dipy_skyline#

Synopsis#

Launch Skyline GUI.

If you want to load only odfs or rois. use dipy_skyline run –odfs <Your ODF files> or dipy_skyline run –rois <Your ROI files> respectively.

These options should be used in stealth mode. For GUI mode, the files can be loaded through the file dialog.

Usage#

dipy_skyline [OPTIONS] input_files

Input Parameters#

  • input_files

    Tuple of path for each image, peak, surface or tractogram to be added to the Skyline viewer.

General Options#

  • --rois

    Tuple of path for each ROI to be added to the Skyline viewer. (default: None)

  • --odfs

    Tuple of path for each ODF to be added to the Skyline viewer. (default: None)

  • --cluster

    Whether to cluster the tractograms. (default: False)

  • --performance_version

    Whether to use the performance version of the tractogram rendering. This will render tractograms as lines instead of tubes, which can improve performance for large tractograms. (default: False)

  • --glass_brain

    Whether to use glass brain mode. This will overwrite the background color to white if not explicitly set by the user. (default: False)

  • --bg_color

    Define the background color of the scene. Colors can be defined with 3 values and should be between [0-1]. For example, a value of (0, 0, 0) would mean the black color. (default: None)

  • --tract_colors

    Define the colors of the tractograms. Colors can be defined with 3 values and should be between [0-1]. String options are ‘random’ for random colors for each tractogram, ‘direction’ for directionally colored streamlines. For example, a value of (1, 0, 0) would mean the red color. (default: None)

  • --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)

  • --cluster_size_thr

    Clusters with size less than cluster_size_thr will be hidden. If -1, it will show all cluster above the 50th percentile of the cluster size distribution. (default: -1)

  • --cluster_length_thr

    Clusters with average length less than cluster_length_thr in mm will be hidden. If -1, it will show all cluster above the 25th percentile of the cluster length distribution. (default: -1)

  • --buan_pvals

    File path for BUAN p-values to be used for BUAN-based coloring of tractograms. (default: None)

  • --stealth

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

  • --rgb

    Enable the colors in the image if 4D data with RGB/RGBA channels. (default: False)

Output Options#

  • --out_dir

    Output directory to save the figure if stealth mode is enabled. (default: current directory)

  • --out_stealth_png

    Filename of saved picture if stealth mode is enabled. (default: out_skyline.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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