mrthreshold [ options ] input output
- input: the input image to be thresholded.
- output: the output binary image mask.
create bitwise image by thresholding image intensity. By default, an optimal threshold is determined using a parameter-free method. Alternatively the threshold can be defined manually by the user or using a histogram-based analysis to cut out the background.
- -abs value specify threshold value as absolute intensity.
- -histogram define the threshold by a histogram analysis to cut out the background. Note that only the first study is used for thresholding.
- -percentile value threshold the image at the ith percentile.
- -top N provide a mask of the N top-valued voxels
- -bottom N provide a mask of the N bottom-valued voxels
- -invert invert output binary mask.
- -toppercent N provide a mask of the N%% top-valued voxels
- -bottompercent N provide a mask of the N%% bottom-valued voxels
- -nan use NaN as the output zero value.
- -ignorezero ignore zero-valued input voxels.
- -mask image compute the optimal threshold based on voxels within a mask.
- -info display information messages.
- -quiet do not display information messages or progress status.
- -debug display debugging messages.
- -force force overwrite of output files. Caution: Using the same file as input and output might cause unexpected behaviour.
- -nthreads number use this number of threads in multi-threaded applications (set to 0 to disable multi-threading)
- -failonwarn terminate program if a warning is produced
- -help display this information page and exit.
- -version display version information and exit.
- If not using the -abs option:Ridgway, G. R.; Omar, R.; Ourselin, S.; Hill, D. L.; Warren, J. D. & Fox, N. C. Issues with threshold masking in voxel-based morphometry of atrophied brains. NeuroImage, 2009, 44, 99-111
Author: J-Donald Tournier (email@example.com)
Copyright: Copyright (c) 2008-2016 the MRtrix3 contributors
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MRtrix is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
For more details, see www.mrtrix.org