BEaST brain extraction tool mincbeast <library dir> <input> <output>


mincbeast will extract brain using library of presegmented images For the detailed explanation of the algorithm see: Eskildsen SF, Coupe P, Fonov V, Manjon JV, Leung KK, Guizard N, Wassef SN, Ostergaard LR, Collins DL; Alzheimer’s Disease Neuroimaging Initiative. BEaST: brain extraction based on nonlocal segmentation technique. Neuroimage. 2012 Feb 1;59(3):2362-73. DOI: j.neuroimage.2011.09.012

Common options

-help Print summary of command-line options and exit.

-clobber Overwrite an existing file.

-version Print the program’s version number and exit.

Algorithm specific options

-probability Output the probability map instead of crisp mask.

-flip Flip images around the mid-sagittal plane to increase patch count.

-load_moments Do not calculate moments instead use precalculated library moments. (for optimization purposes)

-fill Fill holes in the binary output.

-median Apply a median filter on the probability map.

-nlm_filter Apply an NLM filter on the probability map (experimental).

-abspath File paths in the library are absolute (default is relative to library root).

-voxel_size Specify voxel size for calculations (4, 2, or 1). Assumes no multiscale. Use configuration file for multiscale. Default value: 4

-patch_size Specify patch size for single scale approach. Default value: 1

-search_area Specify size of search area for single scale approach. Default value: 2

-alpha Specify confidence level Alpha. Default value: 0.5

-beta Specify smoothness factor Beta. Default value: 0.25

-threshold Specify threshold for patch selection. Default value: 0.95

-selection_num Specify number of selected images. Default value: 20

-positive Specify mask of positive segmentation (inside mask) instead of the default mask.

-output_selection Specify file to output selected files.

-count Specify file to output the patch count.

-configuration Specify configuration file.

-mask Specify a segmentation mask instead of the the default mask.

-same_resolution Output final mask with the same resolution as input file.

-no_mask Do not apply a segmentation mask. Perform the segmentation over the entire image.

-no_positive Do not apply a positive mask.


Simon Fristed Eskildsen, Vladimir S. Fonov, Pierrick Coupe, Jose V. Manjon


Copyright © 2011 Simon Fristed Eskildsen, Vladimir S. Fonov, Pierrick Coupe, Jose V. Manjon