Anatomically realistic volume conductor models of the human head are important for accurate forward modeling of the electric field during transcranial brain stimulation (TBS), electro- (EEG) and ...magnetoencephalography (MEG). In particular, the skull compartment exerts a strong influence on the field distribution due to its low conductivity, suggesting the need to represent its geometry accurately. However, automatic skull reconstruction from structural magnetic resonance (MR) images is difficult, as compact bone has a very low signal in magnetic resonance imaging (MRI). Here, we evaluate three methods for skull segmentation, namely FSL BET2, the unified segmentation routine of SPM12 with extended spatial tissue priors, and the skullfinder tool of BrainSuite. To our knowledge, this study is the first to rigorously assess the accuracy of these state-of-the-art tools by comparison with CT-based skull segmentations on a group of ten subjects. We demonstrate several key factors that improve the segmentation quality, including the use of multi-contrast MRI data, the optimization of the MR sequences and the adaptation of the parameters of the segmentation methods. We conclude that FSL and SPM12 achieve better skull segmentations than BrainSuite. The former methods obtain reasonable results for the upper part of the skull when a combination of T1- and T2-weighted images is used as input. The SPM12-based results can be improved slightly further by means of simple morphological operations to fix local defects. In contrast to FSL BET2, the SPM12-based segmentation with extended spatial tissue priors and the BrainSuite-based segmentation provide coarse reconstructions of the vertebrae, enabling the construction of volume conductor models that include the neck. We exemplarily demonstrate that the extended models enable a more accurate estimation of the electric field distribution during transcranial direct current stimulation (tDCS) for montages that involve extraencephalic electrodes. The methods provided by FSL and SPM12 are integrated into pipelines for the automatic generation of realistic head models based on tetrahedral meshes, which are distributed as part of the open-source software package SimNIBS for field calculations for transcranial brain stimulation.
•Assessment of three methods for the automatic skull segmentation from MR images.•Rigorous test of their accuracy by comparison against CT data of the same subjects.•FSL and SPM12 can achieve reasonable accuracy for the upper part of the head.•A combination of T1- and T2-weighted images, rather than a single T1, is suggested.•Accuracy strongly benefits from optimization of the MRI sequence parameters.
Transcranial brain stimulation (TBS) has been established as a method for modulating and mapping the function of the human brain, and as a potential treatment tool in several brain disorders. ...Typically, the stimulation is applied using a one-size-fits-all approach with predetermined locations for the electrodes, in electric stimulation (TES), or the coil, in magnetic stimulation (TMS), which disregards anatomical variability between individuals. However, the induced electric field distribution in the head largely depends on anatomical features implying the need for individually tailored stimulation protocols for focal dosing. This requires detailed models of the individual head anatomy, combined with electric field simulations, to find an optimal stimulation protocol for a given cortical target. Considering the anatomical and functional complexity of different brain disorders and pathologies, it is crucial to account for the anatomical variability in order to translate TBS from a research tool into a viable option for treatment.
In this article we present a new method, called CHARM, for automated segmentation of fifteen different head tissues from magnetic resonance (MR) scans. The new method compares favorably to two freely available software tools on a five-tissue segmentation task, while obtaining reasonable segmentation accuracy over all fifteen tissues. The method automatically adapts to variability in the input scans and can thus be directly applied to clinical or research scans acquired with different scanners, sequences or settings. We show that an increase in automated segmentation accuracy results in a lower relative error in electric field simulations when compared to anatomical head models constructed from reference segmentations. However, also the improved segmentations and, by implication, the electric field simulations are affected by systematic artifacts in the input MR scans. As long as the artifacts are unaccounted for, this can lead to local simulation differences up to 30% of the peak field strength on reference simulations. Finally, we exemplarily demonstrate the effect of including all fifteen tissue classes in the field simulations against the standard approach of using only five tissue classes and show that for specific stimulation configurations the local differences can reach 10% of the peak field strength.
•We introduce a new automated method for whole-head segmentation.•The method segments 15 different head tissues covering also the neck.•The segmentation accuracy and robustness compare favorably to existing tools.•Choice of scan parameters can cause segmentation and simulation errors up to 30%.•Including extra tissues into the simulation affects the electric field locally.
