Deep-Learning-Based Neural Tissue Segmentation of MRI in Multiple Sclerosis: Effect of Training Set Size

Abstract

Background: The dependence of deep-learning (DL)-based segmentation accuracy of brain MRI on the training size is not known.

Purpose: To determine the required training size for a desired accuracy in brain MRI segmentation in multiple sclerosis (MS) using DL.

Study type: Retrospective analysis of MRI data acquired as part of a multicenter clinical trial.

Study population: In all, 1008 patients with clinically definite MS.

Field strength/sequence: MRIs were acquired at 1.5T and 3T scanners manufactured by GE, Philips, and Siemens with dual turbo spin echo, FLAIR, and T₁ -weighted turbo spin echo sequences.

Assessment: Segmentation results using an automated analysis pipeline and validated by two neuroimaging experts served as the ground truth. A DL model, based on a fully convolutional neural network, was trained separately using 16 different training sizes. The segmentation accuracy as a function of the training size was determined. These data were fitted to the learning curve for estimating the required training size for desired accuracy.

Statistical tests: The performance of the network was evaluated by calculating the Dice similarity coefficient (DSC), and lesion true-positive and false-positive rates.

Results: The DSC for lesions showed much stronger dependency on the sample size than gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF). When the training size was increased from 10 to 800 the DSC values varied from 0.00 to 0.86 ± 0.016 for T₂ lesions, 0.87 ± 009 to 0.94 ± 0.004 for GM, 0.86 ± 0.08 to 0.94 ± 0.005 for WM, and 0.91 ± 0.009 to 0.96 ± 0.003 for CSF.

Data conclusion: Excellent segmentation was achieved with a training size as small as 10 image volumes for GM, WM, and CSF. In contrast, a training size of at least 50 image volumes was necessary for adequate lesion segmentation.

Level of evidence: 1 Technical Efficacy Stage: 1 J. Magn. Reson. Imaging 2020;51:1487-1496.

Keywords: MRI; deep learning; multiple sclerosis; segmentation.