connectome_build

data.connectome_build

Build a structural connectome from a tractogram + parcellation via MRtrix3.

A thin wrapper around MRtrix3’s tck2connectome. Given a streamline tractogram and an integer-labelled parcellation image that already live in the same space, it returns the edge-weight (streamline-count) and mean-tract-length matrices. The inputs are assumed to be co-registered — this module does not register them.

Assembling the matrices into a :class:tvbo.classes.network.Network and writing the …_desc-SC_relmat.h5 + YAML sidecar happens in the caller (tvbo network build); this module only shells out to MRtrix and reads back the CSVs, so it is the single place the tck2connectome invocation is defined.

Attributes

Name	Description
TCK2CONNECTOME

Functions

Name	Description
connectome_from_tractogram	Compute the `(weights, lengths)` matrices for a tractogram + parcellation.
ensure_mrtrix	Raise a friendly `RuntimeError` when the MRtrix command is missing.
mrtrix_available	Return True when the given MRtrix command is on `PATH`.
run_tck2connectome	Run `tck2connectome` twice: edge weights (count) then mean tract lengths.
tck2connectome_commands	Return the two `tck2connectome` argv lists (edge weights, then lengths).

connectome_from_tractogram

data.connectome_build.connectome_from_tractogram(
    tractogram,
    parcellation,
    *,
    symmetric=True,
    zero_diagonal=True,
    extra_args=None,
    assignments_out=None,
)

Compute the (weights, lengths) matrices for a tractogram + parcellation.

Runs tck2connectome in a temporary directory and loads the CSVs it writes. Both inputs must already be co-registered in the same space.

Parameters

tractogram : Path Streamline tractogram MRtrix can read (e.g. .tck). parcellation : Path Integer-labelled parcellation image (e.g. dseg.nii.gz). assignments_out : Path, optional When given, tck2connectome’s -out_assignments is kept at this path.

Returns:

weights, lengths : np.ndarray (N, N) streamline-count and mean-length matrices.

ensure_mrtrix

data.connectome_build.ensure_mrtrix(tool=TCK2CONNECTOME)

Raise a friendly RuntimeError when the MRtrix command is missing.

mrtrix_available

data.connectome_build.mrtrix_available(tool=TCK2CONNECTOME)

Return True when the given MRtrix command is on PATH.

run_tck2connectome

data.connectome_build.run_tck2connectome(
    tractogram,
    parcellation,
    weights_csv,
    lengths_csv,
    assignments_csv=None,
    *,
    symmetric=True,
    zero_diagonal=True,
    force=True,
    extra_args=None,
)

Run tck2connectome twice: edge weights (count) then mean tract lengths.

tck2connectome_commands

data.connectome_build.tck2connectome_commands(
    tractogram,
    parcellation,
    weights_csv,
    lengths_csv,
    assignments_csv=None,
    *,
    symmetric=True,
    zero_diagonal=True,
    force=True,
    extra_args=None,
)

Return the two tck2connectome argv lists (edge weights, then lengths).

The first call counts streamlines between each node pair (edge weights); the second scales each streamline by its length and averages per edge to get mean tract lengths. Returned rather than run so callers can preview them (dry-run).