Generate a fixel-fixel connectivity matrix
fixelconnectivity [ options ] fixel_directory tracks matrix
- fixel_directory: the directory containing the fixels between which connectivity will be quantified
- tracks: the tracks used to determine fixel-fixel connectivity
- matrix: the output fixel-fixel connectivity matrix directory path
This command will generate a directory containing three images, which encodes the fixel-fixel connectivity matrix. Documentation regarding this format and how to use it will come in the future.
Options that influence generation of the connectivity matrix / matrices¶
- -threshold value a threshold to define the required fraction of shared connections to be included in the neighbourhood (default: 0.01)
- -angle value the max angle threshold for assigning streamline tangents to fixels (Default: 45 degrees)
- -mask file provide a fixel data file containing a mask of those fixels to be computed; fixels outside the mask will be empty in the output matrix
- -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.
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 (email@example.com)
Copyright: Copyright (c) 2008-2021 the MRtrix3 contributors.
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For more details, see http://www.mrtrix.org/.