Multi-echo fMRI: A review of applications in fMRI denoising and analysis of BOLD signals

Kundu, Prantik; Voon, Valerie; Balchandani, Priti; Lombardo, Michael; Poser, Benedikt A.; Bandettini, Peter A.

doi:10.1016/j.neuroimage.2017.03.033

Cited by 285 publications

(274 citation statements)

References 68 publications

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“…Since the early seminal studies, a variety of rs‐FMRI data analysis approaches have been proposed to isolate the signal changes because of spontaneous neural activity. The integrated multi‐echo approach applied here combines the advantages of (1) multi‐echo data, and (2) judging the source of each signal component based on its echo‐dependence and removing the non‐BOLD components . The multi‐echo data combination strategy was originally proposed in the early days of FMRI to increase the SNR for task FMRI .…”

Section: Discussionmentioning

confidence: 99%

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Integrated multi‐echo denoising strategy improves identification of inherent language laterality

Amemiya

Yamashita

Takao

et al. 2018

Magnetic Resonance in Med

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Purpose Although increasingly used in both neuroscience and clinical studies, a major challenge facing resting‐state FMRI (rs‐FMRI) still lies in isolating BOLD signal fluctuations resulting from neuronal activity from noise. In this study, we investigated the effect of a newly proposed denoising approach, integrated multi‐echo rs‐FMRI analysis, on language mapping. Methods Multiband multi‐echo rs‐FMRI data were acquired, along with language task FMRI that identified language areas in the left hemisphere of 12 subjects. The language laterality and specificity of the language mapping given by seed‐based correlation analysis were compared among the rs‐FMRI data sets pre‐processed using 3 different approaches: multi‐echo data with integrated multi‐echo independent component analysis, denoising that uses the TE‐dependency of each signal component to judge its origin, and multi‐echo and single‐echo data with conventional denoising. The laterality index was automatically computed without setting any threshold to minimize the arbitrariness and to ensure the generality of the result. Results A repeated measures analysis of variance followed by post hoc tests showed that optimal combination of the 3‐echo data succeeded in increasing the correlation within the targeted language system. With the physically principled multi‐echo denoising approach, the integrated strategy further succeeded in revealing areas of synchronization more specific to the language system compared with conventional denoising approach, which eventually improved the identification of the laterality of the system. Conclusion By successfully reducing non‐specific correlations spreading over the brain, integrated multi‐echo approach improved language mapping and identification of the laterality of the system using rs‐FMRI.

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Section: Discussionmentioning

confidence: 99%

“…and by averaging with a voxel‐wise (

normalv

) weighting

ω

given by Posse et al as follows:

\begin{matrix} ω {()(, {normalT}_{2, v}^{*})}_{normaln} = \frac{{T E}_{normaln} \times \exp (- \frac{{T E}_{normaln}}{{normalT}_{2, v}^{*}})}{\sum_{n}^{normalN} {T E}_{normaln} \times \exp (- \frac{{T E}_{normaln}}{{normalT}_{2, v}^{*}})} . \end{matrix}

…”

Section: Methodsmentioning

confidence: 99%

Integrated multi‐echo denoising strategy improves identification of inherent language laterality

Amemiya

Yamashita

Takao

et al. 2018

Magnetic Resonance in Med

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“…Data were reconstructed using EPTI reconstruction with self‐B 0 variation correction. For each TR, T 2 * was estimated through a mono‐exponential fit of the multi‐contrast images, and a weighted‐average based combination of images acquired at different TEs was also generated by using the method in Posse et al and Kundu et al Statistical analysis was then performed on both the weighted‐average magnitude data and the T 2 * time course using a general linear model (GLM) as implemented in FSL . The data were motion corrected and smoothed with a Gaussian kernel with 5‐mm FWHM, and activation was identified with a standard GLM using the stimulus timing convolved with a canonical double‐gamma hemodynamic response function (HRF) that included a temporal derivative term to account for slight temporal offsets in the response timing.…”

Section: Methodsmentioning

confidence: 99%

Echo planar time‐resolved imaging (EPTI)

