity between the lesion and lateral geniculate nuclei (LGN), and between LGN and visual association cortex compared to controls. Conversely, functional connectivity between brainstem and visual association cortex, and between visual association cortex and prefrontal cortex (PFC) was significantly increased in the patient. Focal damage to the rostrodorsal pons is sufficient to cause RBD and PH in humans, suggesting an overlapping mechanism in both syndromes. This lesion produced a pattern of altered functional connectivity consistent with disrupted visual cortex connectivity via de-afferentation of thalamocortical pathways

Differential Effect of Contrast Polarity Reversals in Closed Squares and Open L-Junctions

Scene segmentation depends on interaction between geometrical and photometric factors. It has been shown that reversals in contrast polarity at points of highest orientation discontinuity along closed contours significantly impair shape discrimination performance, while changes in contrast polarity at straight(er) contour segments do not have such deleterious effects (Spehar, 2002). Here we employ (semi) high resolution fMRI (1.5 mm × 1.5 mm × 1.5 mm) to investigate the neuronal substrate underlying these perception effects. Stimuli consisted of simple elements (a) squares with contrast reversals along straight segments; (b) squares with contrast reversals in the corner (highest orientation discontinuity); (c) L-Junctions with contrast reversals along the straight ends; (d) L-Junctions with contrast reversals in the corner. Element with contrast polarity reversals are easy to distinguish though appear geometrically equivalent. For squares with contrast polarity reversals only along straight lines we find significantly lower BOLD modulation compared to any of the control conditions, which show similar responses to each other. In the light of previous psychophysical work (Elder and Zucker, 1993; Spehar, 2002) we speculate that this effect is due to closure perception. We observe this across a wide range of areas on occipital cortex

Differential Effect of Contrast Polarity Reversals in Closed Squares and Open L-Junctions

Scene segmentation depends on interaction between geometrical and photometric factors. It has been shown that reversals in contrast polarity at points of highest orientation discontinuity along closed contours significantly impair shape discrimination performance, while changes in contrast polarity at straight(er) contour segments do not have such deleterious effects (Spehar, 2002). Here we employ (semi) high resolution fMRI (1.5 mm × 1.5 mm × 1.5 mm) to investigate the neuronal substrate underlying these perception effects. Stimuli consisted of simple elements (a) squares with contrast reversals along straight segments; (b) squares with contrast reversals in the corner (highest orientation discontinuity); (c) L-Junctions with contrast reversals along the straight ends; (d) L-Junctions with contrast reversals in the corner. Element with contrast polarity reversals are easy to distinguish though appear geometrically equivalent. For squares with contrast polarity reversals only along straight lines we find significantly lower BOLD modulation compared to any of the control conditions, which show similar responses to each other. In the light of previous psychophysical work (Elder and Zucker, 1993; Spehar, 2002) we speculate that this effect is due to closure perception. We observe this across a wide range of areas on occipital cortex

Bayesian Dynamic DAG Learning: Application in Discovering Dynamic Effective Connectome of Brain

Understanding the complex mechanisms of the brain can be unraveled by extracting the Dynamic Effective Connectome (DEC). Recently, score-based Directed Acyclic Graph (DAG) discovery methods have shown significant improvements in extracting the causal structure and inferring effective connectivity. However, learning DEC through these methods still faces two main challenges: one with the fundamental impotence of high-dimensional dynamic DAG discovery methods and the other with the low quality of fMRI data. In this paper, we introduce Bayesian Dynamic DAG learning with M-matrices Acyclicity characterization \textbf{(BDyMA)} method to address the challenges in discovering DEC. The presented dynamic causal model enables us to discover bidirected edges as well. Leveraging an unconstrained framework in the BDyMA method leads to more accurate results in detecting high-dimensional networks, achieving sparser outcomes, making it particularly suitable for extracting DEC. Additionally, the score function of the BDyMA method allows the incorporation of prior knowledge into the process of dynamic causal discovery which further enhances the accuracy of results. Comprehensive simulations on synthetic data and experiments on Human Connectome Project (HCP) data demonstrate that our method can handle both of the two main challenges, yielding more accurate and reliable DEC compared to state-of-the-art and baseline methods. Additionally, we investigate the trustworthiness of DTI data as prior knowledge for DEC discovery and show the improvements in DEC discovery when the DTI data is incorporated into the process

