usage: __main__.py [-h] [--distance DISTANCE]
[--labels_to_dilate LABELS_TO_DILATE [LABELS_TO_DILATE ...]]
[--labels_to_fill LABELS_TO_FILL [LABELS_TO_FILL ...]]
[--labels_not_to_dilate LABELS_NOT_TO_DILATE [LABELS_NOT_TO_DILATE ...]]
[--mask MASK] [--processes NBR] [-v [{DEBUG,INFO,WARNING}]]
[-f]
in_file out_file
Dilate regions (with or without masking) from a labeled volume:
- "label_to_dilate" are regions that will dilate over
"label_to_fill" if close enough to it ("distance").
- "label_to_dilate", by default (None) will be all
non-"label_to_fill" and non-"label_not_to_dilate".
- "label_not_to_dilate" will not be changed, but will not dilate.
- "mask" is where the dilation is allowed (constrained)
in addition to "background_label" (logical AND)
>>> scil_labels_dilate.py wmparc_t1.nii.gz wmparc_dil.nii.gz \
--label_to_fill 0 5001 5002 \
--label_not_to_dilate 4 43 10 11 12 49 50 51
Formerly: scil_dilate_labels.py
positional arguments:
in_file Path of the volume (nii or nii.gz).
out_file Output filename of the dilated labels.
options:
-h, --help show this help message and exit
--distance DISTANCE Maximal distance to dilate (in mm) [2.0].
--labels_to_dilate LABELS_TO_DILATE [LABELS_TO_DILATE ...]
Label list to dilate. By default it dilates all
labels not in labels_to_fill nor in labels_not_to_dilate.
--labels_to_fill LABELS_TO_FILL [LABELS_TO_FILL ...]
Background id / labels to be filled [[0]],
the first one is given as output background value.
--labels_not_to_dilate LABELS_NOT_TO_DILATE [LABELS_NOT_TO_DILATE ...]
Label list not to dilate.
--mask MASK Only dilate values inside the mask.
--processes NBR Number of sub-processes to start.
Default: [1]
-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.
References:
[1] Al-Sharif N.B., St-Onge E., Vogel J.W., Theaud G.,
Evans A.C. and Descoteaux M. OHBM 2019.
Surface integration for connectome analysis in age prediction.