fixelfilter

Synopsis

Perform filtering operations on fixel-based data

Usage

fixelfilter [ options ]  input filter output
  • input: the input: either a fixel data file, or a fixel directory (see Description)
  • filter: the filtering operation to perform; options are: connect, smooth
  • output: the output: either a fixel data file, or a fixel directory (see Description)

Description

If the first input to the command is a specific fixel data file, then a filtered version of only that file will be generated by the command. Alternatively, if the input is the location of a fixel directory, then the command will create a duplicate of the fixel directory, and apply the specified filter operation to all fixel data files within the directory.

For the smoothing filter, it is typically recommended that the provided fixel-fixel connectivity matrix should include both streamline-based connection strength and spatial distance between fixels; this can be generated by the MRtrix3 command fixelconnectivity, specifically using the -smoothing option.

Options

  • -matrix file provide a fixel-fixel connectivity matrix for filtering operations that require it

Options specific to the “connect” filter

  • -threshold_value value specify a threshold for the input fixel data file values (default = 0.5)
  • -threshold_connectivity value specify a fixel-fixel connectivity threshold for connected-component analysis (default = 0.10000000000000001)

Options specific to the “smooth” filter

  • -fwhm value the full-width half-maximum (FWHM) of the spatial component of the smoothing filter (default = 10mm)
  • -minweight value apply a minimum threshold to smoothing weights (default = 0.01)
  • -mask image only perform smoothing within a specified binary fixel mask

Standard options

  • -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).
  • -config key value (multiple uses permitted) temporarily set the value of an MRtrix config file entry.
  • -help display this information page and exit.
  • -version display version information and exit.

References

Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch, M.; Christiaens, D.; Jeurissen, B.; Yeh, C.-H. & Connelly, A. MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 2019, 202, 116137


Author: Robert E. Smith (robert.smith@florey.edu.au)

Copyright: Copyright (c) 2008-2020 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/.

Covered Software is provided under this License on an “as is” basis, without warranty of any kind, either expressed, implied, or statutory, including, without limitation, warranties that the Covered Software is free of defects, merchantable, fit for a particular purpose or non-infringing. See the Mozilla Public License v. 2.0 for more details.

For more details, see http://www.mrtrix.org/.