Extract streamlines from a tractogram based on their assignment to parcellated nodes


connectome2tck [ options ]  tracks_in assignments_in prefix_out
  • tracks_in: the input track file
  • assignments_in: text file containing the node assignments for each streamline
  • prefix_out: the output file / prefix


The compulsory input file “assignments_in” should contain a text file where there is one row for each streamline, and each row contains a list of numbers corresponding to the parcels to which that streamline was assigned (most typically there will be two entries per streamline, one for each endpoint; but this is not strictly a requirement). This file will most typically be generated using the tck2connectome command with the -out_assignments option.


Options for determining the content / format of output files

  • -nodes list only select tracks that involve a set of nodes of interest (provide as a comma-separated list of integers)
  • -exclusive only select tracks that exclusively connect nodes from within the list of nodes of interest
  • -files option select how the resulting streamlines will be grouped in output files. Options are: per_edge, per_node, single (default: per_edge)
  • -exemplars image generate a mean connection exemplar per edge, rather than keeping all streamlines (the parcellation node image must be provided in order to constrain the exemplar endpoints)
  • -keep_unassigned by default, the program discards those streamlines that are not successfully assigned to a node. Set this option to generate corresponding outputs containing these streamlines (labelled as node index 0)
  • -keep_self by default, the program will not output streamlines that connect to the same node at both ends. Set this option to instead keep these self-connections.

Options for importing / exporting streamline weights

  • -tck_weights_in path specify a text scalar file containing the streamline weights
  • -prefix_tck_weights_out prefix provide a prefix for outputting a text file corresponding to each output file, each containing only the streamline weights relevant for that track file

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).
  • -help display this information page and exit.
  • -version display version information and exit.

Author: Robert E. Smith (

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

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.

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