dipy_horizon#

Synopsis#

Horizon is deprecated and will be removed with future releases. Please use Skyline with dipy_skyline CLI.

See [1] for further details about Horizon.

Interact with any number of .trx, .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. This will be ignored with Skyline. (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. This will be ignored with Skyline. (default: 1000)

  • --clusters_gt

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

  • --clusters_lt

    Clusters with size less than clusters_lt will be shown. This will be ignored with Skyline. (default: 100000000)

  • --native_coords

    Show results in native coordinates. This will be ignored with Skyline. (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’. This will be ignored with Skyline. (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. This will be ignored with Skyline. (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. This will be ignored with Skyline. (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. This will be ignored with Skyline. (default: (1, 0, 0))

  • --roi_images

    Displays binary images as contours. This will be ignored with Skyline. (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. This will be ignored with Skyline. (default: (1, 0, 0))

Output Options#

  • --out_dir

    Output directory. (default: current directory)

  • --out_stealth_png

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

References#

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.

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