Open-access quantitative MRI data of the spinal cord and reproducibility across

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Data quality

Overall, data quality was satisfactory based on qualitative visual inspection. Criteria included the correctness of field of view prescription, proper selection of receive coils, quality of shimming (assessed by looking at fat saturation performance and the presence of susceptibility distortions), and the presence and severity of motion artifacts. Figure 3 shows examples of good quality data for all sequences. A few operator errors occurred, including: mis-labeled MT0 for MT1 and MT1 for MT0, shim parameters changed between MT0 and MT1 scans (causing different signal intensities, and hence not suitable for MT-based metrics), change of FFT scaling factor between the MT1/MT0 scans and the T1w scan used to compute MTsat and T1 maps (causing different signal quantization and hence not suitable for MT-based metrics unless corrected for), and repositioning of the participants, causing mis-alignment between the images before/after repositioning and violation of the analysis pipeline assumptions (all images are supposed to be acquired with the patient in the same position). These errors were not caught by the BIDS validator, but by the managing team during visual inspection of the data and interpretation of the qMRI metrics results. In future work, the data validator could be made sensitive to these issues. For example, the FFT scaling factor and shim coefficient are sometimes retrievable from the DICOM data and could be checked. Also, the qform (affine matrix present in the NIfTI header) could be checked to ensure consistency across data from the same series, e.g. MT1, MT0, GRE-T1w. Regarding the mis-labeling of MT1/MT0, training a deep learning model to recognize image contrast could address this issue.

Fig. 3
figure3

Axial views of good quality data for all sequences in the spine generic protocol across various slices (the exact coverage along the SC varies because the slice thickness varies across sequences). DWI corresponds to the mean DWI data after motion correction. The images are from different participants. T1w: vuiisAchieva02; T2w: milan01; T2*w (ME-GRE): brnoCeitec01; MT0, MT1, T1w (for the MTS protocol) and DWI : barcelona04. Axial views were automatically generated by SCT’s QC report.

Figure 4 illustrates some of the image artifacts encountered during QC. A list of poor data quality scans is available on the Github’s issues of the dataset under the label “data-quality” (https://github.com/spine-generic/data-multi-subject/labels/data-quality); most of these were caused by patient motion. Mosaics of images for every contrast and every participant are available in the supplementary materials (Figures S1S5). Additional examples of good quality data are also available in the spine generic website (https://spine-generic.rtfd.io/en/latest/data-acquisition.html#example-of-datasets).

Fig. 4
figure4

Axial views of good quality data for all sequences in the spine generic protocol across various slices (the exact coverage along the SC varies because the slice thickness varies across sequences). DWI corresponds to the mean DWI data after motion correction. The images are from different participants. T1w: vuiisAchieva02; T2w: milan01; T2*w (ME-GRE): brnoCeitec01; MT0, MT1, T1w (for the MTS protocol) and DWI : barcelona04. Axial views were automatically generated by SCT’s QC report.

Quantitative results: Single subject

Overall, data quality was satisfactory. All images were visually inspected to ensure that there were no significant errors in the masks used to average the signals in the SC, WM or GM, and any errors were manually corrected. A list of poor quality scans is available on Github in the issues for the dataset, under the label “data-quality” (https://github.com/spine-generic/data-single-subject/labels/data-quality). Complete metrics and statistical tests are available in the r20201130 release assets (https://github.com/spine-generic/data-single-subject/releases/download/r20201130/results.zip).

Figure 5 shows the SC CSA data from the T1w scan, averaged between cervical levels 2 and 3 (C2 and C3), for the single participant across the 19 centers. Within each manufacturer, the inter-site standard deviation ranges from 0.65 mm2 (Siemens) to 1.56 mm2 (GE), which is remarkably small considering that the size of a pixel is 1 mm2. The inter-site COVs were 2.3% for GE, 1.8% for Philips and 0.9% for Siemens. The inter-manufacturer difference was significant (p < 0.01), with the Tukey test showing significant differences between GE and Philips (p-adjusted = 0.03) and between GE and Siemens (p-adjusted < 0.01).

