Pre-processing of Sub-millimeter GE-BOLD fMRI Data for Laminar Applications

Patricia Pais-Roldán; Seong Dae Yun; N Jon Shah

doi:10.3389/fnimg.2022.869454

Pre-processing of Sub-millimeter GE-BOLD fMRI Data for Laminar Applications

Front Neuroimaging. 2022 May 4:1:869454. doi: 10.3389/fnimg.2022.869454. eCollection 2022.

Authors

Patricia Pais-Roldán¹, Seong Dae Yun¹, N Jon Shah^{1

2

3

4}

Affiliations

¹ Institute of Neuroscience and Medicine 4, Medical Imaging Physics, Forschungszentrum Jülich, Jülich, Germany.
² Institute of Neuroscience and Medicine 11, Molecular Neuroscience and Neuroimaging, Jülich Aachen Research Alliance, Forschungszentrum Jülich, Jülich, Germany.
³ Jlich Aachen Research Alliance, Brain - Translational Medicine, Aachen, Germany.
⁴ Department of Neurology, Rheinisch-Westfälische Technische Hochschule Aachen University, Aachen, Germany.

Abstract

Over the past 30 years, brain function has primarily been evaluated non-invasively using functional magnetic resonance imaging (fMRI) with gradient-echo (GE) sequences to measure blood-oxygen-level-dependent (BOLD) signals. Despite the multiple advantages of GE sequences, e.g., higher signal-to-noise ratio, faster acquisitions, etc., their relatively inferior spatial localization compromises the routine use of GE-BOLD in laminar applications. Here, in an attempt to rescue the benefits of GE sequences, we evaluated the effect of existing pre-processing methods on the spatial localization of signals obtained with EPIK, a GE sequence that affords voxel volumes of 0.25 mm³ with near whole-brain coverage. The methods assessed here apply to both task and resting-state fMRI data assuming the availability of reconstructed magnitude and phase images.

Keywords: brain imaging; data cleanup; gradient-echo functional MRI; noise; spatial specificity.