# connectome2tck¶

## Synopsis¶

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

## Usage¶

connectome2tck [ options ]  tracks_in assignments_in prefix_out

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

## Description¶

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.

## Example usages¶

• Default usage:

$connectome2tck tracks.tck assignments.txt edge-  The command will generate one track file for every edge in the connectome, with the name of each file indicating the nodes connected via that edge; for instance, all streamlines connecting nodes 23 and 49 will be written to file “edge-23-49.tck”. • Extract only the streamlines between nodes 1 and 2: $ connectome2tck tracks.tck assignments.txt tracks_1_2.tck -nodes 1,2 -exclusive -files single


Since only a single edge is of interest, this example provides only the two nodes involved in that edge to the -nodes option, adds the -exclusive option so that only streamlines for which both assigned nodes are in the list of nodes of interest are extracted (i.e. only streamlines connecting nodes 1 and 2 in this example), and writes the result to a single output track file.

• Extract the streamlines connecting node 15 to all other nodes in the parcellation, with one track file for each edge:

$tck2connectome tracks.tck assignments.txt from_15_to_ -nodes 15 -keep_self  The command will generate the same number of track files as there are nodes in the parcellation: one each for the streamlines connecting node 15 to every other node; i.e. “from_15_to_1.tck”, “from_15_to_2.tck”, “from_15_to_3.tck”, etc.. Because the -keep_self option is specified, file “from_15_to_15.tck” will also be generated, containing those streamlines that connect to node 15 at both endpoints. • For every node, generate a file containing all streamlines connected to that node: $ connectome2tck tracks.tck assignments.txt node -files per_node


Here the command will generate one track file for every node in the connectome: “node1.tck”, “node2.tck”, “node3.tck”, etc.. Each of these files will contain all streamlines that connect the node of that index to another node in the connectome (it does not select all tracks connecting a particular node, since the -keep_self option was omitted and therefore e.g. a streamline that is assigned to node 41 will not be present in file “node41.tck”). Each streamline in the input tractogram will in fact appear in two different output track files; e.g. a streamline connecting nodes 8 and 56 will be present both in file “node8.tck” and file “node56.tck”.

• Get all streamlines that were not successfully assigned to a node pair:

$connectome2tck tracks.tck assignments.txt unassigned.tck -nodes 0 -keep_self -files single  Node index 0 corresponds to streamline endpoints that were not successfully assigned to a node. As such, by selecting all streamlines that are assigned to “node 0” (including those streamlines for which neither endpoint is assigned to a node due to use of the -keep_self option), the single output track file will contain all streamlines for which at least one of the two endpoints was not successfully assigned to a node. • Generate a single track file containing edge exemplar trajectories: $ tck2connectome tracks.tck assignments.txt exemplars.tck -files single -exemplars nodes.mif


This produces the track file that is required as input when attempting to display connectome edges using the streamlines or streamtubes geometries within the meview connectome tool.

## Options¶

### 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).