Multiresolution data acquisition and detection in functional MRI

Functional Magnetic Resonance Imaging of the Amygdala and Subregions at 3 Tesla: A Scoping Review

The amygdalae are a pair of small brain structures, each of which is composed of three main subregions and whose function is implicated in neuropsychiatric conditions. Functional Magnetic Resonance Imaging (fMRI) has been utilized extensively in investigation of amygdala activation and functional connectivity (FC) with most clinical research sites now utilizing 3 Tesla (3T) MR systems. However, accurate imaging and analysis remains challenging not just due to the small size of the amygdala, but also its location deep in the temporal lobe. Selection of imaging parameters can significantly impact data quality with implications for the accuracy of study results and validity of conclusions. Wide variation exists in acquisition protocols with spatial resolution of some protocols suboptimal for accurate assessment of the amygdala as a whole, and for measuring activation and FC of the three main subregions, each of which contains multiple nuclei with specialized roles. The primary objective of this scoping review is to provide a broad overview of 3T fMRI protocols in use to image the activation and FC of the amygdala with particular reference to spatial resolution. The secondary objective is to provide context for a discussion culminating in recommendations for a standardized protocol for imaging activation of the amygdala and its subregions. As the advantages of big data and protocol harmonization in imaging become more apparent so, too, do the disadvantages of data heterogeneity. EVIDENCE LEVEL: 3 TECHNICAL EFFICACY: Stage 2.

A mixed-effects, spatially varying coefficients model with application to multi-resolution functional magnetic resonance imaging data

Spatial resolution plays an important role in functional magnetic resonance imaging studies as the signal-to-noise ratio increases linearly with voxel volume. In scientific studies, where functional magnetic resonance imaging is widely used, the standard spatial resolution typically used is relatively low which ensures a relatively high signal-to-noise ratio. However, for pre-surgical functional magnetic resonance imaging analysis, where spatial accuracy is paramount, high-resolution functional magnetic resonance imaging may play an important role with its greater spatial resolution. High spatial resolution comes at the cost of a smaller signal-to-noise ratio. This begs the question as to whether we can leverage the higher signal-to-noise ratio of a standard functional magnetic resonance imaging study with the greater spatial accuracy of a high-resolution functional magnetic resonance imaging study in a pre-operative patient. To answer this question, we propose to regress the statistic image from a high resolution scan onto the statistic image obtained from a standard resolution scan using a mixed-effects model with spatially varying coefficients. We evaluate our model via simulation studies and we compare its performance with a recently proposed model that operates at a single spatial resolution. We apply and compare the two models on data from a patient awaiting tumor resection. Both simulation study results and the real data analysis demonstrate that our newly proposed model indeed leverages the larger signal-to-noise ratio of the standard spatial resolution scan while maintaining the advantages of the high spatial resolution scan.

Multi-resolution simulation of focused ultrasound propagation through ovine skull from a single-element transducer

Transcranial focused ultrasound (tFUS) is emerging as a non-invasive brain stimulation modality. Complicated interactions between acoustic pressure waves and osseous tissue introduce many challenges in the accurate targeting of an acoustic focus through the cranium. Image-guidance accompanied by a numerical simulation is desired to predict the intracranial acoustic propagation through the skull; however, such simulations typically demand heavy computation, which warrants an expedited processing method to provide on-site feedback for the user in guiding the acoustic focus to a particular brain region. In this paper, we present a multi-resolution simulation method based on the finite-difference time-domain formulation to model the transcranial propagation of acoustic waves from a single-element transducer (250 kHz). The multi-resolution approach improved computational efficiency by providing the flexibility in adjusting the spatial resolution. The simulation was also accelerated by utilizing parallelized computation through the graphic processing unit. To evaluate the accuracy of the method, we measured the actual acoustic fields through ex vivo sheep skulls with different sonication incident angles. The measured acoustic fields were compared to the simulation results in terms of focal location, dimensions, and pressure levels. The computational efficiency of the presented method was also assessed by comparing simulation speeds at various combinations of resolution grid settings. The multi-resolution grids consisting of 0.5 and 1.0 mm resolutions gave acceptable accuracy (under 3 mm in terms of focal position and dimension, less than 5% difference in peak pressure ratio) with a speed compatible with semi real-time user feedback (within 30 s). The proposed multi-resolution approach may serve as a novel tool for simulation-based guidance for tFUS applications.

