SynBOLD-DisCo: Synthetic BOLD images for distortion correction of fMRI without additional calibration scans.

The blood oxygen level dependent (BOLD) signal from functional magnetic resonance imaging (fMRI) is a noninvasive technique that has been widely used in research to study brain function. However, fMRI suffers from susceptibility-induced off resonance fields which may cause geometric distortions and mismatches with anatomical images. State-of-the-art correction methods require acquiring reverse phase encoded images or additional field maps to enable distortion correction. However, not all imaging protocols include these additional scans and thus cannot take advantage of these susceptibility correction capabilities. As such, in this study we aim to enable state-of-the-art distortion correction with FSL's topup algorithm of historical and/or limited fMRI data that include only a structural image and single phase encoded fMRI. To do this, we use 3D U-net models to synthesize undistorted fMRI BOLD contrast images from the structural image and use this undistorted synthetic image as an anatomical target for distortion correction with topup. We evaluate the efficacy of this approach, named SynBOLD-DisCo (synthetic BOLD images for distortion correction), and show that BOLD images corrected using our approach are geometrically more similar to structural images than the distorted BOLD data and are practically equivalent to state-of-the-art correction methods which require reverse phase encoded data. Future directions include additional validation studies, integration with other preprocessing operations, retraining with broader pathologies, and investigating the effects of spin echo versus gradient echo images for training and distortion correction. In summary, we demonstrate SynBOLD-DisCo corrects distortion of fMRI when reverse phase encoding scans or field maps are not available.

Distortion correction of functional MRI without reverse phase encoding scans or field maps.

Functional magnetic resonance images (fMRI) acquired using echo planar sequences typically suffer from spatial distortions due to susceptibility induced off-resonance fields, which may cause geometric mismatch with structural images and affect subsequent quantification and localization of brain function. State-of-the art distortion correction methods (for example, using FSL's topup or AFNI's 3dQwarp algorithms) require the collection of additional scans - either field maps or images with reverse phase encoding directions (i.e., blip-up/blip-down acquisitions) - to estimate and correct distortions. However, not all imaging protocols acquire these additional data and thus cannot take advantage of these post-acquisition corrections. In this study, we aim to enable state-of-the art processing of historical or limited datasets that do not include specific sequences for distortion correction by using only the acquired functional data and a single commonly acquired structural image. To achieve this, we synthesize an undistorted image with contrast similar to the fMRI data and use the non-distorted synthetic image as an anatomical target for distortion correction. We evaluate the efficacy of this approach, named SynBOLD-DisCo (Synthetic BOLD contrast for Distortion Correction), and show that this distortion correction process yields fMRI data that are geometrically similar to non-distorted structural images, with distortion correction virtually equivalent to acquisitions that do contain both blip-up/blip-down images. Our method is available as a Singularity container, source code, and an executable trained model to facilitate evaluation and integration into existing fMRI preprocessing pipelines.

Vigilance associates with the low-dimensional structure of fMRI data.

The human brain exhibits rich dynamics that reflect ongoing functional states. Patterns in fMRI data, detected in a data-driven manner, have uncovered recurring configurations that relate to individual and group differences in behavioral, cognitive, and clinical traits. However, resolving the neural and physiological processes that underlie such measurements is challenging, particularly without external measurements of brain state. A growing body of work points to underlying changes in vigilance as one driver of time-windowed fMRI connectivity states, calculated on the order of tens of seconds. Here we examine the degree to which the low-dimensional spatial structure of instantaneous fMRI activity is associated with vigilance levels, by testing whether vigilance-state detection can be carried out in an unsupervised manner based on individual BOLD time frames. To investigate this question, we first reduce the spatial dimensionality of fMRI data, and apply Gaussian Mixture Modeling to cluster the resulting low-dimensional data without any a priori vigilance information. Our analysis includes long-duration task and resting-state scans that are conducive to shifts in vigilance. We observe a close alignment between low-dimensional fMRI states (data-driven clusters) and measurements of vigilance derived from concurrent electroencephalography (EEG) and behavior. Whole-brain coactivation analysis revealed cortical anti-correlation patterns that resided primarily during higher behavioral- and EEG-defined levels of vigilance, while cortical activity was more often spatially uniform in states corresponding to lower vigilance. Overall, these findings indicate that vigilance states may be detected in the low-dimensional structure of fMRI data, even within individual time frames.

