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S2: Anatomical Cord Reference

Step Code: S2_anat_cordref
Depends on: S1 (Input Verification)
Required by: S3-S11 (all downstream steps)

Purpose

S2 establishes the anatomical cord reference that anchors all subsequent fMRI processing. The spinal cord presents unique challenges compared to brain imaging: its small cross-sectional area (~50-80 mm²), susceptibility to physiological motion, and variable vertebral anatomy across subjects. This step addresses these challenges by:

  1. Creating a standardized anatomical reference for downstream registration
  2. Segmenting the spinal cord for region-of-interest analyses
  3. Labeling vertebral levels for spatial normalization
  4. Registering to the PAM50 template for group-level analyses

Algorithm Overview

The S2 step consists of four sequential substeps:

Substep Name Description
S2.1 Discovery + Crop Select anatomy, standardize, discover cord, crop
S2.2 Segmentation + Labels Cord segmentation, TotalSpineSeg for vertebrae/discs/canal
S2.3 Rootlets Dorsal nerve rootlet detection (conditional)
S2.4 Registration PAM50 template registration with dual-path strategy

S2.1: Discovery and Cropping

Rationale

Spinal cord MRI often includes significant non-cord tissue (e.g., brainstem, shoulders) that can interfere with segmentation and registration algorithms. The discovery phase identifies the cord location and creates a cropped working volume.

Algorithm

  1. Anatomy Selection - Prefer T2w (better cord-CSF contrast), fallback to T1w
  2. Standardization - Reorient to RPI via sct_image -setorient RPI
  3. Discovery Segmentation - sct_deepseg -task seg_sc_contrast_agnostic
  4. FOV Validation - Reject if cord coverage < 20 slices
  5. Cord-Focused Cropping - sct_crop_image -m <crop_mask>

QC: Crop Box Sagittal

Crop Box Sagittal

What to look for:

  • ✅ Blue contour (cord mask) follows the spinal cord
  • ✅ Red contour (crop box) encompasses the full cord region
  • ❌ FAIL: Crop box extends into brain or misses cord

S2.2: Segmentation and Labeling

Cord Segmentation Methods

Method Command Best For
contrast_agnostic (default) sct_deepseg -task seg_sc_contrast_agnostic CSA consistency
totalspineseg Extract from TSS output All-in-one

TotalSpineSeg Integration

TotalSpineSeg provides automatic instance segmentation:

  • Spinal cord (label 1)
  • Spinal canal (label 2)
  • Vertebrae (labels 11-50: C1 through Sacrum)
  • Intervertebral discs (labels 63-100: C2/C3 through L5/S)

Command: sct_deepseg -task totalspineseg

Metrics Computed

  • Cord volume (mm³), length (mm)
  • CSA: mean, min, max (mm²)
  • Vertebrae/discs detected
  • Canal volume

QC: Cord Segmentation Montage

Cord Mask Montage

What to look for:

  • ✅ Cord mask is continuous across all slices
  • ✅ Mask is centered on the cord
  • ❌ FAIL: Large gaps or leakage into CSF

QC: TotalSpineSeg Montage

TotalSpineSeg Montage

Sagittal view showing colored vertebrae, discs, cord (blue), canal (cyan), with anatomical labels.

What to look for:

  • ✅ Vertebrae are correctly ordered (no label jumps)
  • ✅ Disc labels correspond to adjacent vertebrae
  • ❌ FAIL: Missing vertebrae or shifted labels

S2.3: Rootlets Detection

Eligibility

  • T2w image available
  • Sufficient cord coverage
  • Policy-enabled

Command: sct_deepseg -task seg_spinal_rootlets

QC: Rootlets Montage

Rootlets Montage

What to look for:

  • ✅ Rootlets appear at dorsal-lateral positions
  • ✅ Regular spacing along the cord
  • ❌ FAIL: Rootlets detected ventrally (false positives)

S2.4: Template Registration

Strategy

Dual-path when rootlets available:

  1. Disc-based registration - vertebral disc labels as landmarks
  2. Rootlet-based registration - nerve rootlet entry points

Command: sct_register_to_template

Output Warps

  • *_from-cordref_to-PAM50_warp.nii.gz (forward)
  • *_from-PAM50_to-cordref_warp.nii.gz (inverse)

QC: PAM50 Registration Overlay

PAM50 Registration

This animated GIF alternates between subject anatomy and template overlay.

What to look for:

  • ✅ Cord contours align between subject and template
  • ✅ No large rotational offsets
  • ❌ FAIL: Significant misalignment (>5mm offset)

Outputs

Derivatives

derivatives/spinalfmriprep/{dataset}/sub-{id}/anat/
├── sub-{id}_desc-cordref_{T1w|T2w}.nii.gz
├── sub-{id}_desc-cord_dseg_{T1w|T2w}.nii.gz
├── sub-{id}_desc-canal_dseg_{T1w|T2w}.nii.gz
├── sub-{id}_desc-totalspineseg_dseg_{T1w|T2w}.nii.gz
├── sub-{id}_desc-vertebral_labels_{T1w|T2w}.nii.gz
├── sub-{id}_desc-disc_labels_{T1w|T2w}.nii.gz
└── sub-{id}_desc-rootlets_dseg_{T1w|T2w}.nii.gz (if eligible)

derivatives/spinalfmriprep/{dataset}/sub-{id}/xfm/
├── sub-{id}_from-cordref_to-PAM50_warp.nii.gz
└── sub-{id}_from-PAM50_to-cordref_warp.nii.gz

derivatives/spinalfmriprep/{dataset}/sub-{id}/figures/
├── sub-{id}_desc-S2_crop_box_sagittal.png
├── sub-{id}_desc-S2_cordmask_montage.png
├── sub-{id}_desc-S2_totalspineseg_montage.png
├── sub-{id}_desc-S2_rootlets_montage.gif (conditional)
└── sub-{id}_desc-S2_pam50_reg_overlay.gif

CLI Usage

# Run S2 for a single dataset
poetry run spinalfmriprep run S2_anat_cordref \
  --dataset-key <KEY> \
  --datasets-local config/datasets_local.yaml \
  --out work/wf_001

# Run S2 for all regression datasets
poetry run spinalfmriprep run S2_anat_cordref \
  --scope reg \
  --datasets-local config/datasets_local.yaml \
  --out work/wf_001

# Validate outputs
poetry run spinalfmriprep check S2_anat_cordref --out work/wf_001

References

  1. TotalSpineSeg: Löffler et al. (2024). GitHub
  2. SCT: De Leener et al. NeuroImage 145:24-43 (2017). DOI
  3. PAM50: De Leener et al. NeuroImage 165:170-179 (2018). DOI

Last updated: January 2026