Fig. 5
figure5

Results of the single subject study for the T1w scan. The cross-sectional area (CSA) of the SC was averaged between the C2 and C3 vertebral levels. Sites tokyoSigna2 and oxfordFmrib were excluded from the statistics due to excessive motion.

Figure 6 shows the SC CSA for the T2w scan, again averaged between cervical levels 2 and 3 (C2 and C3). The inter-site COVs were 2.3% for GE, 2.1% for Philips and 1.5% for Siemens. The inter-manufacturer difference was significant (p < 0.01), with the Tukey test showing significant differences between Philips and Siemens (p-adjusted < 0.01).

Fig. 6
figure6

Results of the single subject study for the T2w scan. The cross-sectional area (CSA) of the SC was averaged between the C2 and C3 vertebral levels.

Figure 7 shows the gray matter CSA for the ME-GRE scan, averaged between cervical levels C3 and C4. The inter-site COVs were 2.5% for GE, 3.4% for Philips and 3.4% for Siemens. The inter-manufacturer difference was significant (p < 0.01), with the Tukey test showing significant differences between GE and Philips (p-adjusted < 0.01) and between Philips and Siemens (p-adjusted < 0.01).

Fig. 7
figure7

Results of the single subject study for the ME-GRE scan. Gray matter CSA was computed after automatic gray matter segmentation and averaged between C3 and C4 vertebral levels.

Figure 8a shows the MTR average for the WM between C2 and C5. The inter-site COVs were 8.0% for GE, 4.2% for Philips and 3.6% for Siemens. The inter-manufacturer difference was significant (p < 0.01), but the Tukey test showed no significant difference across pairwised manufacturers.

Fig. 8
figure8

Results of the single subject study for the MT protocol. The mean MTR (a) and MTsat (b) were computed in the white matter between C2 and C5. Sites perform and juntendo750w were excluded from the statistics because the TR for the GRE-MT0 and GRE-MT1 was set to 62 ms (vs. 35ms for the other GE sites), causing drastic decrease of MTR values. These sites were not excluded from MTsat.

Figure 8b shows the MTsat results. The inter-site COVs were 11.3% for GE, 2.9% for Philips and 5.2% for Siemens. The inter-manufacturer difference was significant (p < 0.01), with the Tukey test showing significant differences between GE and Philips (p-adjusted = 0.03), between GE and Siemens (p-adjusted < 0.01), and between Philips and Siemens (p-adjusted < 0.01).

Sites perform and juntendo750w were excluded from the MTR statistics because the TR for the GRE-MT0 and GRE-MT1 was set to 62 ms (vs. 35 ms for the other GE sites), causing a drastic decrease in MTR values. These sites were not excluded from MTsat, because this metric is supposed to account for the T1 recovery effect12 as was indeed observed, with those sites now falling inside the 1σ interval. The site tokyoSigna1 fell outside the 1σ interval because of issues related to image registration.

Figure 9 shows the average fractional anisotropy (FA) in WM across C2 and C5. The inter-site COVs were 0.8% for GE, 4.5% for Philips and 2.8% for Siemens. The inter-manufacturer difference was significant (p < 0.01), but the Tukey test showed no significant difference across pairwised manufacturers. One of the outliers (tokyo750w) was due to the absence of the FOCUS license, which led us to rely on saturation bands to prevent aliasing. However, those were not efficient (likely due to poor shimming in the region), with poor fat saturation efficiency that yielded spurious diffusion tensor fits (e.g. FA >1 or <0).

Fig. 9
figure9

Results of the single subject study for the DWI protocol. The FA in the SC WM was averaged between the C2 and C5 vertebral levels. The following sites were excluded: perform (strong fat aliasing artifact), tokyo750w (poor shimming) and juntendoAchieva (no cardiac gating).

Average +/− standard deviation (SD) and COVs for mean diffusivity were, respectively, (0.62…

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