whole-spine

# Whole-Spine Anatomical MRI dataset & B0 simulations

## Dataset Description

This dataset includes structural MRI (T1-weighted) and simulated ΔB0 field maps for sixty volunteers. Participants were scanned using two Siemens 3T MRI scanners (MAGNETOM Tim Trio and Verio) equipped with head, neck, and spine coils. The scans cover anatomical regions extending from the head to the torso and include lateral torso encompassing most of both lungs.

All data is organized in BIDS format and is available on OpenNeuro.

## Participants
* Total Participants: 60
* Males: 32
* Females: 18
* Undisclosed sex: 10
* Age: Mean = 27.1 years, SD = 6.5, Range = 21-56 years
* Weight: Mean = 66.7 kg, SD = 9.5, Range = 45-90 kg
* Height: Mean = 175.6 cm, SD = 8.8, Range = 155-192 cm

## MRI Acquisition

* Scanner Models: Siemens MAGNETOM Tim Trio and Verio (3T)
* Coils Used: Head, neck, and spine coils
* Structural Images: T1-weighted MPRAGE
* Resolution: 1 mm³
* Field of View (FOV): From head to torso, including lateral regions of both lungs
* Data Processing

## Structural Data Segmentation

1. Automated Segmentation Tools:

* TotalSegmentator MRI: Used for full-body, sinuses, trachea, ear canal, and lungs based on training with 10 manually segmented subjects.
* Samseg: Used for segmenting brain, eyes, and skull.
* TotalSpineSeg: Used for segmenting spinal cord, vertebrae, and intervertebral disks.

2. Post-Processing Steps:

* Tissue islands were removed, holes were closed, and tissue masks for specific regions (skull, brain, eyes, sinus, and ear canal) were smoothed using a custom pipeline ([GitHub repo](https://github.com/shimming-toolbox/b0-fieldmap-realistic-simulation), release v1.1, commit: 4f3c471db542fa9b12f308aaeece401323980965).
* Tissue masks were then merged into a single NIfTI file with the following voxel assignments: background (air), body, brain, spine, lungs, skull, trachea, sinus, ear canal, and eyes.

# Susceptibility Assignment
Each anatomical label in the segmentation volumes was assigned a specific susceptibility value (χ) as defined in [this Github repository](https://github.com/shimming-toolbox/tissue-to-MRproperty):

* Air: 0.35 ppm
* Sinus & Ear Canals: -2 ppm
* Trachea & Lungs: -4.2 ppm
* Brain: -9.04 ppm
* Body & Eyes: -9.05 ppm
* Spinal Canal & Disks: -9.055 ppm
* Skull & Vertebrae: -11 ppm

# Field Map Simulation

Field maps (ΔB0) were generated by applying a convolution in the Fourier domain between the susceptibility maps and an analytical dipole distribution. Key parameters:

* Implementation: Python ([GitHub repo](https://github.com/shimming-toolbox/susceptibility-to-fieldmap-fft))
* Padding:
* Edge-value padding applied on five volume surfaces
* Constant-value padding applied on the dorsal surface
* Padding Size: 50 voxels per surface

# Dataset Files and Structure

This dataset is organized according to the BIDS format. Key directories and files include:

* /sub-<participant_id>/anat: Contains T1-weighted images in NIfTI format
* /derivatives: Includes simulated ΔB0 field maps and segmentation labels

# 全脊柱解剖MRI数据集与B0场模拟

## 数据集说明
本数据集包含60名受试者的结构磁共振成像（T1-weighted，T1加权成像）与模拟ΔB0场图。受试者使用两台配备头部、颈部及脊柱线圈的西门子3T MRI扫描仪（MAGNETOM Tim Trio与Verio）进行扫描。扫描覆盖从头部至躯干的解剖区域，同时包含覆盖双侧大部分肺组织的躯干侧区。

所有数据均按照脑成像数据结构（Brain Imaging Data Structure，BIDS）格式组织，并可在OpenNeuro平台获取。

## 受试者信息
* 总受试者人数：60名
* 男性：32名
* 女性：18名
* 性别未披露：10名
* 年龄：平均27.1岁，标准差6.5，年龄范围21~56岁
* 体重：平均66.7千克，标准差9.5，体重范围45~90千克
* 身高：平均175.6厘米，标准差8.8，身高范围155~192厘米

## MRI采集参数
* 扫描仪型号：西门子MAGNETOM Tim Trio与Verio（3T）
* 使用线圈：头部、颈部及脊柱线圈
* 结构成像序列：T1加权MPRAGE序列
* 分辨率：1 mm³
* 视野（FOV）：覆盖头部至躯干，包含双侧肺的侧区
* 数据处理

## 结构数据分割
1. 自动化分割工具：
* TotalSegmentator MRI工具：基于10例手动分割受试者的训练数据，用于全身、鼻窦、气管、外耳道及肺部的分割
* Samseg工具：用于大脑、眼部及颅骨的分割
* TotalSpineSeg工具：用于脊髓、椎体及椎间盘的分割

2. 后处理步骤：
* 采用自定义流程（[GitHub仓库](https://github.com/shimming-toolbox/b0-fieldmap-realistic-simulation)，版本v1.1，提交哈希：4f3c471db542fa9b12f308aaeece401323980965）移除组织孤岛、闭合孔洞，并对特定区域（颅骨、大脑、眼部、鼻窦及外耳道）的组织掩码进行平滑处理
* 随后将各组织掩码合并为单个NIfTI格式文件，体素按如下规则赋值：背景（空气）、身体组织、大脑、脊柱、肺部、颅骨、气管、鼻窦、外耳道及眼部

# 磁化率赋值
分割体积中的每个解剖标签均被赋予特定的磁化率值（χ），具体定义参考[该GitHub仓库](https://github.com/shimming-toolbox/tissue-to-MRproperty)：
* 空气：0.35 ppm
* 鼻窦与外耳道：-2 ppm
* 气管与肺部：-4.2 ppm
* 大脑：-9.04 ppm
* 身体组织与眼部：-9.05 ppm
* 椎管与椎间盘：-9.055 ppm
* 颅骨与椎体：-11 ppm

# 场图模拟
ΔB0场图通过在傅里叶域对磁化率图与解析偶极子分布进行卷积生成。关键参数如下：
* 实现语言：Python（[GitHub仓库](https://github.com/shimming-toolbox/susceptibility-to-fieldmap-fft)）
* 填充方式：
* 五个体积表面采用边缘值填充
* 背侧表面采用常数值填充
* 填充尺寸：每个表面50个体素

# 数据集文件与结构
本数据集按照BIDS格式组织，主要目录与文件如下：
* /sub-<participant_id>/anat：包含NIfTI格式的T1加权成像文件
* /derivatives：包含模拟ΔB0场图与分割标签

搜集汇总

背景与挑战

背景概述

该数据集是一个包含60名志愿者全脊柱解剖MRI数据及B0场模拟的神经影像数据集。数据采集使用两台西门子3T MRI扫描仪，覆盖头部至躯干区域，包含T1加权结构图像和模拟场图。数据集采用BIDS格式组织，并提供了详细的分割结果和磁化率分配信息，适用于磁共振物理和脊柱成像研究。