usage: __main__.py [-h]
[--streamlines_measures GOLD_STANDARD_STREAMLINES TRACTOGRAM]
[--voxels_measures GOLD_STANDARD_MASK TRACKING MASK]
[--processes NBR] [--reference REFERENCE] [--indent INDENT]
[--sort_keys] [-v [{DEBUG,INFO,WARNING}]] [-f]
in_bundles [in_bundles ...] out_json
This script is intended to score many versions of a same bundle, compared to
ONE ground truth / gold standard.
See also scil_bundle_score_many_bundles_one_tractogram.py to score all bundles
from a single tractogram by comparing each valid bundle to its ground truth.
All tractograms must be in the same space (aligned to one reference).
The measures can be applied to a voxel-wise or streamline-wise representation.
A gold standard must be provided for the desired representation.
A gold standard would be a segmentation from an expert or a group of experts.
If only the streamline-wise representation is provided without a voxel-wise
gold standard, it will be computed from the provided streamlines.
At least one of the two representations is required.
The gold standard tractogram is the tractogram (whole brain most likely) from
which the segmentation is performed.
The gold standard tracking mask is the tracking mask used by the tractography
algorighm to generate the gold standard tractogram.
The computed binary classification measures are:
sensitivity, specificity, precision, accuracy, dice, kappa, youden for both
the streamline and voxel representation (if provided).
Formerly: scil_evaluate_bundles_binary_classification_measures.py
positional arguments:
in_bundles Path of the input bundles.
out_json Path of the output json.
options:
-h, --help show this help message and exit
--streamlines_measures GOLD_STANDARD_STREAMLINES TRACTOGRAM
The gold standard bundle and the original tractogram.
--voxels_measures GOLD_STANDARD_MASK TRACKING MASK
The gold standard mask and the original tracking mask.
--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}]
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.