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Increased fMRI Sensitivity at Equal Data Burden Using Averaged Shifted Echo Acquisition

View Article: PubMed Central - PubMed

ABSTRACT

There is growing evidence as to the benefits of collecting BOLD fMRI data with increased sampling rates. However, many of the newly developed acquisition techniques developed to collect BOLD data with ultra-short TRs require hardware, software, and non-standard analytic pipelines that may not be accessible to all researchers. We propose to incorporate the method of shifted echo into a standard multi-slice, gradient echo EPI sequence to achieve a higher sampling rate with a TR of <1 s with acceptable spatial resolution. We further propose to incorporate temporal averaging of consecutively acquired EPI volumes to both ameliorate the reduced temporal signal-to-noise inherent in ultra-fast EPI sequences and reduce the data burden. BOLD data were collected from 11 healthy subjects performing a simple, event-related visual-motor task with four different EPI sequences: (1) reference EPI sequence with TR = 1440 ms, (2) shifted echo EPI sequence with TR = 700 ms, (3) shifted echo EPI sequence with every two consecutively acquired EPI volumes averaged and effective TR = 1400 ms, and (4) shifted echo EPI sequence with every four consecutively acquired EPI volumes averaged and effective TR = 2800 ms. Both the temporally averaged sequences exhibited increased temporal signal-to-noise over the shifted echo EPI sequence. The shifted echo sequence with every two EPI volumes averaged also had significantly increased BOLD signal change compared with the other three sequences, while the shifted echo sequence with every four EPI volumes averaged had significantly decreased BOLD signal change compared with the other three sequences. The results indicated that incorporating the method of shifted echo into a standard multi-slice EPI sequence is a viable method for achieving increased sampling rate for collecting event-related BOLD data. Further, consecutively averaging every two consecutively acquired EPI volumes significantly increased the measured BOLD signal change and the subsequently calculated activation map statistics.

No MeSH data available.


Schematic illustrating slice excitation and read-out for a typical fMRI EPI sequence (A) and a sequence incorporating a shifted-echo (B). RF, radio frequency. Gs, slice selection gradient. In the typical fMRI EPI sequence data are acquired at a long TE, forcing a long repetition time TR between consecutive RF pulses. In the shifted-echo fMRI EPI sequence, the delay time between the end of the RF excitation and the start of the read-out is used to acquire another slice, effectively reducing the TR to half the time, while maintaining the same long TE for each slice. Gradient spoiling and rephrasing is used to control the signal strength in each slice.
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Figure 1: Schematic illustrating slice excitation and read-out for a typical fMRI EPI sequence (A) and a sequence incorporating a shifted-echo (B). RF, radio frequency. Gs, slice selection gradient. In the typical fMRI EPI sequence data are acquired at a long TE, forcing a long repetition time TR between consecutive RF pulses. In the shifted-echo fMRI EPI sequence, the delay time between the end of the RF excitation and the start of the read-out is used to acquire another slice, effectively reducing the TR to half the time, while maintaining the same long TE for each slice. Gradient spoiling and rephrasing is used to control the signal strength in each slice.

Mentions: Many of these new techniques developed to acquire EPI data with a significantly increased sampling rate require hardware, software, and non-standard data processing pipelines that may not be available to all researchers. One potential and readily available method to collect BOLD-EPI data at a TR of <1 s with an acceptable spatial resolution would be to incorporate the method of shifted echo into a standard multi-slice, gradient echo EPI sequence. The concept of shifted echo is schematically depicted in Figure 1. The transverse magnetization after a slice-selective RF pulse is purposely dephased to suppress signal from that slice during the time between the RF pulse and the typical echo time for fMRI experiments at TE = 40 ms. This allows measuring another slice during that time. The magnetization can be recalled by adding proper gradients prior to each RF pulse, effectively producing an echo time that is shifted by 1 TR (Moonen et al., 1992; Chung and Duerk, 1999). Pulse sequences incorporating a shifted echo typically store the excited magnetization along the transverse axis until spoiler gradients are used to recall it at a later TR interval. The use of shifted echo sequences for the acquisition of BOLD data is not new (Liu et al., 1993a,b; Duyn et al., 1994; Moonen et al., 1994; Chung and Duerk, 1999; Gibson et al., 2006; Chang et al., 2013; Ehses et al., 2015), however, these previous studies have, for example, achieved increased sampling rates at the expense of decreased spatial resolution and/or slice coverage (Gibson et al., 2006), prioritized spatial resolution at the expense of temporal resolution (Ehses et al., 2015), or used a non-standard multi-slice EPI sequence (Liu et al., 1993a; Duyn et al., 1994; Chang et al., 2013; Ehses et al., 2015).