Optimized simultaneous ASL and BOLD functional imaging of the whole brain

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106990/1/jmri24273.pd

Spatial resolution and imaging encoding fMRI settings for optimal cortical and subcortical motor somatotopy in the human brain

There is much controversy about the optimal trade-off between blood-oxygen-level-dependent (BOLD) sensitivity and spatial precision in experiments on brain’s topology properties using functional magnetic resonance imaging (fMRI). The sparse empirical evidence and regional specificity of these interactions pose a practical burden for the choice of imaging protocol parameters. Here, we test in a motor somatotopy experiment the impact of fMRI spatial resolution on differentiation between body part representations in cortex and subcortical structures. Motor somatotopy patterns were obtained in a block-design paradigm and visually cued movements of face, upper and lower limbs at 1.5, 2, and 3 mm spatial resolution. The degree of segregation of the body parts’ spatial representations was estimated using a pattern component model. In cortical areas, we observed the same level of segregation between somatotopy maps across all three resolutions. In subcortical areas the degree of effective similarity between spatial representations was significantly impacted by the image resolution. The 1.5 mm 3D EPI and 3 mm 2D EPI protocols led to higher segregation between motor representations compared to the 2 mm 3D EPI protocol. This finding could not be attributed to differential BOLD sensitivity or delineation of functional areas alone and suggests a crucial role of the image encoding scheme – i.e., 2D vs. 3D EPI. Our study contributes to the field by providing empirical evidence about the impact of acquisition protocols for the delineation of somatotopic areas in cortical and sub-cortical brain regions

The Impact of Echo Time Shifts and Temporal Signal Fluctuations on BOLD Sensitivity in Presurgical Planning at 7 T.

OBJECTIVES: Gradients in the static magnetic field caused by tissues with differing magnetic susceptibilities lead to regional variations in the effective echo time, which modifies both image signal and BOLD sensitivity. Local echo time changes are not considered in the most commonly used metric for BOLD sensitivity, temporal signal-to-noise ratio (tSNR), but may be significant, particularly at ultrahigh field close to air cavities (such as the sinuses and ear canals) and near gross brain pathologies and postoperative sites. MATERIALS AND METHODS: We have studied the effect of local variations in echo time and tSNR on BOLD sensitivity in 3 healthy volunteers and 11 patients with tumors, postoperative cavities, and venous malformations at 7 T. Temporal signal-to-noise ratio was estimated from a 5-minute run of resting state echo planar imaging with a nominal echo time of 22 milliseconds. Maps of local echo time were derived from the phase of a multiecho GE scan. One healthy volunteer performed 10 runs of a breath-hold task. The t-map from this experiment served as a criterion standard BOLD sensitivity measure. Two runs of a less demanding breath-hold paradigm were used for patients. RESULTS: In all subjects, a strong reduction in the echo time (from 22 milliseconds to around 11 milliseconds) was found close to the ear canals and sinuses. These regions were characterized by high tSNR but low t-values in breath-hold t-maps. In some patients, regions of particular interest in presurgical planning were affected by reductions in the echo time to approximately 13-15 milliseconds. These included the primary motor cortex, Broca's area, and auditory cortex. These regions were characterized by high tSNR values (70 and above). Breath-hold results were corrupted by strong motion artifacts in all patients. CONCLUSIONS: Criterion standard BOLD sensitivity estimation using hypercapnic experiments is challenging, especially in patient populations. Taking into consideration the tSNR, commonly used for BOLD sensitivity estimation, but ignoring local reductions in the echo time (eg, from 22 to 11 milliseconds), would erroneously suggest functional sensitivity sufficient to map BOLD signal changes. It is therefore important to consider both local variations in the echo time and temporal variations in signal, using the product metric of these two indices for instance. This should ensure a reliable estimation of BOLD sensitivity and to facilitate the identification of potential false-negative results. This is particularly true at high fields, such as 7 T and in patients with large pathologies and postoperative cavities