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Lesion Filling

Improve volume measurements by reducing intensity contrast within known lesion areas.


This tool takes a user-defined lesion mask (usually created manually) together with a structural image (e.g. T1-weighted image, but it could also be T2-weighted, PD, etc.) and "fills" the lesion area in the structural image with intensities that are similar to those in the non-lesion neighbourhood. It has been shown (see references) that using such a method as part of a pre-processing pipeline can improve the registration and segmentation of pathological brains (particular those with Multiple Sclerosis) and the resultant volumetric measures of brain tissue.


If you use lesion_filling in your research, please make sure that you reference at least the first of the articles listed below, and ideally the complete list.

  • M. Battaglini, M. Jenkinson, and N. De Stefano. Evaluating and reducing the impact of white matter lesions on brain volume measurements. Human Brain Mapping, 33(9):2062–2071, 2012.
  • Chard DT, Jackson JS, Miller DH, Wheeler-Kingshott CA. Reducing the impact of white matter lesions on automated measures of brain gray and white matter volumes. J Magn Reson Imaging 32:223–228, 2010.

Usage and options

The usage of the script is particularly simple and there are no configurable options.

Part of FSL (build 500)
Copyright(c) 2012, University of Oxford (Mark Jenkinson)

lesion_filling [options] -i <intensity image> -l <lesion mask image> -o <output/filled image>

Compulsory arguments (You MUST set one or more of):
        -i,--in input image filename (e.g. T1w image)
        -o,--out        output filename (lesion filled image)
        -l,--lesionmask filename of lesion mask image

Optional arguments (You may optionally specify one or more of):
        -v,--verbose    switch on diagnostic messages
        -h,--help       display this message

2012-09-05 11:30