Fig 1.
Pictorial view of the of the data processing pipeline.
Schematics of the data processing pipeline illustrating the main steps and related toolbox used (SCT or SPM). PhysLogs: physiological log files.
Fig 2.
a) Maps of the tSNR averaged across subjects in the PAM50 space, at levels from C1 to T2. The maps are overlaid on a standard anatomical template. b) tSNR averaged within the spinal cord at vertebral levels from C1 to T2 for images acquired on axial (red) or sagittal (blue) planes. Data are mean and standard error of the mean across subjects. Significant differences are calculated via two-sample paired t-test and shown as * if p ≤ 0.05, and ** if p < 0.001.
Fig 3.
The degree of overlap between spinal cord masks obtained from T1-weighted and EPI scans in a representative subject.
Masks of the spinal cord of a representative subject for axial (red, left) and sagittal planes (blue, center). Overlap (right) is highlighted in purple. The relevant T1 mask, assumed as undistorted reference, is white. Average DSC was 0.43 ± 0.08 for acquisition on the axial plane and 0.44 ± 0.06 for acquisition on the sagittal plane. DSC difference was not significant (t = 0.8, p > 0.4) between scan planes. Beyond distortion, EPI masks have a generally smaller cross-sectional area because EPI masking was performed aggressively to minimize contamination by CSF.
Fig 4.
Reproducibility assessment using inter-subject correlation of unthresholded t maps in spinal cord and central gray matter.
Reproducibility assessed as inter-subject correlation matrices of unthresholded t maps in spinal cord cord (A), including gray matter (GM) and surrounding white matter, and in central gray matter (B). From the inter-subject correlation matrices, the frequency of Pearson’s correlation coefficient values was calculated and displayed in the figure (red: axial, blue: sagittal).
Fig 5.
BOLD response maps and rostrocaudal distribution across axial and sagittal acquisitions in the spinal cord.
A) Maps of the positive functional contrast (BOLD response) at levels C3-C7 in axial (left) and sagittal (right) acquisition (t = 2.4, p > 0.01). B) BOLD response (top 33% most responding voxels) averaged at different rostrocaudal levels, in PAM50 space. The response is expressed as percent of the baseline. The approximate position of the center of each spinal segment is marked on the horizontal axis. The amplitude of BOLD in most responding voxels in axial and sagittal acquisition is mostly overlapped at each spinal level.
Fig 6.
False Discovery Rate estimation as a function of threshold p-value for axial and sagittal acquisitions.
False Discovery Rate was estimated assuming that the fraction of active voxels in WM is repetitive of the fraction of False Positives in gray matter (GM) and displayed as a function of threshold p-value, for images acquired on axial (red) and sagittal (blue) planes.