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dipy_recobundles
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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.