Dual-echo EPI for non-equilibrium fMRI — Implications of different echo combinations and masking procedures

Beißner, Florian; Baudrexel, Simon; Volz, Steffen; Deichmann, Ralf

doi:10.1016/j.neuroimage.2010.04.243

Cited by 16 publications

(23 citation statements)

References 24 publications

(31 reference statements)

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“…Another technically more demanding possibility is cardiac gating, that is, triggering the fMRI acquisition by the pulse [25] and, thus, reducing cardiogenic physiological noise. However, cardiac gating has a number of serious drawbacks that need to be taken into account: First, it does not remove physiological noise related to respiration, second, the varying effective repetition time leads to T1 fluctuations that have to be removed before analyzing the data [26], and third, it requires special magnetic resonance (MR) sequences that may not be widely available.…”

Section: Possible Solutionsmentioning

confidence: 99%

Functional MRI of the Brainstem: Common Problems and their Solutions

Beißner

2015

Clin Neuroradiol

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Functional magnetic resonance imaging (fMRI) of the brainstem is a relatively young field that is rapidly evolving. While it is still difficult to obtain usable fMRI signals from this complicated brain region, the past few years have seen a number of important advances that bring us closer to routine application of this method in the clinical and scientific setting. This review gives an overview of the technical capabilities and limitations of brainstem fMRI. It explains the major brainstem-specific problems and gives advice on how to avoid or counteract them. In particular, I discuss how spatial resolution issues can be overcome by using appropriate sequences, coils, and spatial preprocessing, how the effects of physiological noise can be mitigated by noise modeling and spatial masking, and how the functional heterogeneity of brainstem nuclei needs to be taken into account, when planning a study. Solving these common problems is a prerequisite for any scientist or clinician interested in applying fMRI to measure brainstem activity.

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Section: Possible Solutionsmentioning

confidence: 99%

Functional MRI of the Brainstem: Common Problems and their Solutions

Beißner

2015

Clin Neuroradiol

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“…Consequently, this part of the experiment was excluded from the data analysis as described in this paper. However, it should be noted that activations induced by swallowing can be measured by using dual echo EPI and that this particular part of the study was presented recently (Beissner et al, 2010).…”

Section: Experimental Paradigmmentioning

confidence: 99%

“…A home-written single-shot dualecho EPI sequence (Beissner et al, 2010) was gated to the subject's pulse as measured by a photopletysmograph situated on the index finger. The parameters were: FOV: 192 × 192 mm 2 , matrix size: 64 × 64, in-plane resolution 3 × 3 mm 2 , slice thickness: 2.5 mm, interslice gap: 1.25 mm, effective spatial resolution in slice direction: 3.75 mm, 40 slices for whole brain coverage including the lower brainstem.…”

Section: Fmri Imaging Parametersmentioning

confidence: 99%

“…As shown in a recent paper (Beissner et al, 2010), there are mainly two ways of applying spatial smoothing to dual-echo EPI images, either by smoothing image data before calculating the T 2 * maps, or by smoothing the resulting T 2 * maps. The second way requires an additional joint masking procedure to remove outlier values induced by small denominators in the quotient formation according to Eq.…”

Section: Data Processing 2: Smoothingmentioning

confidence: 99%

“…In particular, one study has exploited the potential of this technique for cardiac-gated fMRI measurements of brainstem activity (Zhang et al, 2006). It has been shown recently that different methods of combining the information from the two echoes may have a significant impact on the activation results obtained with dual-echo EPI (Beissner et al, 2010). A direct calculation of T 2 * was found to be superior to simply calculating the quotient of the images acquired at different echo times (TE).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

fMRI of the brainstem using dual-echo EPI

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On the impact of physiological noise in spinal cord functional MRI

Fratini

Moraschi

Maraviglia

et al. 2013

Magnetic Resonance Imaging

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Functional magnetic resonance imaging (fMRI) techniques are widely exploited for the study of brain activation. In recent years, similar approaches have been attempted for the study of spinal cord function; however, obtaining good functional images of spinal cord still represents a technical and scientific challenge. Some of the main limiting factors can be classified under the broad category of "physiological noise," and are related to 1) the cerebrospinal fluid (CSF) flux in the subarachnoid space surrounding the spinal cord; 2) the cord motion itself; and 3) the small area of the cord, which makes it critical to have a high image resolution. In addition, the different magnetic susceptibility properties of tissues surrounding the spinal cord reduce the local homogeneity of the static magnetic field, causing image distortion, reduction of the effective resolution, and signal loss, all effects that are modulated by motion. For these reasons, a number of methods have been developed for the purpose of denoising spinal cord fMRI time series. In this work, after a short introduction on the relevant features of the spinal cord anatomy, we review the main sources of physiological noise in spinal cord fMRI and discuss the main approaches useful for its mitigation.

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Dual-echo EPI for non-equilibrium fMRI — Implications of different echo combinations and masking procedures

Cited by 16 publications

References 24 publications

Functional MRI of the Brainstem: Common Problems and their Solutions

Functional MRI of the Brainstem: Common Problems and their Solutions

fMRI of the brainstem using dual-echo EPI

On the impact of physiological noise in spinal cord functional MRI

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