Appendix e-1: Magnetic resonance imaging data acquisition
The magnetic resonance imaging (MRI) scans were acquired on a 3.0 T Philips Achieva
whole body scanner (Philips Medical System, Best, The Netherlands) equipped with a
transmit-receive body coil and a commercial eight element sensitivity encoding (SENSE)
head coil array. Two volumetric 3D T1-weighted gradient echo sequence scans were
obtained with a measured spatial resolution of 0.94 x 0.94 x 1 mm (acquisition matrix
256 x 256 pixel, 160 slices). Further imaging parameters were: Field of view FOV = 240 x
240 mm, echo-time TE = 3.7 ms, repetition-time TR = 8.06 ms, flip-angle = 8, SENSE
factor R = 2.1.
Diffusion-weighted spin echo echo-planar (EPI) sequence scans were obtained with a
measured spatial resolution of 2.0 x 2.0 x 2.0 mm (acquisition matrix 112 x 112 pixels,
75 slices). Further imaging parameters were: Field of View FOV: 224 x 224 mm, echo-
time TE = 55 ms, repetition-time TR = 13.006 ms, flip-angle FA = 90, SENSE factor R =
2.1. Diffusion was measured in 32 non-collinear directions preceded by a non-diffusion-
weighted volume (reference volume). The b-value was 1.000 s/mm2.
This method is based on high-resolution 3D MRI scans, registered into a common
surface-based space, and is designed to find significant regional differences in cortical
thickness with submillimeter precision. The technical details of these procedures are
described in prior publications (e1-e12). A longitudinal preprocessing approach was
applied, which has been previously described by (e13, e14). Because of our a priori
hypotheses, we applied for each hemisphere a region of interest (ROI) comprising the
primary motor and somatosensory cortex. This ROI contained all vertices, which are
located within one of the following labels (e15) in FreeSurfer: postcentral sulcus, central
sulcus, precentral gyrus, postcentral gyrus (Figure e-1). Cortical thickness was
measured at each vertex. Procedures for the measurement of cortical thickness have
been validated against histological analysis (e16) and manual measurements (e17, e18).
In order to detect regional differences in cortical thickness between the two time points,
we performed a longitudinal cortical thickness analysis using vertex-wise paired t-tests
with a resel based correction for multiple comparisons (e19, e20). The resel-based
correction considers the spatial smoothness of the data (FWHM = 12 mm), which
reduces and determines the effective number of independent statistical tests. For an
extensive discussion of this method refer to (e19, e20).
Appendix e-2: Fiber tractography and analysis of fractional anisotropy
Fiber tractography was done with the Diffusion Toolkit 0.5 and TrackVis 0.5.1 (e21)
(www.trackvis.org). The preprocessed data from FSL were inserted into the Diffusion
Toolkit. The diffusion tensors for each subject were estimated according to the corrected
gradients. The fiber assignment by continuous tracking (FACT) with the “brute-force”
method was employed (e22, e23). This is an automatic procedure to reconstruct fiber
across the entire white matter by tracking fibers form each voxel in the brain.
Subsequently, fibers were reconstructed by TrackVis, assuming that in each voxel, the
eigenvector associated with the largest eigenvalue of the diagonalized diffusion tensor
represents the orientation of the dominant fiber bundles (e24).
Fiber tracking was performed in each subjects’ native space and terminated when FA
was lower than 0.2 or a trajectory angle between two consecutive voxels was greater
than 45° (e24). The individual color-coded FA maps served for region-of-interest (ROI)
placing in TrackVis. ROI’s were drawn large-sized to include the entire corticospinal
tract (e25) (see also Figure 3A). Analogue to other studies obtaining the corticospinal
tract (e26-e28), the fiber tracts were obtained through a two-ROI approach (seed ROI
and target ROI) with logical AND concatenation (e29, e30) of the two ROIs, such that
only fibers that passed both ROI’s were included in the reconstructed fiber tracts. The
seed ROI was placed around the corona radiata in the axial section according to (e26-
e28). The target ROI was placed in the anterior part of the brainstem, typically located in
the axial view. The reconstruction of the fiber tracts was randomly performed either
first in the left or in the right hemisphere in each subject. Two investigators (NL and JH)
conducted tractography blinded to the subjects and to the time point of examination.
The second investigator reconstructed all tracts for all subjects. Mean FA values
obtained by the first investigator were employed for statistical analysis. Inter-rater
reliability was established by an interclass correlation coefficient. The interclass
correlation coefficient of mean FA values generated by the two observers for all
corticospinal tracts by the two observers were r = 0.88.
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