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BACKGROUND: Functional Magnetic Resonance Imaging (fMRI) is based on theBlood Oxygenation Level Dependent contrast and has been exploited for theindirect study of the neuronal activity within both the brain and the spinalcord. However, the interpretation of spinal cord fMRI (scfMRI) is stillcontroversial and its diffusion is rather limited because of technicallimitations. Overcoming these limitations would have a beneficial effect forthe assessment and follow-up of spinal injuries and neurodegenerative diseases.PURPOSE: This study was aimed at systematically verify whether sagittalscanning in scfMRI using EPI readout is a viable alternative to the more commonaxial scanning, and at optimizing a pipeline for EPI-based scfMRI dataanalysis, based on Spinal Cord Toolbox (SCT). METHODS: Forty-five healthysubjects underwent MRI acquisition in a Philips Achieva 3T MRI scanner.T2*-weighted fMRI data were acquired using a GE-EPI sequence along sagittal andaxial planes during an isometric motor task. Differences on benchmarks wereassessed via paired two-sample t-test at p=0.05. RESULTS: We investigated theimpact of the acquisition strategy by means of various metrics such as TemporalSignal to Noise Ratio (tSNR), Dice Coefficient to assess geometric distortions,Reproducibility and Sensitivity. tSNR was higher in axial than in sagittalscans, 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 withdistortion and functional response, showed no difference between imagesobtained along the axial and sagittal planes. CONCLUSIONS: Quantitative metricsof data quality suggest that axial scanning would be the optimal choice. Weconclude that axial acquisition is advantageous specially to mitigate theeffects of physiological noise and to minimize inter-subject variance.

Influence of scanning plane on Human Spinal Cord functional Magnetic Resonance echo planar imaging