Supplementary material figure legends:
Supplementary Figure 1: Boxplots of magnetisation transfer ratio (MTR) values in each of
the voxel layers analysed. From left to right in each plot: outer exclusion layer – partial
volume with cerebrospinal fluid, inner exclusion layer – interpolation of voxels, outermost
spinal cord voxel layer, white matter and grey matter. Box plots demonstrate these MTR
results in: (A) controls (B) clinically isolated syndrome (C) relapsing remitting multiple
sclerosis (D) secondary progressive multiple sclerosis (E) primary progressive multiple
sclerosis. The MTR values in both the outer and inner ‘exclusion’ layers (on the left of each
box plot) are seen to be lower than those of the outer spinal cord layer, consistent with
contamination with cerebrospinal fluid. These voxel layers were therefore removed and not
considered in analysis of the outermost region of the spinal cord.
Supplementary Figure 2: (A) A histogram of MTR values in the outer exclusion layer (due to
partial volume effects with cerebrospinal fluid). The variation in MTR values in this voxel
layer may be seen in the histogram itself and also by means of the variation in colour
intensities in the two displays of individual pixels (B and C).
Supplementary Figure 3: (A) A histogram display of MTR values in the inner exclusion layer
(due to interpolation of voxels). A reduction in variation of MTR values may be seen in this
image compared to Figure 2, on both the histogram and colour intensity images (B and C).
The presence of lower MTR values seen as orange pixels in (B) and (C) are due to
interpolation of voxels that were originally contained in an area heavily contaminated by
partial volume effects with cerebrospinal fluid.
Supplementary Figure 4: (A) A histogram display of the outermost voxel layer in the spinal
cord. (B) Colour intensity display of this voxel layer (C) A zoomed portion of the colour
intensity display indicated in (B). This voxel layer displays minimal variation in MTR values
following the careful removal of the two layers indicated in Figures 2 and 3.
Supplementary Figure 5: A colour intensity display of the three outer spinal cord voxel
layers, a reduction in variation in signal intensity may be seen moving from the outer
exclusion layer (due to partial volume effects with cerebrospinal fluid) to the inner exclusion
layer (due to interpolation of voxels) to the outer spinal cord voxel layer i.e. the voxel layer
chosen for analysis. A comparison of MTR values in the inner exclusion layer and outermost
voxel layer of the spinal cord did not reveal any differences greater than two standard
deviations in sections sampled on opposite sides of the spinal cord in either an anteriorposterior direction or left-right direction.
Supplementary Figure 6: Demonstrates line profile graphs through MT-off images (A and C)
and MT-on images (B and D). The large matrix size in both directions (matrix 320 x 240 with
a field of view 240 x 180 mm2) in the MTR acquisition was chosen to minimise any potential
effects of artefacts (such as Gibbs-ringing) as these are inversely proportional to the matrix
size. The line profile at the interface between the spinal cord and cerebrospinal fluid
demonstrates a clear difference in signal, without any added imaging artefacts distorting the
line profile in both the anterior/posterior and left/right directions.