A comparison of denoising pipelines in high temporal resolution task-based functional magnetic resonance imaging data.
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ABSTRACT:
SUBMITTER: Mayer AR
PROVIDER: S-EPMC6865567 | biostudies-literature | 2019 Sep
REPOSITORIES: biostudies-literature
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Project description:PurposeTo demonstrate an MRI technique-Submillisecond Periodic Event Encoded Dynamic Imaging (SPEEDI)-for capturing cyclic dynamic events with submillisecond temporal resolution.MethodsThe SPEEDI technique is based on an FID or an echo signal in which each time point in the signal is used to sample a distinct k-space raster, followed by repeated FIDs or echoes to produce the remaining k-space data in each k-space raster. All acquisitions are synchronized with a cyclic event, resulting in a set of time-resolved images of the cyclic event with a temporal resolution determined by the dwell time. In SPEEDI, spatial encoding is accomplished by phase encoding. The SPEEDI technique was demonstrated in two experiments at 3 T to (1) visualize fast-changing electric currents that mimicked the waveform of an action potential, and (2) characterize rapidly decaying eddy currents in an MRI system, with a temporal resolution of 0.2 ms and 0.4 ms, respectively. In both experiments, compressed sensing was incorporated to reduce the scan times. Phase difference maps related to the dynamics of electric currents or eddy currents were then obtained.ResultsIn the first experiment, time-resolved phase maps resulting from the action potential-mimicking current waveform were successfully obtained and agreed well with theoretical calculations (normalized RMS error = 0.07). In the second experiment, spatially resolved eddy current phase maps revealed time constants (27.1 ± 0.2 ms, 41.1 ± 3.5 ms, and 34.8 ± 0.7 ms) that matched well with those obtained from an established method using point sources (26.4 ms, 41.2 ms and 34.8 ms). For both experiments, phase maps from fully sampled and compressed-sensing-accelerated k-space data exhibited a high structural similarity (> 0.8) despite a two-fold to three-fold acceleration.ConclusionsWe have illustrated that SPEEDI can provide submillisecond temporal resolution. This capability will likely lead to future exploration of ultrafast, cyclic biomedical processes using MRI.
| S-EPMC9109937 | biostudies-literature
Project description:Mesial temporal lobe epilepsy (mTLE) is a chronic disorder with spontaneous seizures recurring for years, or even decades. Many structural and functional changes have been detected in both the seizure focus and distal regions throughout the brain over this duration that may reflect the development of epileptogenic networks. Resting state functional magnetic resonance imaging (fMRI) connectivity mapping has the potential to elucidate and quantify these networks. The network between the left and right hippocampus may very likely be one of the most susceptible to changes due to long-term seizure propagation effects. Therefore, the objective of this study was to quantify cross hippocampal influence in mTLE using high temporal resolution fMRI, and to determine its relationship with disease duration.fMRI images were acquired in the resting (interictal) state with 500 ms temporal resolution across the temporal lobes of 19 mTLE patients (13 left, 6 right). The left and right hippocampi were identified on each subject's images using both structurally defined and functionally defined boundaries. The cross hippocampal influence was quantified in two ways for each pair of regions: (1) the nondirectional hippocampal functional connectivity calculated as the Pearson's correlation between the average time series in the left and the right hippocampus regions, and (2) the Granger causality (GC) laterality measure, which implies directional influence by determining temporal precedence. Each of these measures was correlated with age, age of onset, and disease duration across subjects to investigate relationship to disease progression.The hippocampal connectivity was not significantly different between patients with left and right mTLE using either the structurally or the functionally defined regions. Across all patients, hippocampal connectivity was not correlated significantly with age of onset or duration of disease. However, as duration of disease increased after 10 years (nine patients), the hippocampal connectivity increased linearly. Using the functionally defined regions, the GC laterality was increased in the right mTLE over the left mTLE, indicating that the left hippocampus was influencing the right hippocampus more than the right influencing left. This was also positively correlated with age of onset. Furthermore, like hippocampal connectivity, the relationship between GC laterality and duration of disease changes after 10 years duration of disease. After this duration, the GC laterality was positive in the three of three patients with right mTLE (left influencing right), whereas the GC laterality was negative in five of six patients with left mTLE (right influencing left).This study reveals a relationship between fMRI functional connectivity and causal influence of the left and right hippocampi and duration of disease in mTLE. During the interictal state, the interhemispheric hippocampal connectivity initially is disrupted and then linearly increases as the epilepsy progresses longer than 10 years. This increase in connectivity appears to be due to the hippocampus contralateral to the epileptogenic focus exerting more influence over the ipsilateral hippocampus. These findings may have implications in understanding the functional development of epileptic networks and possibly prediction of surgical outcome of mTLE.
