DOI: 10.6084/m9.figshare.13176860.v1
title: FMRI data sets spanning the brain, brainstem, and spinal cord, from two pain studies of healthy females

description: <b>Summary</b>Data sets are from healthy women, from two studies, and are separated into four folders containing fMRI data from the brain (Brain1 and Brain2) and from the brainstem and cervical spinal cord (BSSC1 and BSSC2). The data have already been pre-processed by converting to NIfTI format, and applying co-registration, slice-timing correction, spatial normalization, and physiological noise removal, as detailed below. Each folder contains participant information in terms of the stimulation temperature and pain rating for each fMRI run, and the age of each participant.<b><br></b><b>Details</b> Functional MRI data sets are included from the healthy control groups in two previous studies of pain processing in women, conducted between 2013-2014 (referred to as ‘Study 1’), and between 2018-2019 (referred to as ‘Study 2’). Full details of the methods used for Study 1 have been previously published (11). All participants were free of previous neurological injury or disease, and were free of any contraindications for MRI. Both studies involved noxious hot stimulation of the right hand, with temperatures that were calibrated to elicit moderate pain. Also, both studies involved two sessions, one for brain fMRI, and the other for fMRI of the brainstem and cervical spinal cord. All methods were reviewed and approved by our institutional research ethics board. Study 1 consists of data from 15 females (age range = 21-55, average 39.1 ± 10.2 years (mean ± std)). Study 2 consists of data from 18 females (age range = 21-59, average 36 ± 11.3 years). Multiple fMRI runs were acquired from each participant. Participants in both studies were characterized by completing questionnaires to assess anxiety, depression, pain catastrophizing, social desirability, and health-related factors. Prior to fMRI data collection, each participant underwent a 1-hour training session, during which they were introduced to the experimental pain stimulus and study design, and were trained how to rate their pain using a standardized numerical pain intensity scale (NPS). The scale ranges from 0 to 100 in increments of 5, with verbal descriptors at increments of 10 (11, 43). In both studies, the stimulus consisted of heat applied briefly to the skin overlying the thenar eminence (base of the thumb) on the right hand. The stimulus devices, temperatures, and timings, were different for the two studies, as detailed below. Study 1 Heat stimuli were applied to the hand by means of an MRI-compatible Peltier thermode (Medoc, Ramat Yishai, Israel), which was attached to the participant’s right hand. During heat stimulation, the temperature was rapidly increased and decreased under computer control. Stimulation consisted of 11 heat spikes applied every 3 seconds in order to evoke temporal summation of second pain (TSSP). The stimulation period was preceded by a 52 second rest period and followed by a 65 second rest period. Participants viewed instructions on a rear-projection screen which notified them when a new scan was about to begin, when the application of the heat stimulus would begin, and when to report their ratings for the first and last heat contacts. Study 2 Heat stimuli were applied by means of an MRI-compatible Robotic Contact-Heat Thermal Heat Stimulator (RTS-2) which pneumatically raises and lowers a heated aluminum thermode to make contact with the participants’ skin, with software-controlled timing and temperature. The stimulation paradigm consisted of an initial 60 seconds of “baseline” scanning. This is one condition which was randomly interleaved with a condition without stimulation. Participants were then informed that stimulation would begin 1 minute later, at the 120 second mark, and then 10 heat contacts at the calibrated temperature were administered over 30 seconds. This 30 second stimulation period was followed by a 120 second rest period, for a total time of 4 minutes and 30 seconds. <br> All image data were acquired using a 3 tesla whole-body MRI system (Siemens Magnetom Trio; Siemens, Erlangen, Germany). For all studies, participants were positioned supine and were supported by foam padding as needed to ensure comfort and minimize bulk body movement. Imaging methods were optimized for each region (brain, or BS/SC), due to the different imaging challenges, and were acquired with T2*-weighted imaging in the brain, and T2-weighted imaging in the brainstem and spinal cord, in order to provide an optimal balance of image quality and BOLD sensitivity in both regions (31, 44, 45). Study 1 Brain fMRI Functional images were acquired in 49 contiguous axial slices oriented parallel to the anterior commissure-posterior commissure (AC-PC) line using a T2*-weighted gradient-echo echo-planar imaging (GE-EPI) sequence (TR = 3 s, TE = 30 ms, Flip Angle = 90°, FOV = 192 mm x 192 mm, Matrix = 64 x 64, Resolution = 3 x 3 x 3 mm3). A 12-channel head coil was used for detection of the MRI signal, with a body coil for transmission of RF pulses. A total of 50 volumes were acquired for each imaging run. Five runs of the same type were combined for each fMRI data set. Study 2 Brain fMRI Functional images were acquired in 66 contiguous axial slices using a T2*-weighted GE-EPI sequence (TR = 2 s, TE = 30 ms, Flip Angle = 84°, Multiband = 3, 7/8 Partial Fourier, FOV = 180 mm x 180 mm, Matrix = 90 x 90, Resolution = 2 x 2 x 2 mm3). A 32-channel head coil was used for detection of the MR signal, with a body coil for transmission of RF pulses. A total of 135 volumes were acquired for each imaging run. Three to five runs of the same type were combined for each fMRI data set. Study 1 and Study 2, Brainstem and Spinal Cord fMRI Functional MRI data were acquired with a T2-weighted half-fourier single-shot fast spin-echo (HASTE) sequence. Data were acquired in 9 contiguous sagittal slices with a repetition time (TR) of 0.75 sec/slice, an echo time of 76 msec to optimize the T2-weighted BOLD sensitivity, and a 28 × 21 cm field-of-view with 1.5 × 1.5 × 2 mm3 resolution (45). The imaging volume spanned from the T1 vertebra to above the thalamus, and spanned the entire cervical spinal cord and brainstem left-to-right. Data were acquired using the upper elements of a spine receiver-array coil, a posterior neck coil, and the posterior half of a 12-channel head coil. The receiver elements were adjusted based on the participant’s size, as needed. A body coil was used for transmitting radio-frequency (RF) excitation pulses. In Study 1, a total of 138 volumes were acquired for each condition (over 6 repeated runs). In Study 2, a total of 200 volumes were acquired for each condition (over 5 repeated runs). The image quality was enhanced by means of spatial suppression pulses anterior to the spine to reduce motion artefacts caused by breathing, swallowing, etc, and motion compensating gradients in the head-foot direction.<br>Data were pre-processed in MATLAB using SPM12 for brain data (available at https://www.fil.ion.ucl.ac.uk/spm/software/spm12/ ), and SpinalfMRI9 for brainstem and spinal cord data (available at https://www.queensu.ca/academia/stromanlab/home/fmri-analysis-software ).Data were converted to NIfTI format and pre-processed, including co-registration (i.e. motion correction), slice-timing correction, spatial normalization to standardized templates (MNI152 for brain, and combination of MNI152 and PAM50 for brainstem and cervical spinal cord), and noise removal.<br>The data included in the repository have been pre-processed, and are in separate folders for Study 1 and Study 2, and for brain fMRI data, and brainstem and spinal cord (BSSC) data. Corresponding data of pain ratings and stimulation temperatures for each run are included.<br>