usage: __main__.py [-h] --volume_ids VOLUME_IDS [VOLUME_IDS ...]
[--out_labels_ids OUT_LABELS_IDS [OUT_LABELS_IDS ...] |
--unique | --group_in_m] [--background BACKGROUND]
[--merge_groups] [-v [{DEBUG,INFO,WARNING}]] [-f]
output
Script to combine labels from multiple volumes. If there is overlap, it will
overwrite them based on the input order.
>>> scil_labels_combine.py out_labels.nii.gz
--volume_ids animal_labels.nii 20
--volume_ids DKT_labels.nii.gz 44 53
--out_labels_indices 20 44 53
>>> scil_labels_combine.py slf_labels.nii.gz
--volume_ids a2009s_aseg.nii.gz all
--volume_ids clean/s1__DKT.nii.gz 1028 2028
Formerly: scil_combine_labels.py.
positional arguments:
output Combined labels volume output.
options:
-h, --help show this help message and exit
--volume_ids VOLUME_IDS [VOLUME_IDS ...]
List of volumes directly followed by their labels:
--volume_ids atlasA id1a id2a
--volume_ids atlasB id1b id2b ...
"all" can be used instead of id numbers.
--out_labels_ids OUT_LABELS_IDS [OUT_LABELS_IDS ...]
List of labels indices for output images.
--unique If set, output id with unique labels, excluding first background value.
--group_in_m Add (x * 10 000) to each volume labels, where x is the input volume order number.
--background BACKGROUND
Background id, excluded from output [0],
the value is used as output background value.
--merge_groups Each group from the --volume_ids option will be merged as a single labels.
-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.