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 in mm.

--less_than int

Keep streamlines have length less than this value in mm.

--no_slr

Don’t enable local Streamline-based Linear Registration.

--clust_thr float

MDF distance threshold for all streamlines.

--reduction_thr float

Reduce search space by (mm).

--reduction_distance str

Reduction distance type can be mdf or mam.

--model_clust_thr float

MDF distance threshold for the model bundles.

--pruning_thr float

Pruning after matching.

--pruning_distance str

Pruning distance type can be mdf or mam.

--slr_metric str

Options are None, symmetric, asymmetric or diagonal.

--slr_transform str

Transformation allowed. translation, rigid, similarity or scaling.

--slr_matrix str

Options are ‘nano’, ‘tiny’, ‘small’, ‘medium’, ‘large’, ‘huge’.

--refine

Enable refine recognized bundle.

--r_reduction_thr float

Refine reduce search space by (mm).

--r_pruning_thr float

Refine pruning after matching.

--no_r_slr

Don’t enable Refine local Streamline-based Linear Registration.

Output Arguments(Optional)

--out_dir str

Output directory. (default current directory)

--out_recognized_transf str

Recognized bundle in the space of the model bundle.

--out_recognized_labels str

Indices of recognized bundle in the original tractogram.

References

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.