Wang

Dong

Reese

et al. 2019

Magnetic Resonance in Med

133

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Purpose To develop an efficient distortion‐ and blurring‐free multi‐shot EPI technique for time‐resolved multiple‐contrast and/or quantitative imaging. Methods EPI is a commonly used sequence but suffers from geometric distortions and blurring. Here, we introduce a new multi‐shot EPI technique termed echo planar time‐resolved imaging (EPTI), which has the ability to rapidly acquire distortion‐ and blurring‐free multi‐contrast data set. The EPTI approach performs encoding in ky‐t space and uses a new highly accelerated spatio–temporal CAIPI sampling trajectory to take advantage of signal correlation along these dimensions. Through this acquisition and a B0‐informed parallel imaging reconstruction, hundreds of “time‐resolved” distortion‐ and blurring‐free images at different TEs across the EPI readout window can be created at sub‐millisecond temporal increments using a small number of EPTI shots. Moreover, a method for self‐estimation and correction of shot‐to‐shot B0 variations was developed. Simultaneous multi‐slice acquisition was also incorporated to further improve the acquisition efficiency. Results We evaluated EPTI under varying simulated acceleration factors, B0‐inhomogeneity, and shot‐to‐shot B0 variations to demonstrate its ability to provide distortion‐ and blurring‐free images at multiple TEs. Two variants of EPTI were demonstrated in vivo at 3T: (1) a combined gradient‐ and spin‐echo EPTI for quantitative mapping of T2, T2*, proton density, and susceptibility at 1.1 × 1.1 × 3 mm3 whole‐brain in 28 s (0.8 s/slice), and (2) a gradient‐echo EPTI, for multi‐echo and quantitative T2* fMRI at 2 × 2 × 3 mm3 whole‐brain at a 3.3 s temporal resolution. Conclusion EPTI is a new approach for multi‐contrast and/or quantitative imaging that can provide fast acquisition of distortion‐ and blurring‐free images at multiple TEs.

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“…Our TR was constrained by our fMRI protocol in which we collected dual-echo data allowing us to image magnetic susceptible regions better (Halai et al, 2015; Halai et al, 2014). As technologies improve, e.g., multi-banding multi-echo fMRI, the TR can be reduced much further while maintaining good signal coverage (see Kundu et al (2017) for a review).…”

Section: Limitationsmentioning

confidence: 99%

Relating resting-state hemodynamic changes to the variable language profiles in post-stroke aphasia

Zhao

Ralph

Halai

2018

NeuroImage: Clinical

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Linking both structural lesions and the functional integrity of remaining brain tissue to patients' behavioural profile may be critical in discovering the limits of behavioural recovery post stroke. In the present study, we explored the relationship between temporal hemodynamic changes and language performance in chronic post-stroke aphasia. We collected detailed language and neuropsychological data for 66 patients with chronic (>1 year) post-stroke aphasia. We used principal component analysis to extract their core language-neuropsychological features. From resting-state fMRI scans in 35 patients, we calculated the lag in the time-course of the intact brain voxels in each patient. Finally, variation across the language-cognitive factors was related to both the patients' structural damage and the time-course changes in each patient's intact tissue. Phonological abilities were correlated with the structural integrity of the left superior temporal, angular gyrus, supramarginal gyrus and arcuate fasciculus regions and hemodynamic advance in the left intra-parietal sulcus. Speech fluency related to integrity of premotor regions, plus hemodynamic advance in the left middle/superior temporal gyrus, left middle occipital gyrus, and right angular gyrus. Semantic performance reflected a combination of medial ventral temporal lobe status and hemodynamic delay in the left posterior middle temporal gyrus. Finally, executive abilities correlated with hemodynamic delay in the left middle/inferior frontal gyrus, right rolandic operculum, bilateral supplementary motor areas/middle cingulum areas, and bilateral thalamus/caudate. Following stroke, patients' patterns of chronic language abilities reflects a combination of structural and functional integrity across a distributed network of brain regions. The correlation between hemodynamic changes and behaviours may have clinical importance.

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Multi-echo fMRI: A review of applications in fMRI denoising and analysis of BOLD signals

Cited by 285 publications

References 68 publications

Integrated multi‐echo denoising strategy improves identification of inherent language laterality

Integrated multi‐echo denoising strategy improves identification of inherent language laterality

Echo planar time‐resolved imaging (EPTI)

Relating resting-state hemodynamic changes to the variable language profiles in post-stroke aphasia

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