# 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