dipy_slr

Usage

dipy_slr [-h] [–x0 str] [–rm_small_clusters int]

[–qbx_thr [int [int …]]] [–num_threads int] [–greater_than int] [–less_than int] [–nb_pts int] [–progressive] [–out_dir str] [–out_moved str] [–out_affine str] [–out_stat_centroids str] [–out_moving_centroids str] [–out_moved_centroids str] static_files moving_files

Streamline-based linear registration.

For efficiency we apply the registration on cluster centroids and remove small clusters.

Positional Arguments

static_files moving_files

Optional Arguments

-h, --help

show this help message and exit

--x0 str

rigid, similarity or affine transformation model.

--rm_small_clusters int

Remove clusters that have less than rm_small_clusters.

–qbx_thr [int [int …]]

Thresholds for QuickBundlesX.

--num_threads int

Number of threads to be used for OpenMP parallelization. If None (default) the value of OMP_NUM_THREADS environment variable is used if it is set, otherwise all available threads are used. If < 0 the maximal number of threads minus |num_threads + 1| is used (enter -1 to use as many threads as possible). 0 raises an error. Only metrics using OpenMP will use this variable.

--greater_than int

Keep streamlines that have length greater than this value.

--less_than int

Keep streamlines have length less than this value.

--nb_pts int

Number of points for discretizing each streamline.

–progressive

Output Arguments(Optional)

--out_dir str

Output directory. (default current directory)

--out_moved str

Filename of moved tractogram.

--out_affine str

Filename of affine for SLR transformation.

--out_stat_centroids str

Filename of static centroids.

--out_moving_centroids str

Filename of moving centroids.

--out_moved_centroids str

Filename of moved centroids.

References

Garyfallidis15

Garyfallidis et al. “Robust and efficient linearregistration of white-matter fascicles in the space ofstreamlines”, NeuroImage, 117, 124–140, 2015

Garyfallidis14

Garyfallidis et al., “Direct native-space fiberbundle alignment for group comparisons”, ISMRM, 2014.

Garyfallidis17

Garyfallidis et al. Recognition of white matterbundles using local and global streamline-based registrationand 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.