usage: __main__.py [-h] [--mask MASK] [--apply_config JSON] [-f]
[-v [{DEBUG,INFO,WARNING,ERROR}]]
in_folder in_ref_img out_dir
BundleSeg output visualization tool.
This script allows visualization of segmented bundles and after-the-fact
filtering to explore optimal thresholds for each bundle. It uses
FURY for 3D rendering.
It includes tools to slice images, filter streamlines, and interactively
visualize bundles and a reference image.
This script is intended to be used after running BundleSeg:
scil_tractogram_segment_with_bundleseg
To explore thresholds the option --exploration_mode must be used to segment
using a much higher distance threshold.
positional arguments:
in_folder Folder generated by BundleSeg containing the results.
in_ref_img Background reference image.
out_dir Output directory for filtered bundles.
options:
-h, --help show this help message and exit
--mask MASK Binary mask used to render surfaces (VOI).
--apply_config JSON Apply a configuration file to automatically filter.
-f Force overwriting of the output files.
-v [{DEBUG,INFO,WARNING,ERROR}]
Produces verbose output depending on the provided level.
Default level is warning, default when using -v is info.