  BACKGROUND: Functional Magnetic Resonance Imaging (fMRI) is based on the
Blood Oxygenation Level Dependent contrast and has been exploited for the
indirect study of the neuronal activity within both the brain and the spinal
cord. However, the interpretation of spinal cord fMRI (scfMRI) is still
controversial and its diffusion is rather limited because of technical
limitations. Overcoming these limitations would have a beneficial effect for
the assessment and follow-up of spinal injuries and neurodegenerative diseases.
PURPOSE: This study was aimed at systematically verify whether sagittal
scanning in scfMRI using EPI readout is a viable alternative to the more common
axial scanning, and at optimizing a pipeline for EPI-based scfMRI data
analysis, based on Spinal Cord Toolbox (SCT). METHODS: Forty-five healthy
subjects underwent MRI acquisition in a Philips Achieva 3T MRI scanner.
T2*-weighted fMRI data were acquired using a GE-EPI sequence along sagittal and
axial planes during an isometric motor task. Differences on benchmarks were
assessed via paired two-sample t-test at p=0.05. RESULTS: We investigated the
impact of the acquisition strategy by means of various metrics such as Temporal
Signal to Noise Ratio (tSNR), Dice Coefficient to assess geometric distortions,
Reproducibility and Sensitivity. tSNR was higher in axial than in sagittal
scans, as well as reproducibility within the whole cord mask (t=7.4, p<0.01)
and within the GM mask (t=4.2, p<0.01). The other benchmarks, associated with
distortion and functional response, showed no difference between images
obtained along the axial and sagittal planes. CONCLUSIONS: Quantitative metrics
of data quality suggest that axial scanning would be the optimal choice. We
conclude that axial acquisition is advantageous specially to mitigate the
effects of physiological noise and to minimize inter-subject variance.
