From Brooks JC, Davies WE, Pickering AE. Resolving the Brainstem Contributions to Attentional Analgesia. J Neurosci. 2017;37(9):2279-2291. doi:10.1523/JNEUROSCI.2193-16.2016 *Data acquisition*. Imaging was performed with a 3T Skyra MR system (Siemens Medical Solutions) and 32-channel receive-only head coil. Subjects were instructed to remain as still as possible during scanning, and head motion minimized by placing memory foam padding beside their head. Following acquisition of 3-plane localizer images, T1- and T2-weighted structural scans were acquired for the purpose of spatial normalization and brainstem atlas development, respectively. A sagittal T1-weighted volume scan was acquired with MPRAGE pulse sequence with the following parameters: TE/TI/TR = 2.25/800/1900 ms, flip angle = 9°, averages = 2, GRAPPA acceleration factor = 2, resolution 0.94 × 0.94 × 0.9 mm, and a sagittal T2-weighted volume scan with SPACE (Sampling Perfection with Application optimized Contrasts using different flip angle Evolution) pulse sequence with the following parameters: TE/TI/TR = 388/1800/5000 ms, variable flip angle, GRAPPA acceleration factor = 2, resolution 0.45 × 0.45 × 0.9 mm. The T2-weighted sagittal volume scan was prescribed with its y-axis (i.e., superior-inferior) parallel to the floor of the fourth ventricle. *Data analysis* To aid identification of brainstem nuclei, a gray matter probability map was constructed using the DARTEL (Diffeomorphic Anatomical Registration Through Exponentiated Lie algebra) spatial normalization technique available in SPM8 (Ashburner, 2007) running in MATLAB R2015a software (The MathWorks). Briefly, T2-weighted volumetric data were segmented using the VBM8 toolbox (http://dbm.neuro.uni-jena.de/vbm8) into gray, white, CSF, and other tissue types, and the segmented gray matter maps registered to one another using the DARTEL algorithm. The final result is a probabilistic template specific to the study group, which was then transformed into the space of the MNI atlas. With the threshold for the probabilistic map set at p = 0.7 (i.e., at least 70% gray matter), masks were defined for the PAG, RVM, and LC taking advantage of the inherent high contrast between the gray and white matter structures of the brainstem (see Fig. 2). These were validated with reference to anatomical sections on a human brainstem atlas (Naidich et al., 2009).