usage: __main__.py [-h] [--ignore_voxel_size] [-v [{DEBUG,INFO,WARNING}]] [-f]
[--input_bbox INPUT_BBOX | --output_bbox OUTPUT_BBOX]
in_image out_image
Crop a volume using a given or an automatically computed bounding box. If a
previously computed bounding box file is given, the cropping will be applied
and the affine fixed accordingly.
Warning: This works well on masked images (like with FSL-Bet) volumes since
it's looking for non-zero data. Therefore, you should validate the results on
other types of images that haven't been masked.
Formerly: scil_crop_volume.py
positional arguments:
in_image Path of the nifti file to crop.
out_image Path of the cropped nifti file to write.
options:
-h, --help show this help message and exit
--ignore_voxel_size Ignore voxel size compatibility test between input bounding box and data. Warning, use only if you know what you are doing.
-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.
--input_bbox INPUT_BBOX
Path of the pickle file from which to take the bounding box to crop input file.
--output_bbox OUTPUT_BBOX
Path of the pickle file where to write the computed bounding box. (.pickle extension)