Arousal and salience network connectivity alterations in surgical temporal lobe epilepsy.

OBJECTIVE: It is poorly understood why patients with mesial temporal lobe epilepsy (TLE) have cognitive deficits and brain network changes that extend beyond the temporal lobe, including altered extratemporal intrinsic connectivity networks (ICNs). However, subcortical arousal structures project broadly to the neocortex, are affected by TLE, and thus may contribute to these widespread network effects. The authors' objective was to examine functional connectivity (FC) patterns between subcortical arousal structures and neocortical ICNs, possible neurocognitive relationships, and FC changes after epilepsy surgery. METHODS: The authors obtained resting-state functional magnetic resonance imaging (fMRI) in 50 adults with TLE and 50 controls. They compared nondirected FC (correlation) and directed FC (Granger causality laterality index) within the salience network, default mode network, and central executive network, as well as between subcortical arousal structures; these 3 ICNs were also compared between patients and controls. They also used an fMRI-based vigilance index to relate alertness to arousal center FC. Finally, fMRI was repeated in 29 patients > 12 months after temporal lobe resection. RESULTS: Nondirected FC within the salience (p = 0.042) and default mode (p = 0.0008) networks, but not the central executive network (p = 0.79), was decreased in patients in comparison with controls (t-tests, corrected). Nondirected FC between the salience network and subcortical arousal structures (nucleus basalis of Meynert, thalamic centromedian nucleus, and brainstem pedunculopontine nucleus) was reduced in patients in comparison with controls (p = 0.0028-0.015, t-tests, corrected), and some of these connectivity abnormalities were associated with lower processing speed index, verbal comprehension, and full-scale IQ. Interestingly, directed connectivity measures suggested a loss of top-down influence from the salience network to the arousal nuclei in patients. After resection, certain FC patterns between the arousal nuclei and salience network moved toward control values in the patients, suggesting that some postoperative recovery may be possible. Although an fMRI-based vigilance measure suggested that patients exhibited reduced alertness over time, FC abnormalities between the salience network and arousal structures were not influenced by the alertness levels during the scans. CONCLUSIONS: FC abnormalities between subcortical arousal structures and ICNs, such as the salience network, may be related to certain neurocognitive deficits in TLE patients. Although TLE patients demonstrated vigilance abnormalities, baseline FC perturbations between the arousal and salience networks are unlikely to be driven solely by alertness level, and some may improve after surgery. Examination of the arousal network and ICN disturbances may improve our understanding of the downstream clinical effects of TLE.

fMRI-based detection of alertness predicts behavioral response variability.

Levels of alertness are closely linked with human behavior and cognition. However, while functional magnetic resonance imaging (fMRI) allows for investigating whole-brain dynamics during behavior and task engagement, concurrent measures of alertness (such as EEG or pupillometry) are often unavailable. Here, we extract a continuous, time-resolved marker of alertness from fMRI data alone. We demonstrate that this fMRI alertness marker, calculated in a short pre-stimulus interval, captures trial-to-trial behavioral responses to incoming sensory stimuli. In addition, we find that the prediction of both EEG and behavioral responses during the task may be accomplished using only a small fraction of fMRI voxels. Furthermore, we observe that accounting for alertness appears to increase the statistical detection of task-activated brain areas. These findings have broad implications for augmenting a large body of existing datasets with information about ongoing arousal states, enriching fMRI studies of neural variability in health and disease.

Seizure-onset regions demonstrate high inward directed connectivity during resting-state: An SEEG study in focal epilepsy.