| S-EPMC4428312 | biostudies-literature
Project description:Recently, emerging studies have demonstrated the existence of brain resting-state spontaneous activity at frequencies higher than the conventional 0.1 Hz. A few groups utilizing accelerated acquisitions have reported persisting signals beyond 1 Hz, which seems too high to be accommodated by the sluggish hemodynamic process underpinning blood oxygen level-dependent contrasts (the upper limit of the canonical model is ∼0.3 Hz). It is thus questionable whether the observed high-frequency (HF) functional connectivity originates from alternative mechanisms (e.g., inflow effects, proton density changes in or near activated neural tissue) or rather is artificially introduced by improper preprocessing operations. In this study, we examined the influence of a common preprocessing step-whole-band linear nuisance regression (WB-LNR)-on resting-state functional connectivity (RSFC) and demonstrated through both simulation and analysis of real dataset that WB-LNR can introduce spurious network structures into the HF bands of functional magnetic resonance imaging (fMRI) signals. Findings of present study call into question whether published observations on HF-RSFC are partly attributable to improper data preprocessing instead of actual neural activities.
| S-EPMC5312601 | biostudies-literature
Project description:The goal of this article is to model multisubject task-induced functional magnetic resonance imaging (fMRI) response among predefined regions of interest (ROIs) of the human brain. Conventional approaches to fMRI analysis only take into account temporal correlations, but do not rigorously model the underlying spatial correlation due to the complexity of estimating and inverting the high dimensional spatio-temporal covariance matrix. Other spatio-temporal model approaches estimate the covariance matrix with the assumption of stationary time series, which is not always feasible. To address these limitations, we propose a double-wavelet approach for modeling the spatio-temporal brain process. Working with wavelet coefficients simplifies temporal and spatial covariance structure because under regularity conditions, wavelet coefficients are approximately uncorrelated. Different wavelet functions were used to capture different correlation structures in the spatio-temporal model. The main advantages of the wavelet approach are that it is scalable and that it deals with nonstationarity in brain signals. Simulation studies showed that our method could reduce false-positive and false-negative rates by taking into account spatial and temporal correlations simultaneously. We also applied our method to fMRI data to study activation in prespecified ROIs in the prefontal cortex. Data analysis showed that the result using the double-wavelet approach was more consistent than the conventional approach when sample size decreased.
| S-EPMC6771256 | biostudies-literature
Project description:The preprocessing of functional magnetic resonance imaging (fMRI) data is necessary to remove unwanted artifacts and transform the data into a standard format. There are several neuroimaging data processing tools that are widely used, such as SPM, AFNI, FSL, FreeSurfer, Workbench, and fMRIPrep. Different data preprocessing pipelines yield differing results, which might reduce the reproducibility of neuroimaging studies. Here, we developed a preprocessing pipeline for T1-weighted structural MRI and fMRI data by combining components of well-known software packages to fully incorporate recent developments in MRI preprocessing into a single coherent software package. The developed software, called FuNP (Fusion of Neuroimaging Preprocessing) pipelines, is fully automatic and provides both volume- and surface-based preprocessing pipelines with a user-friendly graphical interface. The reliability of the software was assessed by comparing resting-state networks (RSNs) obtained using FuNP with pre-defined RSNs using open research data (n = 90). The obtained RSNs were well-matched with the pre-defined RSNs, suggesting that the pipelines in FuNP are reliable. In addition, image quality metrics (IQMs) were calculated from the results of three different software packages (i.e., FuNP, FSL, and fMRIPrep) to compare the quality of the preprocessed data. We found that our FuNP outperformed other software in terms of temporal characteristics and artifacts removal. We validated our pipeline with independent local data (n = 28) in terms of IQMs. The IQMs of our local data were similar to those obtained from the open research data. The codes for FuNP are available online to help researchers.
