Generate a connectome matrix from a streamlines file and a node parcellation image


tck2connectome [ options ]  tracks_in nodes_in connectome_out
  • tracks_in: the input track file
  • nodes_in: the input node parcellation image
  • connectome_out: the output .csv file containing edge weights


Structural connectome streamline assignment option

  • -assignment_end_voxels use a simple voxel lookup value at each streamline endpoint
  • -assignment_radial_search radius perform a radial search from each streamline endpoint to locate the nearest node.Argument is the maximum radius in mm; if no node is found within this radius, the streamline endpoint is not assigned to any node. Default search distance is 2mm.
  • -assignment_reverse_search max_dist traverse from each streamline endpoint inwards along the streamline, in search of the last node traversed by the streamline. Argument is the maximum traversal length in mm (set to 0 to allow search to continue to the streamline midpoint).
  • -assignment_forward_search max_dist project the streamline forwards from the endpoint in search of a parcellation node voxel. Argument is the maximum traversal length in mm.
  • -assignment_all_voxels assign the streamline to all nodes it intersects along its length (note that this means a streamline may be assigned to more than two nodes, or indeed none at all)

Structural connectome metric options

  • -scale_length scale each contribution to the connectome edge by the length of the streamline
  • -scale_invlength scale each contribution to the connectome edge by the inverse of the streamline length
  • -scale_invnodevol scale each contribution to the connectome edge by the inverse of the two node volumes
  • -scale_file path scale each contribution to the connectome edge according to the values in a vector file

Options for outputting connectome matrices

  • -symmetric Make matrices symmetric on output
  • -zero_diagonal Set matrix diagonal to zero on output

Other options for tck2connectome

  • -stat_edge statistic statistic for combining the values from all streamlines in an edge into a single scale value for that edge (options are: sum,mean,min,max; default=sum)
  • -tck_weights_in path specify a text scalar file containing the streamline weights
  • -keep_unassigned By default, the program discards the information regarding those streamlines that are not successfully assigned to a node pair. Set this option to keep these values (will be the first row/column in the output matrix)
  • -out_assignments path output the node assignments of each streamline to a file; this can be used subsequently e.g. by the command connectome2tck
  • -vector output a vector representing connectivities from a given seed point to target nodes, rather than a matrix of node-node connectivities

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.


If using the default streamline-parcel assignment mechanism (or -assignment_radial_search option): Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. The effects of SIFT on the reproducibility and biological accuracy of the structural connectome. NeuroImage, 2015, 104, 253-265

If using -scale_invlength or -scale_invnodevol options: Hagmann, P.; Cammoun, L.; Gigandet, X.; Meuli, R.; Honey, C.; Wedeen, V. & Sporns, O. Mapping the Structural Core of Human Cerebral Cortex. PLoS Biology 6(7), e159

Author: Robert E. Smith (

Copyright: Copyright (c) 2008-2018 the MRtrix3 contributors.

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