OBJECTIVE: In patients with medically refractory focal epilepsy, stereotactic-electroencephalography (SEEG) can aid in localizing epileptogenic regions for surgical treatment. SEEG, however, requires long hospitalizations to record seizures, and ictal interpretation can be incomplete or inaccurate. Our recent work showed that non-directed resting-state analyses may identify brain regions as epileptogenic or uninvolved. Our present objective is to map epileptogenic networks in greater detail and more accurately identify seizure-onset regions using directed resting-state SEEG connectivity. METHODS: In 25 patients with focal epilepsy who underwent SEEG, 2 minutes of resting-state, artifact-free, SEEG data were selected and functional connectivity was estimated. Using standard clinical interpretation, brain regions were classified into four categories: ictogenic, early propagation, irritative, or uninvolved. Three non-directed connectivity measures (mutual information [MI] strength, and imaginary coherence between and within regions) and four directed measures (partial directed coherence [PDC] and directed transfer function [DTF], inward and outward strength) were calculated. Logistic regression was used to generate a predictive model of ictogenicity. RESULTS: Ictogenic regions had the highest and uninvolved regions had the lowest MI strength. Although both PDC and DTF inward strengths were highest in ictogenic regions, outward strengths did not differ among categories. A model incorporating directed and nondirected connectivity measures demonstrated an area under the receiver-operating characteristic (ROC) curve (AUC) of 0.88 in predicting ictogenicity of individual regions. The AUC of this model was 0.93 when restricted to patients with favorable postsurgical seizure outcomes. SIGNIFICANCE: Directed connectivity measures may help identify epileptogenic networks without requiring ictal recordings. Greater inward but not outward connectivity in ictogenic regions at rest may represent broad inhibitory input to prevent seizure generation.

Brainstem Functional Connectivity Disturbances in Epilepsy may Recover After Successful Surgery.

BACKGROUND: Focal seizures in temporal lobe epilepsy (TLE) are associated with widespread brain network perturbations and neurocognitive problems. OBJECTIVE: To determine whether brainstem connectivity disturbances improve with successful epilepsy surgery, as recent work has demonstrated decreased brainstem connectivity in TLE that is related to disease severity and neurocognitive profile. METHODS: We evaluated 15 adult TLE patients before and after (>1 yr; mean, 3.4 yr) surgery, and 15 matched control subjects using magnetic resonance imaging to measure functional and structural connectivity of ascending reticular activating system (ARAS) structures, including cuneiform/subcuneiform nuclei (CSC), pedunculopontine nucleus (PPN), and ventral tegmental area (VTA). RESULTS: TLE patients who achieved long-term postoperative seizure freedom (10 of 15) demonstrated increases in functional connectivity between ARAS structures and fronto-parietal-insular neocortex compared to preoperative baseline (P = .01, Kruskal-Wallis), with postoperative connectivity patterns resembling controls' connectivity. No functional connectivity changes were detected in 5 patients with persistent seizures after surgery (P = .9, Kruskal-Wallis). Among seizure-free postoperative patients, larger increases in CSC, PPN, and VTA functional connectivity were observed in individuals with more frequent seizures before surgery (P < .05 for each, Spearman's rho). Larger postoperative increases in PPN functional connectivity were seen in patients with lower baseline verbal IQ (P = .03, Spearman's rho) or verbal memory (P = .04, Mann-Whitney U). No changes in ARAS structural connectivity were detected after successful surgery. CONCLUSION: ARAS functional connectivity disturbances are present in TLE but may recover after successful epilepsy surgery. Larger increases in postoperative connectivity may be seen in individuals with more severe disease at baseline.

Resting-State SEEG May Help Localize Epileptogenic Brain Regions.

BACKGROUND: Stereotactic electroencephalography (SEEG) is a minimally invasive neurosurgical method to localize epileptogenic brain regions in epilepsy but requires days in the hospital with interventions to trigger several seizures. OBJECTIVE: To make initial progress in the development of network analysis methods to identify epileptogenic brain regions using brief, resting-state SEEG data segments, without requiring seizure recordings. METHODS: In a cohort of 15 adult focal epilepsy patients undergoing SEEG, we evaluated functional connectivity (alpha-band imaginary coherence) across sampled regions using brief (2 min) resting-state data segments. Bootstrapped logistic regression was used to generate a model to predict epileptogenicity of individual regions. RESULTS: Compared to nonepileptogenic structures, we found increased functional connectivity within epileptogenic regions (P < .05) and between epileptogenic areas and other structures (P < .01, paired t-tests, corrected). Epileptogenic areas also demonstrated higher clustering coefficient (P < .01) and betweenness centrality (P < .01), and greater decay of functional connectivity with distance (P < .05, paired t-tests, corrected). Our functional connectivity model to predict epileptogenicity of individual regions demonstrated an area under the curve of 0.78 and accuracy of 80.4%. CONCLUSION: Our study represents a preliminary step towards defining resting-state SEEG functional connectivity patterns to help localize epileptogenic brain regions ahead of neurosurgical treatment without requiring seizure recordings.

