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
- -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 (email@example.com)
Copyright: Copyright (c) 2008-2018 the MRtrix3 contributors.
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