Constrained source space imaging: application to fast, region-based functional MRI

A new technique called constrained source space imaging is introduced that holds promise for ultrafast acquisition of functional magnetic resonance imaging data. A sparse set of arbitrarily positioned, coarse voxels is first localized using radiofrequency selective excitation, from which magnetization signals are separated using only the spatial sensitivities of multichannel receiver coils, without the need for k-space encoding using imaging gradients. This method permits very fast acquisitions of targeted magnetization without complex or time-consuming image reconstruction techniques. Furthermore, because the data acquisition is performed without imaging gradients, T2* decays can be densely sampled and processed for contrast enhancement to improve functional magnetic resonance imaging data quality. Here, the constrained source space imaging technique is validated in proof-of-concept form, for a simple functional magnetic resonance imaging motor task using a prototype dual-band stimulated echo acquisition mode excitation to image four voxels at TR = 250 ms. Results demonstrate good voxel signal separation and good characterization of hemodynamic responses in primary motor cortices (M1) and supplementary motor areas through T2* fitting of the measured signals. With further refinement, the constrained source space imaging method has potential utility in a priori ROI-based functional magnetic resonance imaging experiments with TR values under 100 ms. Rapid, multivoxel measurements of other sources of MR signal contrast are also possible.

Magnitude and phase behavior of multiresolution BOLD signal

High spatial resolution fMRI provides a more precise estimate of brain activity than low resolution fMRI. The magnitude and phase parts of the BOLD signals are impacted differently by changes in the scan resolution. In this paper, we report on a numerical simulation to show the impact of spatial resolution upon the complex-valued BOLD signal in terms of magnitude and phase variation. We generate realistic capillary networks in cortex voxels, calculate the BOLD-induced magnetic field disturbance and the complex BOLD signals for the voxel and its subvoxels, and thereby characterize the magnitude and phase behaviors across multiple grid resolutions. Our results show that: 1) at higher spatial resolution there is greater spatial variation in the phase of the BOLD signal as compared to its magnitude; 2) the spatial variation of the phase signal monotonically increases with respect to spatial resolution while for the magnitude the spatial variation may reach a maximum at some resolution level; 3) voxels containing large capillaries have higher phase spatial variation than those with smaller capillaries; 4) the amplitude spatial variation at a resolution level increases with respect to relaxation time whereas the phase variation is generally unaffected.

Spectral-spatial pulse design for through-plane phase precompensatory slice selection in T2*-weighted functional MRI

T(2)*-weighted functional MR images suffer from signal loss artifacts caused by the magnetic susceptibility differences between air cavities and brain tissues. We propose a novel spectral-spatial pulse design that is slice-selective and capable of mitigating the signal loss. The two-dimensional spectral-spatial pulses create precompensatory phase variations that counteract through-plane dephasing, relying on the assumption that resonance frequency offset and through-plane field gradient are spatially correlated. The pulses can be precomputed before functional MRI experiments and used repeatedly for different slices in different subjects. Experiments with human subjects showed that the pulses were effective in slice selection and loss mitigation at different brain regions.

High spatial resolution increases the specificity of block-design BOLD fMRI studies of overt vowel production

Functional MRI (fMRI) studies of tasks involving orofacial motion, such as speech, are prone to problems related to motion-induced magnetic field variations. Orofacial motion perturbs the static magnetic field, leading to signal changes that correlate with the task and corrupt activation maps with false positives or signal loss. These motion-induced signal changes represent a contraindication for the implementation of fMRI to study the neurophysiology of orofacial motion. An fMRI experiment of a structured, non-semantic vowel production task was performed using four different voxel volumes and three different slice orientations in an attempt to find a set of acquisition parameters leading to activation maps with maximum specificity. Results indicate that the use of small voxel volumes (2 x 2 x 3 mm(3)) yielded a significantly higher percentage of true positive activation compared to the use of larger voxel volumes. Slice orientation did not have as great an impact as spatial resolution, although coronal slices appeared superior at high spatial resolutions. Furthermore, it was found that combining the strategy of high spatial resolution with an optimum task duration and post-processing methods for separating true and false positives greatly improved the specificity of single-subject, block-design fMRI studies of structured, overt vowel production.

