usage: __main__.py [-h] [--streamline_dice] [--ignore_zeros_in_BA]
[--disable_streamline_distance]
[--single_compare SINGLE_COMPARE] [--keep_tmp] [--ratio]
[--processes NBR] [--reference REFERENCE] [--indent INDENT]
[--sort_keys] [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
in_bundles [in_bundles ...] out_json
Evaluate pairwise similarity measures of bundles.
All tractograms must be in the same space (aligned to one reference).
Our bundle tractometry analysis scripts
---------------------------------------
- scil_bundle_pairwise_comparison:
- can compare any pair (any combo) from the input list.
- can compare the input list against a single file (--single_compare)
- scil_bundle_score_many_bundles_one_tractogram:
- scores files against their individual ground truth.
- scil_bundle_score_same_bundle_many_segmentations:
- compare many versions of a single bundle.
* If you have volumes associated to your bundles, the following script could be
of interest for you: scil_volume_pairwise_comparison
Computed metrics
----------------
In this script, metrics can be based on the coverage masks of the bundles or
directly on the streamlines:
- For the voxel representation, the computed similarity measures are:
bundle_adjacency_voxels, dice_voxels, w_dice_voxels, density_correlation
volume_overlap, volume_overreach
The same measures are also evaluated for the endpoints.
- For the streamline representation, the computed similarity measures are:
bundle_adjacency_streamlines, dice_streamlines, streamlines_count_overlap,
streamlines_count_overreach
positional arguments:
in_bundles Path of the input bundles.
out_json Path of the output json file.
options:
-h, --help show this help message and exit
--streamline_dice Compute streamline-wise dice coefficient.
Tractograms must be identical [False].
--ignore_zeros_in_BA If set, do not count zeros in the average bundle adjacency (BA).
--disable_streamline_distance
Will not compute the streamlines distance
[False].
--single_compare SINGLE_COMPARE
Compare inputs to this single file.
--keep_tmp Will not delete the tmp folder at the end.
--ratio Compute overlap and overreach as a ratio over the reference volume rather than volume.
Can only be used if also using --single_compare`.
--processes NBR Number of sub-processes to start.
Default: [1]
--reference REFERENCE
Reference anatomy for tck/vtk/fib/dpy file
support (.nii or .nii.gz).
-v [{DEBUG,INFO,WARNING,ERROR}]
Produces verbose output depending on the provided level.
Default level is warning, default when using -v is info.
-f Force overwriting of the output files.
Json options:
--indent INDENT Indent for json pretty print.
--sort_keys Sort keys in output json.
2.2.2