Characterization of postsurgical functional connectivity changes in temporal lobe epilepsy.

OBJECTIVE: Seizure outcome after mesial temporal lobe epilepsy (mTLE) surgery is complex and diverse, even across patients with homogeneous presurgical clinical profiles. The authors hypothesized that this is due in part to variations in network connectivity across the brain before and after surgery. Although presurgical network connectivity has been previously characterized in these patients, the objective of this study was to characterize presurgical to postsurgical functional network connectivity changes across the brain after mTLE surgery. METHODS: Twenty patients with drug-refractory unilateral mTLE (5 left side, 10 female, age 39.3 ± 13.5 years) who underwent either selective amygdalohippocampectomy (n = 13) or temporal lobectomy (n = 7) were included in the study. Presurgical and postsurgical (36.6 ± 14.3 months after surgery) functional connectivity (FC) was measured with 3-T MRI and compared with findings in age-matched healthy controls (n = 44, 21 female, age 39.3 ± 14.3 years). Postsurgical connectivity changes were then related to seizure outcome, type of surgery, and presurgical disease parameters. RESULTS: The results demonstrated significant decreases of FC from control group values across the brain after surgery that were not present before surgery, including many contralateral hippocampal connections distal to the surgical site. Postsurgical impairment of contralateral precuneus to ipsilateral occipital connectivity was associated with seizure recurrence. Presurgical impairment of the contralateral precuneus to contralateral temporal lobe connectivity was associated with those who underwent selective amygdalohippocampectomy compared to those who had temporal lobectomy. Finally, changes in thalamic connectivity after surgery were linearly related to duration of epilepsy and frequency of consciousness-impairing seizures prior to surgery. CONCLUSIONS: The widespread contralateral hippocampal FC changes after surgery may be a reflection of an ongoing epileptogenic progression that has been altered by the surgery, rather than a direct result of the surgery itself. This network evolution may contribute to long-term seizure outcome. Therefore, the combination of presurgical network mapping with the understanding of the dynamic effects of surgery on the networks may ultimately be used to create predictors of the likelihood of long-term seizure recurrence in individual patients after mTLE surgery.

Thalamic arousal network disturbances in temporal lobe epilepsy and improvement after surgery.

OBJECTIVE: The effects of temporal lobe epilepsy (TLE) on subcortical arousal structures remain incompletely understood. Here, we evaluate thalamic arousal network functional connectivity in TLE and examine changes after epilepsy surgery. METHODS: We examined 26 adult patients with TLE and 26 matched control participants and used resting-state functional MRI (fMRI) to measure functional connectivity between the thalamus (entire thalamus and 19 bilateral thalamic nuclei) and both neocortex and brainstem ascending reticular activating system (ARAS) nuclei. Postoperative imaging was completed for 19 patients >1 year after surgery and compared with preoperative baseline. RESULTS: Before surgery, patients with TLE demonstrated abnormal thalamo-occipital functional connectivity, losing the normal negative fMRI correlation between the intralaminar central lateral (CL) nucleus and medial occipital lobe seen in controls (p < 0.001, paired t-test). Patients also had abnormal connectivity between ARAS and CL, lower ipsilateral intrathalamic connectivity, and smaller ipsilateral thalamic volume compared with controls (p < 0.05 for each, paired t-tests). Abnormal brainstem-thalamic connectivity was associated with impaired visuospatial attention (ρ = -0.50, p = 0.02, Spearman's rho) while lower intrathalamic connectivity and volume were related to higher frequency of consciousness-sparing seizures (p < 0.02, Spearman's rho). After epilepsy surgery, patients with improved seizures showed partial recovery of thalamo-occipital and brainstem-thalamic connectivity, with values more closely resembling controls (p < 0.01 for each, analysis of variance). CONCLUSIONS: Overall, patients with TLE demonstrate impaired connectivity in thalamic arousal networks that may be involved in visuospatial attention, but these disturbances may partially recover after successful epilepsy surgery. Thalamic arousal network dysfunction may contribute to morbidity in TLE.