Three-dimensional spiral technique for high-resolution functional MRI

For high-resolution functional MRI (fMRI) studies, signal-to-noise ratio (SNR) plays an important role. Any method that results in an improvement in SNR will be able to improve the quality of activation maps. Three-dimensional (3D) acquisition methods in general can provide higher SNR than that of 2D methods due to volume excitation. To demonstrate the superiority of 3D methods for high-resolution fMRI scans, a comparison study between 3D and 2D spiral methods was performed using a contrast-reversing checkerboard visual stimulus. A 3-inch surface coil was used to limit the in-plane FOV to 14 cm x 14 cm so that 32 1-mm slices with an in-plane voxel size of 1.1 mm x 1.1 mm could be acquired within 5.76 seconds. Results showed that average numbers of activated voxels were 407 and 841 for 2D and 3D methods, respectively (P < 0.01). Therefore, the 3D technique may be a useful alternative to the conventional 2D method for high resolution fMRI studies.

Restricted field of view magnetic resonance imaging of a dynamic time series

A restricted field of view (rFOV) approach for imaging a dynamic time series of volumes of limited spatial extent within a larger subject is described. The shorter readout with rFOV-MRI can be exploited to either limit image artifacts or increase spatial resolution. To accomplish rFOV imaging of a multislice volume for a dynamic series, an outer volume suppression (OVS) preparation that saturates signal external to a cylinder through the subject is followed by slice-selective excitation and a spiral readout. The pass- and stopband efficiencies of the OVS in an agar gel phantom were 97% (+/-1.5%) and 3% (+/-1%), respectively. Profiles of the temporal signal-to-noise ratio (SNR) were measured in a phantom and an adult brain. The rFOV sequence reduced distortions from off-resonance signal and T2*-induced blurring compared to a conventional sequence. Sequence utility is demonstrated for high-resolution rFOV functional MRI (fMRI) in the visual cortex. The rFOV sequence may prove to be useful for other multislice dynamic and high-resolution imaging applications.

Rater-dependent accuracy in predicting the spatial location of functional centers on anatomical MR images

OBJECTIVES

The determination of eloquent cortex is essential when planning neurosurgical approaches to brain lesions. This study examined the abilities of medical personnel of various backgrounds to predict the location of functional cortex using anatomical information provided by MR imaging.

PATIENTS AND METHODS

Neurosurgeons, neuroscientists, neuroradiologists, medical students and MR technologists viewed anatomical MR images acquired from patients with brain tumors and healthy controls. These five groups of raters were then asked to locate the primary motor hand, supplementary motor and primary auditory areas and their predictions were compared to fMRI data acquired from the same subjects.

RESULTS

The overall mean distance from the center of the fMRI activation was 2.38 cm. The neuroscientists performed the best and MR technologists performed the worst (mean distance from center of 1.83 and 3.04 cm, respectively, p<0.05). The difference between patients and controls was not significant. The mean distance by ROI was primary motor hand 2.03 cm, auditory area 2.06 cm and supplementary motor area 3.18 cm (p<0.05). Raters also performed best in the medial-lateral direction, compared to superior-inferior and anterior-posterior directions (mean distances from center 0.42, 1.04 and 1.81 cm, respectively). Finally, the approximate minimum fields of view necessary to capture the entire fMRI activations using the raters' predictions ranged from 5 to 15 cm, or 3 to 12 cm larger than the fMRI activations.

CONCLUSION

Medical personnel of various training perform poorly when using only anatomical information to predict the location of functional areas of cortex.

Advanced three-dimensional tailored RF pulse for signal recovery in T2*-weighted functional magnetic resonance imaging

T(2) (*)-weighted functional MR images are plagued by signal loss artifacts caused by susceptibility-induced through-plane dephasing. We present major advances to the original three-dimensional tailored RF (3DTRF) pulse method that pre-compensates the dephasing using three-dimensional selective excitation. The proposed 3DTRF pulses are designed iteratively with off-resonance incorporation and with a novel echo-volumar trajectory that frequency-encodes in z and phase-encodes in x,y. We also propose a computational scheme to accelerate the pulse design process. We demonstrate effective signal recovery in a 5-mm slice in both phantom and inferior brain, using 3DTRF pulses that are only 15.4 ms long. Compared to the original method, the new approach leads to significantly reduced pulse length and enhancement in slice selectivity. 3D images of the slice volume confirm fidelity of the excited phase pattern and slice profile.

