VOXEL SEGMENTATION-BASED PARTIAL VOLUME CORRECTION USING FSL: THEORY AND IMPLEMENTATION

Abstract

The use of a relatively large and straight-edged voxel to acquire spectra from rather small and curved brain structures leads to data contamination in magnetic resonance spectroscopy (MRS), known as partial volume effect (PVE). PVE arises due to the inclusion of cerebrospinal fluid (CSF) in the voxel, leading to underestimation of metabolite concentrations in quantitative MRS. Among the PVE correction techniques available, voxel segmentation to remove the CSF fraction appears to be the most reproducible and reliable method. However, there has not been a comprehensive documented procedure of this technique to guide its implementation, particularly among scientists who may be interested in brain research using quantitative MRS, but lack the skill in the implementation of PVE correction, which is one of the most important corrections of the MR spectra in quantitative MRS. This paper details the procedure for PVE correction, using an example in vivo acquired spectra. A method to deal with tilted voxel placements is also suggested. Thus, this paper may serve as a step-by-step guide to the implementation of PVE correction in single-voxel