dipy_horizon

Usage

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.

Positional Arguments

input_files

Optional Arguments

-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)

Output Arguments(Optional)

--out_dir str

Output directory. Default current directory.

--out_stealth_png str

Filename of saved picture.

References

Horizon_ISMRM19

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.