The impact of post-processing on spinal cord diffusion tensor imaging.

Siawoosh Mohammadi,Thorsten Feiweier,Patrick Freund,Nikolaus Weiskopf,Armin Curt

doi:10.1016/j.neuroimage.2012.12.058

Abstract

Diffusion tensor imaging (DTI) provides information about the microstructure in the brain and spinal cord. While new neuroimaging techniques have significantly advanced the accuracy and sensitivity of DTI of the brain, the quality of spinal cord DTI data has improved less. This is in part due to the small size of the spinal cord (ca. 1 cm diameter) and more severe instrumental (e.g. eddy current) and physiological (e.g. cardiac pulsation) artefacts present in spinal cord DTI. So far, the improvements in image quality and resolution have resulted from cardiac gating and new acquisition approaches (e.g. reduced field-of-view techniques). The use of retrospective correction methods is not well established for spinal cord DTI. The aim of this paper is to develop an improved post-processing pipeline tailored for DTI data of the spinal cord with increased quality. For this purpose, we compared two eddy current and motion correction approaches using three-dimensional affine (3D-affine) and slice-wise registrations. We also introduced a new robust-tensor-fitting method that controls for whole-volume outliers. Although in general 3D-affine registration improves data quality, occasionally it can lead to misregistrations and biassed tensor estimates. The proposed robust tensor fitting reduced misregistration-related bias and yielded more reliable tensor estimates. Overall, the combination of slice-wise motion correction, eddy current correction, and robust tensor fitting yielded the best results. It increased the contrast-to-noise ratio (CNR) in FA maps by about 30% and reduced intra-subject variation in fractional anisotropy (FA) maps by 18%. The higher quality of FA maps allows for a better distinction between grey and white matter without increasing scan time and is compatible with any multi-directional DTI acquisition scheme.

Highlights

Physiological artefacts caused by bulk motion of the cord and cerebrospinal fluid (CSF) pulsation can result in slice-to-slice displacement, deformation, and signal-loss due to a shift of the echo centre in k-space (Chung et al, 2010; Mohammadi et al, 2012a; Skare and Andersson, 2001)
Using no pre-processing and ordinary least square tensor fitting resulted in poor contrast between the butterfly-shaped grey matter (GM) and surrounding white matter (WM) and localised artificial reductions of WM fractional anisotropy (FA), which can lead to a bias in the overall WM FA towards lower values
Robust tensor fitting compensated for the artificial FA reduction even if no motion and eddy current correction were employed

Summary

Introduction

More sophisticated imaging techniques such as functional (Eippert et al, 2009; Lotze et al, 2006; Sprenger et al, 2012; Wietek et al, 2008) and diffusion magnetic resonance imaging (MRI) (Agosta et al, 2007; Budde et al, 2007; Ciccarelli et al, 2007; Mulcahey et al, 2012) have become available for imaging the spinal cord. Most diagnostic studies in the spinal cord were limited by the quality and resolution of the DTI reconstruction (e.g. equal to or more than 1 mm in-plane resolution (Agosta et al, 2007; Budde et al, 2007; Ciccarelli et al, 2007; Freund et al, 2011; Mulcahey et al, 2012; Roser et al, 2010)). Physiological artefacts caused by bulk motion of the cord and cerebrospinal fluid (CSF) pulsation can result in slice-to-slice displacement, deformation, and signal-loss due to a shift of the echo centre in k-space (Chung et al, 2010; Mohammadi et al, 2012a; Skare and Andersson, 2001). Instrumental artefacts caused by eddy currents (Haselgrove and Moore, 1996; Jezzard et al, 1998; Mohammadi et al, 2010), gradient inhomogeneities (Bammer et al, 2003; Mohammadi et al, 2012d; Nagy et al, 2007), vibration artefacts (Gallichan et al, 2010; Mohammadi et al, 2012c), and RF

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