RecoBundlesFlow

Parameters

streamline_files : string

The path of streamline files where you want to recognize bundles

model_bundle_files : string

The path of model bundle files

greater_than : int, optional

Keep streamlines that have length greater than this value (default 50) in mm.

less_than : int, optional

Keep streamlines have length less than this value (default 1000000) in mm.

no_slr : bool, optional

Don’t enable local Streamline-based Linear Registration (default False).

clust_thr : float, optional

MDF distance threshold for all streamlines (default 15)

reduction_thr : float, optional

Reduce search space by (mm) (default 15)

reduction_distance : string, optional

Reduction distance type can be mdf or mam (default mdf)

model_clust_thr : float, optional

MDF distance threshold for the model bundles (default 2.5)

pruning_thr : float, optional

Pruning after matching (default 8).

pruning_distance : string, optional

Pruning distance type can be mdf or mam (default mdf)

slr_metric : string, optional

Options are None, symmetric, asymmetric or diagonal (default symmetric).

slr_transform : string, optional

Transformation allowed. translation, rigid, similarity or scaling (Default ‘similarity’).

slr_matrix : string, optional

Options are ‘nano’, ‘tiny’, ‘small’, ‘medium’, ‘large’, ‘huge’ (default ‘small’)

refine : bool, optional

Enable refine recognized bunle (default False)

r_reduction_thr : float, optional

Refine reduce search space by (mm) (default 12)

r_pruning_thr : float, optional

Refine pruning after matching (default 6).

no_r_slr : bool, optional

Don’t enable Refine local Streamline-based Linear Registration (default False).

out_dir : string, optional

Output directory (default input file directory)

out_recognized_transf : string, optional

Recognized bundle in the space of the model bundle (default ‘recognized.trk’)

out_recognized_labels : string, optional

Indices of recognized bundle in the original tractogram (default ‘labels.npy’)

References