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TR-external EPI phase correction to reduce the required minimum TE in EPI

9th March 2020

Seong Dae Yun, N. Jon Shah

Functional magnetic resonance imaging (fMRI) is a non-invasive technique used to measure cerebral blood flow and neuronal activation in the brain and is particularly useful for understanding how the brain works both in health and disease.

A number of different techniques can be used to obtain fMRI images, but echo-planar imaging (EPI) is the most widely used due to its speed. However, it is rather vulnerable to magnetic field inhomogineities and its application often results in ghost artefacts. It is possible to correct for these artefacts using three navigator echoes, and although this scheme is effective, as the matrix size increases for high-resolution imaging, the navigator echoes can significantly contribute to increasing the required minimum echo time (TE).

To overcome this issue, the work carried out in this study proposes the use of an alternative navigator echo scheme called the “TR-external” scheme. For a given matrix size (288 × 288), the TR-external scheme allows a substantially shorter TE (5.94 ms). In the context of fMRI measurements at 3T with a desired TE of 35 ms this enables submillimetre-resolution (0.73 × 0.73 mm2). The fMRI results show that activated voxels are well localised along the cortical ribbon (see the figure below).

First level analysis results of submillimeter-resolution (0.73x0.73mm2) fMRI

This figure shows first-level analysis results of submillimeter-resolution (0.73 × 0.73 mm2) fMRI. Activated voxels overlaid on the preprocessed EPI scans; three representative slices were chosen out of the entire slice set (1) and time course data were examined at the voxel ([x, y, z] = [15.22, −94.48, 5.90]),showing the maximum t-score (9.69) (2). Its signal behaviour shows clear hemodynamic response changes according to the designed baseline and activation blocks

Original publication:

Analysis of EPI phase correction with low flip-angle excitation to reduce the required minimum TE: Application to whole-brain, submillimeter-resolution fMRI at 3 T


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