usage: __main__.py [-h] [--ignore_zeros_in_BA] [--single_compare FILE]
[--ratio] [--labels_to_mask] [--processes NBR]
[--indent INDENT] [--sort_keys]
[-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
[in_volumes ...] out_json
Evaluate pair-wise similarity measures of masks and atlas.
All volumes must be co-registered in the same space.
Support multiple input volume. The following command will compare all
combinations of the input volumes (1-2, 1-3, 2-3):
scil_volume_pairwise_comparison mask1.nii.gz mask2.nii.gz mask3.nii.gz out.json
The following command will compare all input of the input volumes to a single
volume (1-ref, 2-ref, 3-ref):
scil_volume_pairwise_comparison mask1.nii.gz mask2.nii.gz mask3.nii.gz out.json --single_compare ref.nii.gz
This can work for BET mask, WMPARC, bundle label maps. The datatype of the
input volumes must be uint8 (mask) or uint16 (label map and atlas).
The computed similarity measures are:
adjacency_voxels, dice_voxels, volume_overlap, volume_overreach.
For each measure, an entry in the json file will be created and for each unique
value present in the input volumes there will be an entry under the measure.
(i.e. a binary mask will have one entries for each measure, 1).
If you specify --single_compare, the script will compute the overreach wrt
the reference volume and not both.
If you have streamlines to compare, the following script could be
of interest for you: scil_bundle_pairwise_comparison
positional arguments:
in_volumes Path of the input volumes.
out_json Path of the output json file.
options:
-h, --help show this help message and exit
--ignore_zeros_in_BA If set, do not count zeros in the average bundle adjacency (BA).
--single_compare FILE
Compare inputs to this single file.
--ratio Compute overlap and overreach as a ratio over the reference volume rather than as an absolute.
Can only be used if also using --single_compare`.
--labels_to_mask Allows for comparison between labels and single binary mask. Can only be used with --single_compare.
--processes NBR Number of sub-processes to start.
Default: [1]
-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