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 can either be streamlines, binary bundle map, or a bundle voxel
label map.
To be considered a valid lesion, the lesion volume must be at least
min_lesion_vol mm3. This avoid the detection of thousand of single voxel
lesions if an automatic lesion segmentation tool is used.
Formerly: scil_analyse_lesions_load.py
positional arguments:
in_lesion Binary mask of the lesion(s) (.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.