Mapping the MRI voxel volume in which thermal noise matches physiological noise--implications for fMRI

This work addresses the choice of the imaging voxel volume in blood oxygen level dependent (BOLD) functional magnetic resonance imaging (fMRI). Noise of physiological origin that is present in the voxel time course is a prohibitive factor in the detection of small activation-induced BOLD signal changes. If the physiological noise contribution dominates over the temporal fluctuation contribution in the imaging voxel, further increases in the voxel signal-to-noise ratio (SNR) will have diminished corresponding increases in temporal signal-to-noise (TSNR), resulting in reduced corresponding increases in the ability to detect activation induced signal changes. On the other hand, if the thermal and system noise dominate (suggesting a relatively low SNR) further decreases in SNR can prohibit detection of activation-induced signal changes. Here we have proposed and called the "suggested" voxel volume for fMRI the volume where thermal plus system-related and physiological noise variances are equal. Based on this condition we have created maps of fMRI suggested voxel volume from our experimental data at 3T, since this value will spatially vary depending on the contribution of physiologic noise in each voxel. Based on our fast EPI segmentation technique we have found that for gray matter (GM), white matter (WM), and cerebral spinal fluid (CSF) brain compartments the mean suggested cubical voxel volume is: (1.8 mm)3, (2.1 mm)3 and (1.4 mm)3, respectively. Serendipitously, (1.8 mm)3 cubical voxel volume for GM approximately matches the cortical thickness, thus optimizing BOLD contrast by minimizing partial volume averaging. The introduced suggested fMRI voxel volume can be a useful parameter for choice of imaging volume for functional studies.

Functional asymmetry in human primary auditory cortex: Identified from longitudinal fMRI study

The leftward hemispheric dominance in language processing may be associated with fundamental functional asymmetry in the primary auditory cortex (PAC). Based on repeated functional MRI (fMRI) measurements, we investigated the presence of functional asymmetry in the human PAC using binaural presentation of linguistic sounds (two-syllable nouns) and simple tonal stimulation. Eight right-handed volunteers underwent nine fMRI sessions, approximately eight weeks apart, spanning the duration of more than a year. The PAC from each hemisphere was manually segmented and the volume of activation, detected within the segmented region-of-interest, was measured across the subjects and sessions to generate functional laterality indices. Although variations existed in activation volume between sessions and subjects, we found predominant and consistent leftward functional asymmetry in PAC during both linguistic and non-linguistic sound stimulations.

Spatiotemporal wavelet analysis for functional MRI

Characterizing the spatiotemporal behavior of the BOLD signal in functional Magnetic Resonance Imaging (fMRI) is a central issue in understanding brain function. While the nature of functional activation clusters is fundamentally heterogeneous, many current analysis approaches use spatially invariant models that can degrade anatomic boundaries and distort the underlying spatiotemporal signal. Furthermore, few analysis approaches use true spatiotemporal continuity in their statistical formulations. To address these issues, we present a novel spatiotemporal wavelet procedure that uses a stimulus-convolved hemodynamic signal plus correlated noise model. The wavelet fits, computed by spatially constrained maximum-likelihood estimation, provide efficient multiscale representations of heterogeneous brain structures and give well-identified, parsimonious spatial activation estimates that are modulated by the temporal fMRI dynamics. In a study of both simulated data and actual fMRI memory task experiments, our new method gave lower mean-squared error and seemed to result in more localized fMRI activation maps compared to models using standard wavelet or smoothing techniques. Our spatiotemporal wavelet framework suggests a useful tool for the analysis of fMRI studies.

Evaluating requirements for spatial resolution of fMRI for neurosurgical planning

The unambiguous localization of eloquent functional areas is necessary to decrease the neurological morbidity of neurosurgical procedures. We explored the minimum spatial resolution requirements for functional magnetic resonance imaging (fMRI) data acquisition when brain mapping is used in neurosurgical planning and navigation. Using a 1.5 Tesla clinical MRI scanner, eight patients with brain tumors underwent fMRI scans using spatial resolution of approximately 4 x 4 x 4 mm(3) to map the eloquent motor and language areas during the performance of cognitive/sensorimotor tasks. The fMRI results were then used intra-operatively in an open MRI system to delineate eloquent areas. Retrospectively, activation patterns were visually inspected by a neurosurgeon to determine qualitatively whether ambiguity with respect to the activation boundaries, due to low spatial resolution, could be of potential significance for surgical guidance. A significant degree of ambiguity in both the extent and shape of activation was judged to be present in data from six of the eight patients. Analysis of fMRI data at multiple resolutions from a normal volunteer showed that at 3 mm isotropic resolution, eloquent areas were better localized within the gray matter although there was still some potential for ambiguity caused by activations appearing to cross a sulcus. The data acquired with 2-mm isotropic voxels significantly enhanced the spatial localization of activation to within the gray matter. Thus, isotropic spatial resolution on the order of 2 x 2 x 2 mm(3), which is much higher than the resolutions used in typical fMRI examinations, may be needed for the unambiguous identification of cortical activation with respect to tumors and important anatomical landmarks.

