dipy_recobundles

Usage

dipy_recobundles [-h] [–greater_than int] [–less_than int] [–no_slr]

[–clust_thr float] [–reduction_thr float] [–reduction_distance str] [–model_clust_thr float] [–pruning_thr float] [–pruning_distance str] [–slr_metric str] [–slr_transform str] [–slr_matrix str] [–refine] [–r_reduction_thr float] [–r_pruning_thr float] [–no_r_slr] [–out_dir str] [–out_recognized_transf str] [–out_recognized_labels str] streamline_files model_bundle_files

Recognize bundles

Positional Arguments

streamline_files The path of streamline files where you want to recognize bundles model_bundle_files The path of model bundle files

Optional Arguments

-h, --help

show this help message and exit

--greater_than int

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

--less_than int

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

--no_slr

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

--clust_thr float

MDF distance threshold for all streamlines (default 15)

--reduction_thr float

Reduce search space by (mm) (default 15)

--reduction_distance str

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

--model_clust_thr float

MDF distance threshold for the model bundles (default 2.5)

--pruning_thr float

Pruning after matching (default 8).

--pruning_distance str

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

--slr_metric str

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

--slr_transform str

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

--slr_matrix str

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

--refine

Enable refine recognized bunle (default False)

--r_reduction_thr float

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

--r_pruning_thr float

Refine pruning after matching (default 6).

--no_r_slr

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

Output Arguments(Optional)

--out_dir str

Output directory (default input file directory)

--out_recognized_transf str

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

--out_recognized_labels str

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

References

Garyfallidis17

Garyfallidis et al. Recognition of white matter bundles using local and global streamline-based registration and clustering, Neuroimage, 2017.

Garyfallidis, E., M. Brett, B. Amirbekian, A. Rokem, S. Van Der Walt, M. Descoteaux, and I. Nimmo-Smith. Dipy, a library for the analysis of diffusion MRI data. Frontiers in Neuroinformatics, 1-18, 2014.