Reference·CLI

network

cli.network

tvbo network — build brain-network connectomes from tractograms.

Attributes

Name	Description
app

Functions

Name	Description
build	Build a structural connectome (SC) from a tractogram + parcellation.

build

cli.network.build(
    tractogram=typer.Argument(..., help='Streamline tractogram MRtrix can read (e.g. .tck). Must be in the same space as the parcellation.'),
    parcellation=typer.Argument(..., help='Integer-labelled parcellation image (e.g. dseg.nii.gz), in the same space as the tractogram.'),
    output=typer.Option(None, '-o', '--output', help='Sidecar output path (.yaml); the .h5 companion is written next to it. Default: a BIDS-derived name in the current directory.'),
    atlas=typer.Option(None, '--atlas', help='Parcellation/atlas name (metadata + filename entity).'),
    space=typer.Option(None, '--space', help='Coordinate space both inputs share (e.g. FSLMNI152). Recorded as the template entity; the build assumes the inputs are already co-registered.'),
    cohort=typer.Option(None, '--cohort', help='Cohort/dataset entity (e.g. HCPYA).'),
    reconstruction=typer.Option(None, '--reconstruction', '--rec', help='Tractography pipeline name (e.g. dTOR); recorded as the tractogram and reconstruction entity.'),
    segmentation=typer.Option(None, '--seg', help='Segmentation entity (e.g. 17Networks).'),
    scale=typer.Option(None, '--scale', help='Scale entity (e.g. 1000).'),
    labels=typer.Option(None, '--labels', help='Optional node labels: a text file with one label per line, ordered by parcellation label (1..N).'),
    symmetric=typer.Option(True, '--symmetric/--no-symmetric', help='Pass -symmetric to tck2connectome.'),
    zero_diagonal=typer.Option(True, '--zero-diagonal/--no-zero-diagonal', help='Pass -zero_diagonal to tck2connectome.'),
    keep_assignments=typer.Option(None, '--keep-assignments', help="Also save tck2connectome's -out_assignments to this path."),
    mrtrix_arg=typer.Option(None, '--mrtrix-arg', help='Extra raw argument forwarded to both tck2connectome calls (repeatable).'),
    overwrite=typer.Option(False, '--overwrite', help='Overwrite existing output.'),
    dry_run=typer.Option(False, '--dry-run', help='Print the tck2connectome commands and exit without running them.'),
)

Build a structural connectome (SC) from a tractogram + parcellation.

A thin wrapper around MRtrix3 tck2connectome: it counts streamlines between parcellation nodes (edge weights) and their mean lengths, then writes a tvbo network (…_desc-SC_relmat.h5 + YAML sidecar) you can load with tvbo.Network(...). The tractogram and parcellation must already be in the same space — this command does not register them.