Selection of voxel size and slice orientation for fMRI in the presence of susceptibility field gradients: application to imaging of the amygdala

The impact of voxel geometry on the blood oxygenation level-dependent (BOLD) signal detectability in the presence of field inhomogeneity is assessed and a quantitative approach to selecting appropriate voxel geometry is developed in this report. Application of the developed technique to BOLD sensitivity improvement of the human amygdala is presented. Field inhomogeneity was measured experimentally at 1.5 T and 3 T and the dominant susceptibility field gradient in the human amygdala was observed approximately along the superior-inferior direction. Based on the field mapping studies, an optimal selection for the slice orientation would be an oblique pseudo-coronal plane with its frequency-encoding direction parallel to the field gradient measured from each subject. Experimentally this was confirmed by comparing the normalized standard deviation of time-series echo-planar imaging signals acquired with different slice orientations, in the absence of a functional stimulus. A further confirmation with a carefully designed functional magnetic resonance imaging study is needed. Although the BOLD sensitivity may generally be improved by a voxel size commensurable with the activation volume, our quantitative analysis shows that the optimal voxel size also depends on the susceptibility field gradient and is usually smaller than the activation volume. The predicted phenomenon is confirmed with a hybrid simulation, in which the functional activation was mathematically added to the experimentally acquired rest-period echo-planar imaging data.

Real-time fMRI of temporolimbic regions detects amygdala activation during single-trial self-induced sadness

Temporolimbic circuits play a crucial role in the regulation of human emotion. A highly sensitive single-shot multiecho functional magnetic resonance imaging (fMRI) technique with gradient compensation of local magnetic field inhomogeneities and real-time data analysis were used to measure increases in amygdala activation during single 60-s trials of self-induced sadness. Six healthy male and female subjects performed a validated mood induction paradigm with randomized presentation of sad or neutral faces in 10 trials per scan. Subjects reported the intensity of experienced sadness after each trial. Immediate feedback of amygdala activation was given to the subjects during the ongoing scan to reinforce mood induction. Correspondence between increased intensity of predominantly left sided amygdala activation and self-rating of sadness was found in 78% of 120 sad trials, in contrast to only 14% of neutral trials. Amygdala activation was reproducible during repeated scanning sessions and displayed the strongest correlation with self-rating among all regions. These results suggest that amygdala activation may be closely associated with self-induced sadness. This novel real-time fMRI technology is applicable to a wide range of neuroscience studies, particularly those of the limbic system, and to neuropsychiatric conditions, such as depression, in which pathology of the amygdala has been implicated.

Single-shot T(2)* mapping with 3D compensation of local susceptibility gradients in multiple regions

Macroscopic magnetic field inhomogeneities severely limit sensitivity of blood oxygenation level-dependent (BOLD) functional MRI (fMRI) in frontal and central brain regions close to brain stem. A single-shot multiecho echo-planar imaging method (TurboPEPSI) was developed that combines quantitative T(2)* mapping with gradient compensation of local susceptibility inhomogeneities in multiple volumes of interest (VOIs). Gradient compensation was optimized in individual subjects based on magnetic field mapping and applied at selected echo times, interleaved with acquisition of uncompensated echoes. Intrinsic T(2)* values from uncompensated echoes were obtained in real-time simultaneously with effective T(2)* values from gradient compensated echoes. It is demonstrated that up to three VOIs can be compensated in a single excitation, in addition to collecting uncompensated data, using 8-echo acquisition on a clinical 1.5 Tesla scanner. A theory was developed to optimize the sequence of uncompensated and compensated echoes to achieve maximum BOLD sensitivity. Gradient compensation increased effective T(2)* values in left and right amygdala on average by 18.8 +/- 7.5 ms, while maintaining sensitivity in uncompensated brain areas. In orbitofrontal cortex effective T(2)* values increased by 22.2 +/- 5.3 ms. A CO(2) challenge paradigm was used to demonstrate that this gradient compensation method significantly enhances BOLD signal changes in amygdala as compared to conventional echo-planar imaging (EPI) and uncompensated TurboPEPSI.