scil_lesions_info.py

usage: __main__.py [-h]
                   [--bundle BUNDLE | --bundle_mask BUNDLE_MASK | --bundle_labels_map BUNDLE_LABELS_MAP]
                   [--min_lesion_vol MIN_LESION_VOL] [--out_lesion_atlas FILE]
                   [--out_lesion_stats FILE] [--out_streamlines_stats FILE]
                   [--indent INDENT] [--sort_keys] [--reference REFERENCE]
                   [-v [{DEBUG,INFO,WARNING}]] [-f]
                   in_lesion out_json

This script will output informations about lesion load in bundle(s).
The input lesion file is a labeled volume (.nii.gz) where each lesion is
represented by a unique label. To label a lesion file use
scil_labels_from_mask.py

Then, the second input can either be streamlines, binary bundle mask, or a
bundle voxel label map.

Formerly: scil_analyse_lesions_load.py

positional arguments:
  in_lesion             Lesions file as labels (.nii.gz).
  out_json              Output file for lesion information (.json).

options:
  -h, --help            show this help message and exit
  --bundle BUNDLE       Path of the bundle file (.trk).
  --bundle_mask BUNDLE_MASK
                        Path of the bundle binary mask (.nii.gz).
  --bundle_labels_map BUNDLE_LABELS_MAP
                        Path of the bundle labels map (.nii.gz).
  --min_lesion_vol MIN_LESION_VOL
                        Minimum lesion volume in mm3 [7].
  --out_lesion_atlas FILE
                        Save the labelized lesion(s) map (.nii.gz).
  --out_lesion_stats FILE
                        Save the lesion-wise volume measure (.json).
  --out_streamlines_stats FILE
                        Save the lesion-wise streamline count (.json).
  --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.

Scilpy version: 2.0.2