Fast and accurate semi-automated segmentation method of spinal cord MR images at 3T applied to the construction of a cervical spinal cord template.

Mélanie Pélégrini-Issac,Bogdan Draganski,Noémie Villard,Stéphanie Trunet,Pierre-François Pradat,Brice Tiret,Stéphane Lehéricy,Habib Benali,Raphaël Chen,Mohamed-Mounir El Mendili

doi:10.1371/journal.pone.0122224

Abstract

ObjectiveTo design a fast and accurate semi-automated segmentation method for spinal cord 3T MR images and to construct a template of the cervical spinal cord.Materials and MethodsA semi-automated double threshold-based method (DTbM) was proposed enabling both cross-sectional and volumetric measures from 3D T2-weighted turbo spin echo MR scans of the spinal cord at 3T. Eighty-two healthy subjects, 10 patients with amyotrophic lateral sclerosis, 10 with spinal muscular atrophy and 10 with spinal cord injuries were studied. DTbM was compared with active surface method (ASM), threshold-based method (TbM) and manual outlining (ground truth). Accuracy of segmentations was scored visually by a radiologist in cervical and thoracic cord regions. Accuracy was also quantified at the cervical and thoracic levels as well as at C2 vertebral level. To construct a cervical template from healthy subjects’ images (n=59), a standardization pipeline was designed leading to well-centered straight spinal cord images and accurate probability tissue map.ResultsVisual scoring showed better performance for DTbM than for ASM. Mean Dice similarity coefficient (DSC) was 95.71% for DTbM and 90.78% for ASM at the cervical level and 94.27% for DTbM and 89.93% for ASM at the thoracic level. Finally, at C2 vertebral level, mean DSC was 97.98% for DTbM compared with 98.02% for TbM and 96.76% for ASM. DTbM showed similar accuracy compared with TbM, but with the advantage of limited manual interaction.ConclusionA semi-automated segmentation method with limited manual intervention was introduced and validated on 3T images, enabling the construction of a cervical spinal cord template.

Highlights

At C2 vertebral level, mean Dice similarity coefficient (DSC) was 97.98% for double threshold-based method (DTbM) compared with 98.02% for threshold-based method (TbM) and 96.76% for active surface method (ASM)
Spinal cord atrophy is a neuroimaging feature that is associated with motor neuron diseases such as amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA) [1,2,3,4,5], inflammatory diseases such as multiple sclerosis (MS) [6,7,8], and spinal cord injuries (SCI) [9,10,11]
The present study has two main objectives: 1) To construct and validate a new fast and accurate segmentation method with minimal manual intervention benefitting from the high robustness of TbM to its initialization procedure; 2) As an application, to extend existing work at 1.5 and 3T [25, 26] to the construction of an accurate MRI template of the cervical spinal cord using a large sample of 3T images

Summary

Materials and Methods

A semi-automated double threshold-based method (DTbM) was proposed enabling both cross-sectional and volumetric measures from 3D T2-weighted turbo spin echo MR scans of the spinal cord at 3T. Eighty-two healthy subjects, 10 patients with amyotrophic lateral sclerosis, 10 with spinal muscular atrophy and 10 with spinal cord injuries were studied. DTbM was compared with active surface method (ASM), threshold-based method (TbM) and manual outlining (ground truth). Accuracy of segmentations was scored visually by a radiologist in cervical and thoracic cord regions. Accuracy was quantified at the cervical and thoracic levels as well as at C2 vertebral level. To construct a cervical template from healthy subjects’ images (n=59), a standardization pipeline was designed leading to well-centered straight spinal cord images and accurate probability tissue map

Results

Introduction

Evaluation

Method

Discussion

Limitations and future directions