A BIDS-compatible extended version of this tool is available at https://github.com/mrfil/lesion-mapper-bids. The new version can utilize outputs from Freesurfer and/or fMRIPrep and distinguishes between deep white matter lesions and periventricular lesions.

lesion_mapper - A tool for mappping white matter hyperintensities. Publication at: Wetter, Hubbard, Motl, Sutton. Brain Behav. 2016 Jan 28;6(3):e00440. https://doi.org/10.1002/brb3.440

For research purposes only! Please see LICENSE.txt

Nate Wetter [email protected] Brad Sutton [email protected] Magnetic Resonance Functional Imaging Lab <mrfil.bioen.illinois.edu> University of Illinois at Urbana-Champaign <illinois.edu>

Create the directory structure for each participant's data before running. This can be achieved using file_structure.sh

Use: lesion_mapper -in [options]

Required parameters: -in : FLAIR input image. Needs to already be skull-stripped.

Options: -wmthr : White matter propability threshold for standard space masking. Between 0 and 1. Higher numbers increase false negatives. Lower numbers increase false positives. Default is 0.7. Use -1 to skip this step. -midline : Remove lesions that are within millimeters of touching the saggital midline plane. Should be greater than or equal to zero. If set to zero, lesions crossing the midline will be removed. Default is 4. Use -1 to skip this step. Will be skipped if -wmthr is skipped. -midmax : Only remove parts of midline lesions that are within mm of midline. Should be greater than or equal to -midline. Default is 9. Use -1 to skip this constraint and allow all lesions contiguous with those selected via -midline to be removed. -no2fast : Skip secondary fast step. Results should be more sensitive and less specific. -v : Verbose. -png : Generate png image outputs.