The experimental manipulation of neural activity by neurostimulation techniques overcomes the inherent limitations of correlative recordings, enabling the researcher to investigate causal ...brain-behavior relationships. But only when stimulation and recordings are combined, the direct impact of the stimulation on neural activity can be evaluated. In humans, this can be achieved non-invasively through the concurrent combination of transcranial magnetic stimulation (TMS) with functional magnetic resonance imaging (fMRI). Concurrent TMS-fMRI allows the assessment of the neurovascular responses evoked by TMS with excellent spatial resolution and full-brain coverage. This enables the functional mapping of both local and remote network effects of TMS in cortical as well as deep subcortical structures, offering unique opportunities for basic research and clinical applications. The purpose of this review is to introduce the reader to this powerful tool. We will introduce the technical challenges and state-of-the art solutions and provide a comprehensive overview of the existing literature and the available experimental approaches. We will highlight the unique insights that can be gained from concurrent TMS-fMRI, including the state-dependent assessment of neural responsiveness and inter-regional effective connectivity, the demonstration of functional target engagement, and the systematic evaluation of stimulation parameters. We will also discuss how concurrent TMS-fMRI during a behavioral task can help to link behavioral TMS effects to changes in neural network activity and to identify peripheral co-stimulation confounds. Finally, we will review the use of concurrent TMS-fMRI for developing TMS treatments of psychiatric and neurological disorders and suggest future improvements for further advancing the application of concurrent TMS-fMRI.
Comparing electric field simulations from individualized head models against in-vivo intra-cranial recordings is considered the gold standard for direct validation of computational field modeling for ...transcranial brain stimulation and brain mapping techniques such as electro- and magnetoencephalography. The measurements also help to improve simulation accuracy by pinning down the factors having the largest influence on the simulations. Here we compare field simulations from four different automated pipelines against intracranial voltage recordings in an existing dataset of 14 epilepsy patients. We show that modeling differences in the pipelines lead to notable differences in the simulated electric field distributions that are often large enough to change the conclusions regarding the dose distribution and strength in the brain. Specifically, differences in the automatic segmentations of the head anatomy from structural magnetic resonance images are a major factor contributing to the observed field differences. However, the differences in the simulated fields are not reflected in the comparison between the simulations and intra-cranial measurements. This apparent mismatch is partly explained by the noisiness of the intra-cranial measurements, which renders comparisons between the methods inconclusive. We further demonstrate that a standard regression analysis, which ignores uncertainties in the simulations, leads to a strong bias in the estimated linear relationship between simulated and measured fields. Ignoring this bias leads to the incorrect conclusion that the models systematically misestimate the field strength in the brain. We propose a new Bayesian regression analysis of the data that yields unbiased parameter estimates, along with their uncertainties, and gives further insights to the fit between simulations and measurements. Specifically, the unbiased results give only weak support for systematic misestimations of the fields by the models.
•Fields from different head modeling pipelines can differ up to 49%.•However, all modeling pipelines perform similarly in predicting the measurements.•Bayesian analysis robustly estimates the fit between simulations and recordings.•Previous standard regression analyses of the fit suffered from a systematic bias.•New results do not support a systematic “misestimation” of the fields by the models.
Uncertainty surrounding ohmic tissue conductivity impedes accurate calculation of the electric fields generated by non-invasive brain stimulation. We present an efficient and generic technique for ...uncertainty and sensitivity analyses, which quantifies the reliability of field estimates and identifies the most influential parameters. For this purpose, we employ a non-intrusive generalized polynomial chaos expansion to compactly approximate the multidimensional dependency of the field on the conductivities. We demonstrate that the proposed pipeline yields detailed insight into the uncertainty of field estimates for transcranial magnetic stimulation (TMS) and transcranial direct current stimulation (tDCS), identifies the most relevant tissue conductivities, and highlights characteristic differences between stimulation methods. Specifically, we test the influence of conductivity variations on (i) the magnitude of the electric field generated at each gray matter location, (ii) its normal component relative to the cortical sheet, (iii) its overall magnitude (indexed by the 98th percentile), and (iv) its overall spatial distribution. We show that TMS fields are generally less affected by conductivity variations than tDCS fields. For both TMS and tDCS, conductivity uncertainty causes much higher uncertainty in the magnitude as compared to the direction and overall spatial distribution of the electric field. Whereas the TMS fields were predominantly influenced by gray and white matter conductivity, the tDCS fields were additionally dependent on skull and scalp conductivities. Comprehensive uncertainty analyses of complex systems achieved by the proposed technique are not possible with classical methods, such as Monte Carlo sampling, without extreme computational effort. In addition, our method has the advantages of directly yielding interpretable and intuitive output metrics and of being easily adaptable to new problems.
Purpose
The diffusion‐weighted SPLICE (split acquisition of fast spin‐echo signals) sequence employs split‐echo rapid acquisition with relaxation enhancement (RARE) readout to provide images almost ...free of geometric distortions. However, due to the varying T2$$ {}_2 $$‐weighting during k‐space traversal, SPLICE suffers from blurring. This work extends a method for controlling the spatial point spread function (PSF) while optimizing the signal‐to‐noise ratio (SNR) achieved by adjusting the flip angles in the refocusing pulse train of SPLICE.
