136 Chapter 5 directions with b = 1000 s/mm2and one unweighted b = 0 s/mm2 image, each. Acquisition time was 6.2 min for T1-weighted scans and 5.9 min for each DTI scan. One experienced reviewer (JKG), blinded to the scan identity, inspected the unprocessed T1-weigthed and DTI scans and processing steps as mentioned hereafter. Subcortical segmentations, cortical parcellations and the registration of ROIs to DTI subject space were additionally manually corrected if needed. T1-weighted image processing After visual examination of the T1-weighted images for artefacts and macroscopic brain abnormalities, the intensity was normalized and Freesurfer’s MRI analysis software package (v5.3.0 Developmental) was used to automatically generate subcortical segmentations and cortical parcellations [218, 219]. ROIs were determined a priori on the basis of previously reported neuroimaging results (Appendix A, Supplementary Table 1) and included regions likely related to narcolepsy complaints. All regions were part of the sleep-wake regulation, limbic or reward system and consisted of the hypothalamus, ventral diencephalon, thalamus, midbrain, amygdala, parahippocampal, anterior cingulate (merged rostral and caudal anterior cingulate WM), medial and lateral orbitofrontal WM. The hypothalamus was manually segmented in both hemispheres using standardized criteria [220]. The anterior boundary of the hypothalamus consisted of the first coronal slice posterior of where the anterior commissure became discontinuous. Posteriorly, the last slice was where the mammillary bodies (included) diverted one another in the mid-sagittal plane. The hypothalamus inferiorly ended where the optic chiasm and infundibular stalk began and the anterior–posterior commissure plane was used for the superior delineation, which in itself was not included. Laterally, the segmentation was limited by WM of the internal capsule. Hypothalamus segmentation was blindly performed, twice for every subject. Corresponding maps were visually compared and combined to form the eventual segmentation. Diffusion tensor image processing After automatic brain extraction [221], DTI scans were corrected for susceptibility-, eddy current- and subject movement-induced distortions with the FMRIB Software Library’s (FSL, v5.0) topup and eddy tools [222, 223]. Calculated off-resonance field maps were applied and ‘dropout-slices’ were
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