FMRI data sets spanning the brain, brainstem, and spinal cord, from two pain studies of healthy females

<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>

摘要
本数据集来源于两项针对健康女性的研究，分为四个文件夹，分别存储大脑（Brain1、Brain2）以及脑干与颈髓（BSSC1、BSSC2）的功能磁共振成像（functional magnetic resonance imaging，fMRI）数据。所有数据已完成预处理：转换为NIfTI格式，并进行了共配准、切片时间校正、空间标准化以及生理噪声去除，具体细节如下。每个文件夹中包含受试者信息，包括每次fMRI扫描的刺激温度、疼痛评分，以及每位受试者的年龄。

详细信息
本数据集包含两项既往女性疼痛加工研究中健康对照组的fMRI数据，两项研究分别开展于2013-2014年（记为“研究1”）与2018-2019年（记为“研究2”）。研究1的完整方法细节已在既往文献中发表（11）。所有受试者均无既往神经系统损伤或疾病史，且无磁共振成像检查禁忌证。两项研究均对受试者右手施加伤害性热刺激，刺激温度经过校准以引发中度疼痛。此外，两项研究均包含两个扫描阶段：一个用于大脑fMRI扫描，另一个用于脑干与颈髓的fMRI扫描。所有研究方案均已通过本机构研究伦理委员会的审查与批准。

研究1共纳入15名女性受试者，年龄范围为21-55岁，平均年龄为39.1±10.2岁（均值±标准差）。研究2共纳入18名女性受试者，年龄范围为21-59岁，平均年龄为36±11.3岁。每位受试者均完成多次fMRI扫描。两项研究的受试者均通过填写问卷评估焦虑、抑郁、疼痛灾难化思维、社会期望性以及健康相关因素。

在fMRI数据采集前，每位受试者均接受1小时的培训课程：向其介绍实验性疼痛刺激与研究设计，并培训其使用标准化数字疼痛强度量表（Numerical Pain Scale，NPS）进行疼痛评分。该量表评分范围为0-100，以5为增量，每10分增量配有文字描述（11, 43）。两项研究的刺激均为短暂加热右侧大鱼际肌（拇指根部）皮肤区域。两项研究的刺激设备、温度与时间参数均不相同，具体细节如下。

研究1：热刺激通过兼容磁共振成像的帕尔贴温控刺激器（Medoc™，拉马特甘，以色列）施加于受试者右手，该设备固定于受试者右手。热刺激过程中，温度在计算机控制下快速升降。刺激方案为每3秒施加一次热脉冲，共11次，以诱发继发性疼痛的时间总和效应（temporal summation of second pain，TSSP）。刺激阶段前有52秒的静息期，后有65秒的静息期。受试者通过背投屏幕查看指令，以知晓新扫描即将开始、热刺激开始的时间，以及首次与末次热接触时的评分上报时机。

研究2：热刺激通过兼容磁共振成像的机器人接触式热刺激器（Robotic Contact-Heat Thermal Heat Stimulator，RTS-2）施加，该设备通过气动方式升降加热的铝制温控探头以接触受试者皮肤，软件控制刺激时间与温度。刺激范式包含初始60秒的“基线”扫描，该条件与无刺激条件随机交替呈现。随后告知受试者刺激将在1分钟后，即第120秒时开始，随后在30秒内施加10次校准温度的热接触。该30秒刺激阶段后为120秒的静息期，总时长为4分30秒。

所有影像数据均采用3特斯拉全身磁共振成像系统（Siemens Magnetom Trio；西门子，埃尔兰根，德国）采集。两项研究中，受试者均取仰卧位，必要时使用泡沫垫支撑以确保舒适并减少躯体移动。由于大脑与脑干/脊髓的成像挑战不同，针对两个区域分别优化了成像方案：大脑采用T2*加权成像，脑干与脊髓采用T2加权成像，以在两个区域实现图像质量与血氧水平依赖（Blood Oxygenation Level Dependent，BOLD）敏感性的最优平衡（31, 44, 45）。

研究1 大脑fMRI：采用T2*加权梯度回波平面成像（gradient-echo echo-planar imaging，GE-EPI）序列，采集与前联合-后联合线（anterior commissure-posterior commissure line，AC-PC）平行的49层连续轴位影像，参数如下：重复时间（TR）=3秒，回波时间（TE）=30ms，翻转角=90°，视野（FOV）=192mm×192mm，矩阵=64×64，分辨率=3×3×3mm³。采用12通道头部线圈采集磁共振信号，体线圈发射射频脉冲。每次成像运行共采集50个容积数据。每项fMRI数据集合并5次相同类型的扫描运行。

研究2 大脑fMRI：采用T2*加权GE-EPI序列，采集66层连续轴位影像，参数如下：TR=2秒，TE=30ms，翻转角=84°，多波段因子=3，7/8部分傅里叶变换，FOV=180mm×180mm，矩阵=90×90，分辨率=2×2×2mm³。采用32通道头部线圈采集磁共振信号，体线圈发射射频脉冲。每次成像运行共采集135个容积数据。每项fMRI数据集合并3-5次相同类型的扫描运行。

研究1与研究2 脑干与脊髓fMRI：采用T2加权半傅里叶单次激发快速自旋回波（half-fourier single-shot fast spin-echo，HASTE）序列采集fMRI数据。采集9层连续矢状位影像，每层重复时间（TR）=0.75秒，回波时间（TE）=76ms以优化T2加权BOLD敏感性，视野为28×21cm，分辨率为1.5×1.5×2mm³（45）。成像范围覆盖T1椎体至丘脑上方，包含整个颈髓与左右侧脑干。采用脊柱接收阵列线圈的上部元件、后颈线圈以及12通道头部线圈的后半部分采集数据，接收元件可根据受试者体型进行调整。体线圈用于发射射频（RF）激发脉冲。研究1中，每种条件共采集138个容积数据（共6次重复运行）。研究2中，每种条件共采集200个容积数据（共5次重复运行）。通过脊柱前方的空间抑制脉冲减少呼吸、吞咽等导致的运动伪影，并采用头足方向的运动补偿梯度提升图像质量。

数据预处理：大脑数据采用MATLAB中的SPM12工具（可从https://www.fil.ion.ucl.ac.uk/spm/software/spm12/ 获取），脑干与脊髓数据采用SpinalfMRI9工具（可从https://www.queensu.ca/academia/stromanlab/home/fmri-analysis-software 获取）完成。数据先转换为NIfTI格式，随后进行预处理，包括共配准（即运动校正）、切片时间校正、空间标准化至标准化模板（大脑采用MNI152模板，脑干与颈髓采用MNI152与PAM50模板的组合）以及噪声去除。

本仓库中包含的数据均已完成预处理，按研究1、研究2，以及大脑fMRI数据、脑干与脊髓（BSSC）数据分为不同文件夹。同时包含每次扫描对应的疼痛评分与刺激温度的对应数据。