tck2connectome¶

Synopsis¶

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

Description¶

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

Options¶

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

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
-zero_diagonal set all diagonal entries in the matrix to zero (these represent streamlines that connect to the same node at both ends)
-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.
-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)
-failonwarn terminate program if a warning is produced
-help display this information page and exit.
-version display version information and exit.

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

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/

MRtrix 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.

For more details, see www.mrtrix.org