Framework for integrated MRI average of the spinal cord white and gray matter: The MNI–Poly–AMU template

Abstract

The field of spinal cord MRI is lacking a common template, as existing for the brain, which would allow extraction of multi-parametric data (diffusion-weighted, magnetization transfer, etc.) without user bias, thereby facilitating group analysis and multi-center studies. This paper describes a framework to produce an unbiased average anatomical template of the human spinal cord. The template was created by co-registering T2-weighted images (N = 16 healthy volunteers) using a series of pre-processing steps followed by non-linear registration. A white and gray matter probabilistic template was then merged to the average anatomical template, yielding the MNI-Poly-AMU template, which currently covers vertebral levels C1 to T6. New subjects can be registered to the template using a dedicated image processing pipeline. Validation was conducted on 16 additional subjects by comparing an automatic template-based segmentation and manual segmentation, yielding a median Dice coefficient of 0.89. The registration pipeline is rapid (~15 min), automatic after one C2/C3 landmark manual identification, and robust, thereby reducing subjective variability and bias associated with manual segmentation. The template can notably be used for measurements of spinal cord cross-sectional area, voxel-based morphometry, identification of anatomical features (e.g., vertebral levels, white and gray matter location) and unbiased extraction of multi-parametric data.

Clinically Feasible Microstructural MRI to Quantify Cervical Spinal Cord Tissue Injury Using DTI, MT, and T2*-Weighted Imaging: Assessment of Normative Data and Reliability

“…In keeping with prior reports, significant relationships were found between age and FA 5,7,8 and MTR, 8 but not CSA. 8,23 However, we also identified univariate relationships between MR imaging metrics and sex, height, weight, and cervical cord length, for which we are not aware of previous reports. The relationship between CSA and cervical cord length likely indicates that CSA is related to overall body size because height and weight also showed positive (nonsignificant) correlations.…”

“…Images were nonlinearly registered to the MNI-Poly-AMU template/ atlas in SCT. 23 T2WIs were used to automatically calculate cervical cord length (from the top of C1 to the bottom of the C7 vertebral levels) and SC CSA. DTI was motion-corrected with regularized registration, and diffusion tensors were calculated with outlier rejection by using the RESTORE (robust estimation of tensors by outlier rejection) method.…”

MRI Atlas-Based Measurement of Spinal Cord Injury Predicts Outcome in Acute Flaccid Myelitis

“…7,9,11,21,23,28 This proof-of-concept study demonstrates the prognostic validity of this approach and how segmented analysis of SC subregions (ie, %GM and %WM) may reflect the underlying pathophysiology of disease.…”

“…The MNI-Poly-AMU template is an image of the SC averaged across multiple patients and is used as a reference point for registration of patient SCs and atlas-based MR signal quantification. 7 Registration was done in 4 steps. In step 1, a nonlinear transformation was estimated to straighten the SC (to match the MNI-Poly-AMU straight template).…”

“…However, in a variety of SC pathologies, defining the pattern and extent of signal abnormality on MR imaging can aid in diagnosis and prognosis. 6 The recent development of a standard SC template 7 -as part of the Spinal Cord Toolbox (SCT) 8 -that includes probabilistic maps of GM and WM 9 now makes it possible to quantify the severity of SC injury. [10][11][12] We aimed to measure the proportion of GM and WM damage in patients with AFM occurring in association with the EV-D68 outbreak.…”