Improve volume measurements by reducing intensity contrast within known lesion areas. It is intended for use with "small" lesions, such as those typical in Multiple Sclerosis.
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 a white matter mask in order to "fill" the lesion area in the structural image with intensities that are similar to those in the non-lesion neighbourhood (restricted to white matter only). 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.
A white matter mask is necessary so that lesions that touch areas of non-brain tissue, such as the ventricles, only fill the lesions with intensities from immediately surrounding white matter.
If you use lesion_filling in your research, please make sure that you reference the article below.
- 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.
Usage and options
The usage of the script is particularly simple and there are no configurable options.
Part of FSL (build 509) lesion_filling Copyright(c) 2012, University of Oxford (Mark Jenkinson) Usage: 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 -w,--wmmask filename of white matter mask image Optional arguments (You may optionally specify one or more of): -v,--verbose switch on diagnostic messages -h,--help display this message