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. Author manuscript; available in PMC: 2022 Oct 1.
Published in final edited form as: Nat Protoc. 2021 Aug 16;16(10):4611–4632. doi: 10.1038/s41596-021-00588-0

Table 1.

Purpose, pros and cons of sequences of the spine generic protocol.

Purpose Pros Cons
T1w (3D sagittal)

  • Measuring SC CSA and/or volume

  • Registering to a template (preferred for disc labeling)

  • Assessing lesions

  • Measuring brain atrophy

  • Efficient SNR per unit time

  • High SC/CSF contrast (good for SC segmentation)

  • 320 mm2 FOV in ~5min at 1 mm iso with full brain and cervical-spine coverage

  • Low specific absorption rate (SAR)

  • High WM/GM contrast in the brain (good for cortical surface segmentation)

  • Vertebral discs are well contrasted

  • Sensitive to motion (pulsatile, swallowing)

  • Poor WM/GM contrast in the SC
T2w (3D sagittal)

  • Measuring SC CSA and/or volume (preferred over the 3D T1w due to higher spatial resolution)

  • Registering to a template registration (preferred for cord segmentation)

  • Assessing lesions and compression

  • Very high SC/CSF contrast

  • Less sensitive to motion than the 3D T1w

  • Better spatial resolution than the 3D T1w (0.8 mm vs. 1 mm)

  • High SAR

  • Poor WM/GM contrast in the SC

  • Cannot cover full brain in <10 min at 0.8 mm iso

  • Poor visibility of vertebral discs

  • More prone to Gibbs ringing artifact at high-contrast SC/CSF interface
DWI (2D axial)

  • Computing DTI metrics (fractional anisotropy (FA), mean diffusivity (MD), radial diffusivity (RD), axial diffusivity (AD)) that are sensitive to axonal damage, demyelination and degeneration69.

  • Quantify SC neural tissue microstructural properties

  • Sensitive to WM pathologies (e.g. degenerative demyelination, injury, edema, tumor)

  • Longitudinal monitoring of patient-specific SC microstructure (i.e. disease progression)

  • Detect origin of microstructural damage before non-reversible changes (e.g. T2w hyperintensities, appearance of clinical symptoms)

  • Short acquisition time (<5 min)

  • Sensitive to B0 inhomogeneities (EPI readout)

  • DTI metrics are biased by SNR 70
GRE-MT1/MT0/T1w (3D axial)

  • Computing MTR, MT-CSF and MTsat (requires T1w to partially compensate for B1+ homogeneity and T1 effects on the MTR 71)

  • Detecting WM 61 and GM pathology (myelopathy)

  • Quantify SC neural tissue microstructural properties

  • Sensitive to WM pathologies (e.g. degenerative demyelination, injury, edema, tumor)

  • Longitudinal monitoring of patient-specific SC microstructure (i.e. disease progression)

  • Detect origin of microstructural damage before non-reversible changes (e.g. T2w hyperintensities, appearance of clinical symptoms)

  • High in-plane axial resolution (good for atlas-based analysis of various WM tracts)

  • The combined echoes provide high WM/GM contrast (depending on parameters).

  • Fast

  • Low SAR (except for the MT sequence)

  • Sensitive to motion

  • Sensitive to B0 inhomogeneities (signal drop-out due to intra-voxel dephasing, can be mitigated using thinner slices)

  • Quantitative metrics sensitive to B1 (except for the ME-GRE sequence)
ME-GRE (2D axial)

  • Segmenting the SC and GM for measuring cord/WM/GM CSA

  • Registering to a template and accounting for GM shape

  • Measuring SC and GM CSA