A football helmet prototype that reduces linear and rotational acceleration with the addition of an outer shell.

OBJECTIVEAmid the public health controversy surrounding American football, a helmet that can reduce linear and rotational acceleration has the potential to decrease forces transmitted to the brain. The authors hypothesized that a football helmet with an outer shell would reduce both linear and rotational acceleration. The authors' objectives were to 1) determine an optimal material for a shock-absorbing outer shell and 2) examine the ability of an outer shell to reduce linear and/or rotational acceleration.METHODSA laboratory-based investigation was undertaken using an extra-large Riddell Revolution football helmet. Two materials (Dow Corning Dilatant Compound and Sorbothane) were selected for their non-Newtonian properties (changes in viscosity with shear stress) to develop an outer shell. External pads were attached securely to the helmet at 3 locations: the front boss, the side, and the back. The helmet was impacted 5 times per location at 6 m/sec with pneumatic ram testing. Two-sample t-tests were used to evaluate linear/rotational acceleration differences between a helmet with and a helmet without the outer shell.RESULTSSorbothane was superior to the Dow Corning compound in force reduction and recovered from impact without permanent deformation. Of 5 different grades, 70-duro (a unit of hardness measured with a durometer) Sorbothane was found to have the greatest energy dissipation and stiffness, and it was chosen as the optimal outer-shell material. The helmet prototype with the outer shell reduced linear acceleration by 5.8% (from 75.4g to 71.1g; p < 0.001) and 10.8% (from 89.5g to 79.8g; p = 0.033) at the side and front boss locations, respectively, and reduced rotational acceleration by 49.8% (from 9312.8 rad/sec2 to 4671.7 rad/sed2; p < 0.001) at the front boss location.CONCLUSIONSSorbothane (70 duro) was chosen as the optimal outer-shell material. In the outer-shell prototype helmet, the results demonstrated a 5%-10% reduction in linear acceleration at the side and front boss locations, and a 50% reduction in rotational acceleration at the front boss location. Given the paucity of publicly reported helmet-design literature and the importance of rotational acceleration in head injuries, the substantial reduction seen in rotational acceleration with this outer-shell prototype holds the potential for future helmet-design improvements.

A system for automatic monitoring of surgical instruments and dynamic, non-rigid surface deformations in breast cancer surgery.

When negative tumor margins are achieved at the time of resection, breast conserving therapy (lumpectomy followed with radiation therapy) offers patients improved cosmetic outcomes and quality of life with equivalent survival outcomes to mastectomy. However, high reoperation rates ranging 10-59% continue to challenge adoption and suggest that improved intraoperative tumor localization is a pressing need. We propose to couple an optical tracker and stereo camera system for automated monitoring of surgical instruments and non-rigid breast surface deformations. A bracket was designed to rigidly pair an optical tracker with a stereo camera, optimizing overlap volume. Utilizing both devices allowed for precise instrument tracking of multiple objects with reliable, workflow friendly tracking of dynamic breast movements. Computer vision techniques were employed to automatically track fiducials, requiring one-time initialization with bounding boxes in stereo camera images. Point based rigid registration was performed between fiducial locations triangulated from stereo camera images and fiducial locations recorded with an optically tracked stylus. We measured fiducial registration error (FRE) and target registration error (TRE) with two different stereo camera devices using a phantom breast with five fiducials. Average FREs of 2.7 ± 0.4 mm and 2.4 ± 0.6 mm with each stereo-camera device demonstrate considerable promise for this approach in monitoring the surgical field. Automated tracking was shown to reduce error when compared to manually selected fiducial locations in stereo camera image-based localization. The proposed instrumentation framework demonstrated potential for the continuous measurement of surgical instruments in relation to the dynamic deformations of a breast during lumpectomy.