usage: __main__.py [-h] [--nb_ring NB_RING] [--ring_thickness RING_THICKNESS]
[--mask MASK] [--split_4D OUT_DIR]
[-v [{DEBUG,INFO,WARNING}]] [-f]
in_image out_image
The NAWM (Normal Appearing White Matter) is the white matter that is
neighboring a lesion. It is used to compute metrics in the white matter
surrounding lesions.
This script will generate concentric rings around the lesions, with the rings
going from 2 to nb_ring + 2, with the lesion being 1.
The optional mask is used to compute the rings only in the mask
region. This can be useful to avoid useless computation.
If the lesion_atlas is binary, the output will be 3D. If the lesion_atlas
is a label map, the output will be either:
- 4D, with each label having its own NAWM.
- 3D, if using --split_4D and saved into a folder as multiple 3D files.
WARNING: Voxels must be isotropic.
positional arguments:
in_image Lesions file as mask OR labels (.nii.gz).
(must be uint8 for mask, uint16 for labels).
out_image Output NAWM file (.nii.gz).
If using --split_4D, this will be the prefix of the output files.
options:
-h, --help show this help message and exit
--nb_ring NB_RING Integer representing the number of rings to be created.
--ring_thickness RING_THICKNESS
Integer representing the thickness (in voxels) of the rings to be created.
--mask MASK Mask where to compute the NAWM (e.g WM mask).
--split_4D OUT_DIR Provided lesions will be split into multiple files.
The output files will be named using out_image as a prefix.
-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.
Scilpy version: 2.0.2