Fully automated open-source lesion mapping of T2-FLAIR images with FSL correlates with clinical disability in MS

Nathan C. Wetter, Elizabeth A. Hubbard, Robert W. Motl, Bradley P. Sutton

Research output: Contribution to journalArticlepeer-review


Background: T2 Lesion Volume (T2LV) has been an important biomarker for multiple sclerosis (MS). Current methods available to quantify lesions from MR images generally require manual adjustments or multiple images with different contrasts. Further, implementations are often not easily or openly accessible. Objective: We created a fully unsupervised, single T2 FLAIR image T2LV quantification package based on the popular open-source imaging toolkit FSL. Methods: By scripting various processing tools in FSL, we developed an image processing pipeline that distinguishes normal brain tissue from CSF and lesions. We validated our method by hierarchical multiple regression (HMR) with a preliminary study to see if our T2LVs correlate with clinical disability measures in MS when controlled for other variables. Results: Pearson correlations between T2LV and Expanded Disability Status Scale (EDSS: r = 0.344, P = 0.013), Six-Minute Walk (6MW: r = -0.513, P = 0.000), Timed 25-Foot Walk (T25FW: r = -0.438, P =000), and Symbol Digit Modalities Test (SDMT: r = -0.499, P = 0.000) were all significant. Partial correlations controlling for age were significant between T2LV and 6MW (r = -0.433, P = 0.002), T25FW (r = -0.392, P = 0.004), and SDMT (r = -0.450, P = 0.001). In HMR, T2LV explained significant additional variance in 6MW (R2 change = 0.082, P = 0.020), after controlling for confounding variables such as age, white matter volume (WMV), and gray matter volume (GMV). Conclusion: Our T2LV quantification software produces T2LVs from a single FLAIR image that correlate with physical disability in MS and is freely available as open-source software.

Original languageEnglish (US)
Pages (from-to)1-9
Number of pages9
JournalBrain and Behavior
Issue number3
StatePublished - Mar 1 2016


  • Atrophy
  • Magnetic resonance imaging
  • Multiple sclerosis
  • Outcome measurement
  • T2 lesions

ASJC Scopus subject areas

  • Behavioral Neuroscience


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