| S-EPMC6378808 | biostudies-literature
Project description:BackgroundMyocardial deformation analyses using cardiovascular magnetic resonance (CMR) feature tracking (CMR-FT) have incremental value in the assessment of cardiac function beyond volumetric analyses. Since guidelines do not recommend specific imaging parameters, we aimed to define optimal spatial and temporal resolutions for CMR cine images to enable reliable post-processing.MethodsIntra- and inter-observer reproducibility was assessed in 12 healthy subjects and 9 heart failure (HF) patients. Cine images were acquired with different temporal (20, 30, 40 and 50 frames/cardiac cycle) and spatial resolutions (high in-plane 1.5 × 1.5 mm through-plane 5 mm, standard 1.8 × 1.8 x 8mm and low 3.0 × 3.0 x 10mm). CMR-FT comprised left ventricular (LV) global and segmental longitudinal/circumferential strain (GLS/GCS) and associated systolic strain rates (SR), and right ventricular (RV) GLS.ResultsTemporal but not spatial resolution did impact absolute strain and SR. Maximum absolute changes between lowest and highest temporal resolution were as follows: 1.8% and 0.3%/s for LV GLS and SR, 2.5% and 0.6%/s for GCS and SR as well as 1.4% for RV GLS. Changes of strain values occurred comparing 20 and 30 frames/cardiac cycle including LV and RV GLS and GCS (p < 0.001-0.046). In contrast, SR values (LV GLS/GCS SR) changed significantly comparing all successive temporal resolutions (p < 0.001-0.013). LV strain and SR reproducibility was not affected by either temporal or spatial resolution, whilst RV strain variability decreased with augmentation of temporal resolution.ConclusionTemporal but not spatial resolution significantly affects strain and SR in CMR-FT deformation analyses. Strain analyses require lower temporal resolution and 30 frames/cardiac cycle offer consistent strain assessments, whilst SR measurements gain from further increases in temporal resolution.
| S-EPMC8127257 | biostudies-literature
Project description:Task-based functional neuroimaging methods are increasingly being used to identify biomarkers of treatment response in psychiatric disorders. To facilitate meaningful interpretation of neural correlates of tasks and their potential changes with treatment over time, understanding the reliability of the blood-oxygen-level dependent (BOLD) signal of such tasks is essential. We assessed test-retest reliability of an emotional conflict task in healthy participants collected as part of the Canadian Biomarker Integration Network in Depression. Data for 36 participants, scanned at three time points (weeks 0, 2, and 8) were analyzed, and intra-class correlation coefficients (ICC) were used to quantify reliability. We observed moderate reliability (median ICC values between 0.5 and 0.6), within occipital, parietal, and temporal regions, specifically for conditions of lower cognitive complexity, that is, face, congruent or incongruent trials. For these conditions, activation was also observed within frontal and sub-cortical regions, however, their reliability was poor (median ICC < 0.2). Clinically relevant prognostic markers based on task-based fMRI require high predictive accuracy at an individual level. For this to be achieved, reliability of BOLD responses needs to be high. We have shown that reliability of the BOLD response to an emotional conflict task in healthy individuals is moderate. Implications of these findings to further inform studies of treatment effects and biomarker discovery are discussed.
| S-EPMC7267954 | biostudies-literature
Project description:IntroductionDecoding brain activities is one of the most popular topics in neuroscience in recent years. And deep learning has shown high performance in fMRI data classification and regression, but its requirement for large amounts of data conflicts with the high cost of acquiring fMRI data.MethodsIn this study, we propose an end-to-end temporal contrastive self-supervised learning algorithm, which learns internal spatiotemporal patterns within fMRI and allows the model to transfer learning to datasets of small size. For a given fMRI signal, we segmented it into three sections: the beginning, middle, and end. We then utilized contrastive learning by taking the end-middle (i.e., neighboring) pair as the positive pair, and the beginning-end (i.e., distant) pair as the negative pair.ResultsWe pretrained the model on 5 out of 7 tasks from the Human Connectome Project (HCP) and applied it in a downstream classification of the remaining two tasks. The pretrained model converged on data from 12 subjects, while a randomly initialized model required 100 subjects. We then transferred the pretrained model to a dataset containing unpreprocessed whole-brain fMRI from 30 participants, achieving an accuracy of 80.2 ± 4.7%, while the randomly initialized model failed to converge. We further validated the model's performance on the Multiple Domain Task Dataset (MDTB), which contains fMRI data of 26 tasks from 24 participants. Thirteen tasks of fMRI were selected as inputs, and the results showed that the pre-trained model succeeded in classifying 11 of the 13 tasks. When using the 7 brain networks as input, variations of the performance were observed, with the visual network performed as well as whole brain inputs, while the limbic network almost failed in all 13 tasks.DiscussionOur results demonstrated the potential of self-supervised learning for fMRI analysis with small datasets and unpreprocessed data, and for analysis of the correlation between regional fMRI activity and cognitive tasks.
