SlrWithQbxFlow

Parameters

static_files : string moving_files : string x0 : string, optional

rigid, similarity or affine transformation model (default affine)

rm_small_clusters : int, optional

Remove clusters that have less than rm_small_clusters (default 50)

qbx_thr : variable int, optional

Thresholds for QuickBundlesX (default [40, 30, 20, 15])

num_threads : int, optional

Number of threads. If None (default) then all available threads will be used. Only metrics using OpenMP will use this variable.

greater_than : int, optional

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

less_than : int, optional

Keep streamlines have length less than this value (default 250)

np_pts : int, optional

Number of points for discretizing each streamline (default 20)

progressive : boolean, optional

(default True)

out_dir : string, optional

Output directory (default input file directory)

out_moved : string, optional

Filename of moved tractogram (default ‘moved.trk’)

out_affine : string, optional

Filename of affine for SLR transformation (default ‘affine.txt’)

out_stat_centroids : string, optional

Filename of static centroids (default ‘static_centroids.trk’)

out_moving_centroids : string, optional

Filename of moving centroids (default ‘moving_centroids.trk’)

out_moved_centroids : string, optional

Filename of moved centroids (default ‘moved_centroids.trk’)

Notes

The order of operations is the following. First short or long streamlines are removed. Second the tractogram or a random selection of the tractogram is clustered with QuickBundlesX. Then SLR [Garyfallidis15] is applied.

References

registration of white-matter fascicles in the space of streamlines”, NeuroImage, 117, 124–140, 2015

bundle alignment for group comparisons”, ISMRM, 2014.

bundles using local and global streamline-based registration and clustering, Neuroimage, 2017.