Perform filtering operations on 3D / 4D mask images
maskfilter [ options ] input filter output
- input: the input image.
- filter: the type of filter to be applied (clean, connect, dilate, erode, median)
- output: the output image.
The available filters are: clean, connect, dilate, erode, median.
Each filter has its own unique set of optional parameters.
Options for mask cleaning filter¶
- -scale value the maximum scale used to cut bridges. A certain maximum scale cuts bridges up to a width (in voxels) of 2x the provided scale. (Default: 2)
Options for connected-component filter¶
- -axes axes specify which axes should be included in the connected components. By default only the first 3 axes are included. The axes should be provided as a comma-separated list of values.
- -largest only retain the largest connected component
- -connectivity use 26-voxel-neighbourhood connectivity (Default: 6)
Options for dilate / erode filters¶
- -npass value the number of times to repeatedly apply the filter
Options for median filter¶
- -extent voxels specify the extent (width) of kernel size in voxels. This can be specified either as a single value to be used for all axes, or as a comma-separated list of the extent for each axis. The default is 3x3x3.
- -strides spec specify the strides of the output data in memory; either as a comma-separated list of (signed) integers, or as a template image from which the strides shall be extracted and used. The actual strides produced will depend on whether the output image format can support it.
- -info display information messages.
- -quiet do not display information messages or progress status. Alternatively, this can be achieved by setting the MRTRIX_QUIET environment variable to a non-empty string.
- -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).
- -help display this information page and exit.
- -version display version information and exit.
Copyright: Copyright (c) 2008-2018 the MRtrix3 contributors.
This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, you can obtain one at http://mozilla.org/MPL/2.0/
MRtrix3 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 http://www.mrtrix.org/