- dipy_horizon [-h] [–cluster] [–cluster_thr float] [–random_colors]
[–length_gt float] [–length_lt float] [–clusters_gt int] [–clusters_lt int] [–native_coords] [–stealth] [–emergency_header str] [–bg_color [float [float …]]] [–disable_order_transparency] [–buan] [–buan_thr float] [–buan_highlight [float [float …]]] [–out_dir str] [–out_stealth_png str] input_files [input_files …]
Interactive medical visualization - Invert the Horizon!
Interact with any number of .trk, .tck or .dpy tractograms and anatomy files .nii or .nii.gz. Cluster streamlines on loading.
- -h, --help
show this help message and exit
- --cluster
Enable QuickBundlesX clustering
- --cluster_thr float
Distance threshold used for clustering. Default value 15.0 for small animal brains you may need to use something smaller such as 2.0. The distance is in mm. For this parameter to be active
cluster
should be enabled- --random_colors
Given multiple tractograms have been included then each tractogram will be shown with different color
- --length_gt float
Clusters with average length greater than
length_gt
amount in mm will be shown- --length_lt float
Clusters with average length less than
length_lt
amount in mm will be shown- --clusters_gt int
Clusters with size greater than
clusters_gt
will be shown.- --clusters_lt int
Clusters with size less than
clusters_gt
will be shown.- --native_coords
Show results in native coordinates
- --stealth
Do not use interactive mode just save figure.
- --emergency_header str
If no anatomy reference is provided an emergency header is provided. Current options ‘icbm_2009a’ and ‘icbm_2009c’.
- –bg_color [float [float …]]
Define the background color of the scene. Colors can be defined with 1 or 3 values and should be between [0-1]. Default is black (e.g –bg_color 0 0 0 or –bg_color 0).
- --disable_order_transparency
Default False. Use depth peeling to sort transparent objects. If True also enables anti-aliasing.
- --buan
Enables BUAN framework visualization. Default is False.
- --buan_thr float
Default 0.5. Uses the threshold value to highlight segments on the bundle which have pvalues less than this threshold.
- –buan_highlight [float [float …]]
Define the bundle highlight area color. Colors can be defined with 1 or 3 values and should be between [0-1]. Default is red (e.g –buan_highlight 1 0 0)
- --out_dir str
Output directory. Default current directory.
- --out_stealth_png str
Filename of saved picture.
Garyfallidis E., M-A. Cote, B.Q. Chandio, S. Fadnavis, J. Guaje, R. Aggarwal, E. St-Onge, K.S. Juneja, S. Koudoro, D. Reagan, DIPY Horizon: fast, modular, unified and adaptive visualization, Proceedings of: International Society of Magnetic Resonance in Medicine (ISMRM), Montreal, Canada, 2019.
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.