Increased fMRI Sensitivity at Equal Data Burden Using Averaged Shifted Echo Acquisition
Schematic illustrating slice excitation and read-out for a typical fMRI EPI sequence (A) and a sequence incorporating a shifted-echo (B). RF, radio frequency. Gs, slice selection gradient. In the typical fMRI EPI sequence data are acquired at a long TE, forcing a long repetition time TR between consecutive RF pulses. In the shifted-echo fMRI EPI sequence, the delay time between the end of the RF excitation and the start of the read-out is used to acquire another slice, effectively reducing the TR to half the time, while maintaining the same long TE for each slice. Gradient spoiling and rephrasing is used to control the signal strength in each slice.
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Related In: Results  -  Collection

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Figure 1: Schematic illustrating slice excitation and read-out for a typical fMRI EPI sequence (A) and a sequence incorporating a shifted-echo (B). RF, radio frequency. Gs, slice selection gradient. In the typical fMRI EPI sequence data are acquired at a long TE, forcing a long repetition time TR between consecutive RF pulses. In the shifted-echo fMRI EPI sequence, the delay time between the end of the RF excitation and the start of the read-out is used to acquire another slice, effectively reducing the TR to half the time, while maintaining the same long TE for each slice. Gradient spoiling and rephrasing is used to control the signal strength in each slice.
Mentions: Many of these new techniques developed to acquire EPI data with a significantly increased sampling rate require hardware, software, and non-standard data processing pipelines that may not be available to all researchers. One potential and readily available method to collect BOLD-EPI data at a TR of <1 s with an acceptable spatial resolution would be to incorporate the method of shifted echo into a standard multi-slice, gradient echo EPI sequence. The concept of shifted echo is schematically depicted in Figure 1. The transverse magnetization after a slice-selective RF pulse is purposely dephased to suppress signal from that slice during the time between the RF pulse and the typical echo time for fMRI experiments at TE = 40 ms. This allows measuring another slice during that time. The magnetization can be recalled by adding proper gradients prior to each RF pulse, effectively producing an echo time that is shifted by 1 TR (Moonen et al., 1992; Chung and Duerk, 1999). Pulse sequences incorporating a shifted echo typically store the excited magnetization along the transverse axis until spoiler gradients are used to recall it at a later TR interval. The use of shifted echo sequences for the acquisition of BOLD data is not new (Liu et al., 1993a,b; Duyn et al., 1994; Moonen et al., 1994; Chung and Duerk, 1999; Gibson et al., 2006; Chang et al., 2013; Ehses et al., 2015), however, these previous studies have, for example, achieved increased sampling rates at the expense of decreased spatial resolution and/or slice coverage (Gibson et al., 2006), prioritized spatial resolution at the expense of temporal resolution (Ehses et al., 2015), or used a non-standard multi-slice EPI sequence (Liu et al., 1993a; Duyn et al., 1994; Chang et al., 2013; Ehses et al., 2015).

View Article: PubMed Central - PubMed

ABSTRACT

There is growing evidence as to the benefits of collecting BOLD fMRI data with increased sampling rates. However, many of the newly developed acquisition techniques developed to collect BOLD data with ultra-short TRs require hardware, software, and non-standard analytic pipelines that may not be accessible to all researchers. We propose to incorporate the method of shifted echo into a standard multi-slice, gradient echo EPI sequence to achieve a higher sampling rate with a TR of &lt;1 s with acceptable spatial resolution. We further propose to incorporate temporal averaging of consecutively acquired EPI volumes to both ameliorate the reduced temporal signal-to-noise inherent in ultra-fast EPI sequences and reduce the data burden. BOLD data were collected from 11 healthy subjects performing a simple, event-related visual-motor task with four different EPI sequences: (1) reference EPI sequence with TR = 1440 ms, (2) shifted echo EPI sequence with TR = 700 ms, (3) shifted echo EPI sequence with every two consecutively acquired EPI volumes averaged and effective TR = 1400 ms, and (4) shifted echo EPI sequence with every four consecutively acquired EPI volumes averaged and effective TR = 2800 ms. Both the temporally averaged sequences exhibited increased temporal signal-to-noise over the shifted echo EPI sequence. The shifted echo sequence with every two EPI volumes averaged also had significantly increased BOLD signal change compared with the other three sequences, while the shifted echo sequence with every four EPI volumes averaged had significantly decreased BOLD signal change compared with the other three sequences. The results indicated that incorporating the method of shifted echo into a standard multi-slice EPI sequence is a viable method for achieving increased sampling rate for collecting event-related BOLD data. Further, consecutively averaging every two consecutively acquired EPI volumes significantly increased the measured BOLD signal change and the subsequently calculated activation map statistics.

No MeSH data available.