Methods
An algorithm based on extended phase graph (EPG) simulations optimizes the flip angles by maximizing SNR for a flexibly chosen predefined target PSF that describes the desired k‐space density weighting and spatial resolution. An optimized flip angle scheme and a corresponding post‐processing correction filter which together achieve the target PSF was tested by healthy subject brain imaging using a clinical 1.5 T scanner.
Results
Brain images showed a clear and consistent improvement over those obtained with a standard constant flip angle scheme. SNR was increased and apparent diffusion coefficient estimates were more accurate. For a modified Hann k‐space weighting example, considerable benefits resulted from acquisition weighting by flip angle control.
Conclusion
The presented flexible method for optimizing SPLICE flip angle schemes offers improved MR image quality of geometrically accurate diffusion‐weighted images that makes the sequence a strong candidate for radiotherapy planning or stereotactic surgery.
Phasic dopamine release from mid-brain dopaminergic neurons is thought to signal errors of reward prediction (RPE). If reward maximisation is to maintain homeostasis, then the value of primary ...rewards should be coupled to the homeostatic errors they remediate. This leads to the prediction that RPE signals should be configured as a function of homeostatic state and thus diminish with the attenuation of homeostatic error. To test this hypothesis, we collected a large volume of functional MRI data from five human volunteers on four separate days. After fasting for 12 hours, subjects consumed preloads that differed in glucose concentration. Participants then underwent a Pavlovian cue-conditioning paradigm in which the colour of a fixation-cross was stochastically associated with the delivery of water or glucose via a gustometer. This design afforded computation of RPE separately for better- and worse-than expected outcomes during ascending and descending trajectories of serum glucose fluctuations. In the parabrachial nuclei, regional activity coding positive RPEs scaled positively with serum glucose for both ascending and descending glucose levels. The ventral tegmental area and substantia nigra became more sensitive to negative RPEs when glucose levels were ascending. Together, the results suggest that RPE signals in key brainstem structures are modulated by homeostatic trajectories of naturally occurring glycaemic flux, revealing a tight interplay between homeostatic state and the neural encoding of primary reward in the human brain.
Movement artifacts compromise image quality and may interfere with interpretation, especially in magnetic resonance imaging (MRI) applications with low signal-to-noise ratio such as functional MRI or ...diffusion tensor imaging, and when imaging small lesions. High image resolution has high sensitivity to motion artifacts and often prolongs scan time that again aggravates movement artifacts. During the scan fast imaging techniques and sequences, optimal receiver coils, careful patient positioning, and instruction may minimize movement artifacts. Physiological noise sources are motion from respiration, flow and pulse coupled to cardiac cycles, from the swallowing reflex and small spontaneous head movements. Par example, in resting-state functional MRI spontaneous neuronal activity adds 1-2% of signal change, even under optimal conditions signal contributions from physiological noise remain a considerable fraction hereof. Movement tracking during imaging may allow for prospective correction or postprocessing steps separating signal and noise.
Purpose
To demonstrate a novel method for tracking of head movements during MRI using electroencephalography (EEG) hardware for recording signals induced by native imaging gradients.
Theory and ...Methods
Gradient switching during simultaneous EEG–fMRI induces distortions in EEG signals, which depend on subject head position and orientation. When EEG electrodes are interconnected with high‐impedance carbon wire loops, the induced voltages are linear combinations of the temporal gradient waveform derivatives. We introduce head tracking based on these signals (CapTrack) involving 3 steps: (1) phantom scanning is used to characterize the target sequence and a fast calibration sequence; (2) a linear relation between changes of induced signals and head pose is established using the calibration sequence; and (3) induced signals recorded during target sequence scanning are used for tracking and retrospective correction of head movement without prolonging the scan time of the target sequence. Performance of CapTrack is compared directly to interleaved navigators.
Results
Head‐pose tracking at 27.5 Hz during echo planar imaging (EPI) was demonstrated with close resemblance to rigid body alignment (mean absolute difference: 0.14 0.38 0.15‐mm translation, 0.30 0.27 0.22‐degree rotation). Retrospective correction of 3D gradient‐echo imaging shows an increase of average edge strength of 12%/−0.39% for instructed/uninstructed motion with CapTrack pose estimates, with a tracking interval of 1561 ms and high similarity to interleaved navigator estimates (mean absolute difference: 0.13 0.33 0.12 mm, 0.28 0.15 0.22 degrees).
Conclusion
Motion can be estimated from recordings of gradient switching with little or no sequence modification, optionally in real time at low computational burden and synchronized to image acquisition, using EEG equipment already found at many research institutions.
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