dipy_horizon

Synopsis

Interactive medical visualization - Invert the Horizon!

See [1] for further details about Horizon. Interact with any number of .trk, .tck or .dpy tractograms and anatomy files .nii or .nii.gz. Cluster streamlines on loading.

Usage

dipy_horizon [OPTIONS] input_files

Input Parameters

• input_files

  Filenames.

General Options

• --cluster

  Enable QuickBundlesX clustering. (default: False)

• --rgb

  Enable the color image (rgb only, alpha channel will be ignored). (default: False)

• --cluster_thr

  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. (default: 15.0)

• --random_colors

  Given multiple tractograms and/or ROIs then each tractogram and/or ROI will be shown with different color. If no value is provided, both the tractograms and the ROIs will have a different random color generated from a distinguishable colormap. If the effect should only be applied to one of the 2 types, then use the options ‘tracts’ and ‘rois’ for the tractograms and the ROIs respectively. (default: None)

• --length_gt

  Clusters with average length greater than length_gt amount in mm will be shown. (default: 0)

• --length_lt

  Clusters with average length less than length_lt amount in mm will be shown. (default: 1000)

• --clusters_gt

  Clusters with size greater than clusters_gt will be shown. (default: 0)

• --clusters_lt

  Clusters with size less than clusters_gt will be shown. (default: 100000000)

• --native_coords

  Show results in native coordinates. (default: False)

• --stealth

  Do not use interactive mode just save figure. (default: False)

• --emergency_header

  If no anatomy reference is provided an emergency header is provided. Current options ‘icbm_2009a’ and ‘icbm_2009c’. (default: icbm_2009a)

• --bg_color

  Define the background color of the scene. Colors can be defined with 1 or 3 values and should be between [0-1]. (default: (0, 0, 0))

• --disable_order_transparency

  Use depth peeling to sort transparent objects. If True also enables anti-aliasing. (default: False)

• --buan

  Enables BUAN framework visualization. (default: False)

• --buan_thr

  Uses the threshold value to highlight segments on the bundle which have pvalues less than this threshold. (default: 0.5)

• --buan_highlight

  Define the bundle highlight area color. Colors can be defined with 1 or 3 values and should be between [0-1]. For example, a value of (1, 0, 0) would mean the red color. (default: (1, 0, 0))

• --roi_images

  Displays binary images as contours. (default: False)

• --roi_colors

  Define the color for the roi images. Colors can be defined with 1 or 3 values and should be between [0-1]. For example, a value of (1, 0, 0) would mean the red color. (default: (1, 0, 0))

Output Options

• --out_dir

  Output directory. (default: current directory)

• --out_stealth_png

  Filename of saved picture. (default: tmp.png)

References

[1]

Eleftherios Garyfallidis, Marc-Alexandre Côté, Bramsh Qamar Chandio, Shreyas Fadnavis, Javier Guaje, Ranveer Aggarwal, Etienne St-Onge, Karandeep Singh Juneja, Serge Koudoro, and David Reagan. DIPY Horizon: fast, modular, unified and adaptive visualization. In ISMRM 27th Annual Meeting & Exhibition SMRT 28th Annual Meeting, volume. Montréal, Canada, 2019. International Society for Magnetic Resonance in Medicine (ISMRM).

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.