Mouse BSE
This is an adaptation of BrainSuite’s Brain Surface Extractor (BSE), a skull-stripping tool originally developed for human MRI (Shattuck et al., 2001; Shattuck and Leahy, 2002). BSE has been used in several preclinical imaging studies, and we have adapted the BSE code based on our experience applying it to rodent imaging.
Examples
Usage
mousebse v.25a
Copyright (C) 2025 The Regents of the University of California and the University of Southern California
Created by David W. Shattuck, Ahmanson-Lovelace Brain Mapping Center
Dept. of Neurology, David Geffen School of Medicine, UCLA.
This program is free software and is released under a GNU General Public License; Version 2.
For more details, run the program with the argument --license.
mouse brain surface extractor (mouseBSE)
This program performs automated skull and scalp removal on T1-weighted MRI volumes.
mouseBSE is adapted from the BrainSuite collection of tools.
For more information, please see: http://brainsuite.org
Compiled at 20:46:46 on Feb 9 2025 (#3d76374)
usage: mousebse [settings]
required settings:
-i <input filename> input MRI volume
optional settings:
--license show the license information
-o <output filename> output brain-masked MRI volume
--xmin xplane zeros out data for x < xplane [default: 0]
--ymin yplane zeros out data for y < yplane [default: 0]
--zmin zplane zeros out data for z < zplane [default: 0]
--xmax xplane zeros out data for x > xplane [default: 2147483647]
--ymax yplane zeros out data for y > yplane [default: 2147483647]
--zmax zplane zeros out data for z > zplane [default: 2147483647]
--zpad nslices zeropad the image by nslices [default: 0]
-d <float> diffusion constant [default: 50]
-n <iterations> diffusion iterations [default: 10]
-s <edge sigma> edge detection constant [default: 0.64]
-r <size> radius of erosion/dilation filter [default: 1]
-c <size> closing size [default: 8]
-p dilation_radius dilate final mask by dilation_radius (0==don't dilate) [default: 0]
--mask <filename> save smooth brain mask
--init <filename> initial brain mask
--select region select region from connected components [default: -1]
--adf <filename> diffusion filter output
--eroded <filename> eroded edge map output
--edge <filename> edge map output
-v <number> verbosity level (0=silent) [default: 1]
--norotate retain original orientation (default behavior will auto-rotate input NII files to RAS orientation
--timer show timing
example:
mousebse -i input_mri.img -o skull_stripped_mri.img