| S-EPMC10330812 | biostudies-literature
Project description:ObjectiveLocalization of focal epilepsy is critical for surgical treatment of refractory seizures. There remains a great need for noninvasive techniques to localize seizures for surgical decision-making. We investigate the use of deep learning using resting state functional magnetic resonance imaging (RS-fMRI) to identify the hemisphere of seizure onset in temporal lobe epilepsy (TLE) patients.MethodsA total of 2132 healthy controls and 32 preoperative TLE patients were studied. All participants underwent structural MRI and RS-fMRI. Healthy control data were used to generate training samples for a three-dimensional convolutional neural network (3DCNN). RS-fMRI was synthetically altered in randomly lateralized regions in the healthy control participants. The model was then trained to classify the hemisphere containing synthetic noise. Finally, the model was tested on TLE patients to assess its performance for detecting biological seizure onset zones, and gradient-weighted class activation mapping (Grad-CAM) identified the strongest predictive regions.ResultsThe 3DCNN classified healthy control hemispheres known to contain synthetic noise with 96% accuracy, and TLE hemispheres clinically identified to be seizure onset zones with 90.6% accuracy. Grad-CAM identified a range of temporal, frontal, parietal, and subcortical regions that were strong anatomical predictors of the seizure onset zone, and the resting state networks that colocalized with Grad-CAM results included default mode, medial temporal, and dorsal attention networks. Lastly, in an analysis of a subset of patients with postsurgical outcomes, the 3DCNN leveraged a more focal set of regions to achieve classification in patients with Engel Class >I compared to Engel Class I.SignificanceNoninvasive techniques capable of localizing the seizure onset zone could improve presurgical planning in patients with intractable epilepsy. We have demonstrated the ability of deep learning to identify the correct hemisphere of the seizure onset zone in TLE patients using RS-fMRI with high accuracy. This approach represents a novel technique of seizure lateralization that could improve preoperative surgical planning.
| S-EPMC9177812 | biostudies-literature
Project description:Task-based functional magnetic resonance imaging (tfMRI) has developed as a common alternative in epilepsy surgery to the intracarotid amobarbital procedure, also known as the Wada procedure. Prior studies have implicated tfMRI as a comparable predictor of postsurgical cognitive outcomes. However, the predictive validity of tfMRI has not been established. This preregistered systematic review and meta-analysis (CRD42020183563) synthesizes the literature predicting postsurgical cognitive outcomes in temporal lobe epilepsy (TLE) using tfMRI. The PubMed and PsycINFO literature databases were queried for English-language articles published between January 1, 2009 and December 31, 2020 associating tfMRI laterality indices or symmetry of task activation with outcomes in TLE. Their references were reviewed for additional relevant literature, and unpublished data from our center were incorporated. Nineteen studies were included in the meta-analysis. tfMRI studies predicted postsurgical cognitive outcomes in left TLE ( ρ̂ = -.27, 95% confidence interval [CI] = -.32 to -.23) but not right TLE ( ρ̂ = -.02, 95% CI = -.08 to .03). Among studies of left TLE, language tfMRI studies were more robustly predictive of postsurgical cognitive outcomes ( ρ̂ = -.27, 95% CI = -.33 to -.20) than memory tfMRI studies ( ρ̂ = -.27, 95% CI = -.43 to -.11). Further moderation by cognitive outcome domain indicated language tfMRI predicted confrontation naming ( ρ̂ = -.32, 95% CI = -.41 to -.22) and verbal memory ( ρ̂ = -.26, 95% CI = -.35 to -.17) outcomes, whereas memory tfMRI forecasted only verbal memory outcomes ( ρ̂ = -.37, 95% CI = -.57 to -.18). Surgery type, birth sex, level of education, age at onset, disease duration, and hemispheric language dominance moderated study outcomes. Sensitivity analyses suggested the interval of postsurgical follow-up, and reporting and methodological practices influenced study outcomes as well. These findings intimate tfMRI is a modest predictor of outcomes in left TLE that should be considered in the context of a larger surgical workup.
| S-EPMC9944224 | biostudies-literature