Quantifying brain tissue volume in multiple sclerosis with automated lesion segmentation and filling

Sergi Valverde*, Arnau Oliver, Eloy Roura, Deborah Pareto, Joan C. Vilanova, Lluís Ramió-Torrentà, Jaume Sastre-Garriga, Xavier Montalban, Àlex Rovira, Xavier Lladó

*Corresponding author for this work

Research output: Contribution to journalArticleResearchpeer-review

24 Citations (Scopus)


Lesion filling has been successfully applied to reduce the effect of hypo-intense T1-w Multiple Sclerosis (MS) lesions on automatic brain tissue segmentation. However, a study of fully automated pipelines incorporating lesion segmentation and lesion filling on tissue volume analysis has not yet been performed. Here, we analyzed the % of error introduced by automating the lesion segmentation and filling processes in the tissue segmentation of 70 clinically isolated syndrome patient images. First of all, images were processed using the LST and SLS toolkits with different pipeline combinations that differed in either automated or manual lesion segmentation, and lesion filling or masking out lesions. Then, images processed following each of the pipelines were segmented into gray matter (GM) and white matter (WM) using SPM8, and compared with the same images where expert lesion annotations were filled before segmentation. Our results showed that fully automated lesion segmentation and filling pipelines reduced significantly the % of error in GM and WM volume on images of MS patients, and performed similarly to the images where expert lesion annotations were masked before segmentation. In all the pipelines, the amount of misclassified lesion voxels was the main cause in the observed error in GM and WM volume. However, the % of error was significantly lower when automatically estimated lesions were filled and not masked before segmentation. These results are relevant and suggest that LST and SLS toolboxes allow the performance of accurate brain tissue volume measurements without any kind of manual intervention, which can be convenient not only in terms of time and economic costs, but also to avoid the inherent intra/inter variability between manual annotations.

Original languageEnglish
Pages (from-to)640-647
Number of pages8
JournalNeuroImage: Clinical
Publication statusPublished - 2015


  • Automated tissue segmentation
  • Brain
  • Brain atrophy
  • Lesion filling
  • MRI
  • Multiple sclerosis
  • White matter lesions


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