.. _scil_volume_crop:

scil_volume_crop
================

::

	usage: __main__.py [-h] [--ignore_voxel_size]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   [--input_bbox INPUT_BBOX | --output_bbox OUTPUT_BBOX | --use_deprecated_pickle]
	                   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.
	
	To:
	    - interpolate/reslice to an arbitrary voxel size, use
	      scil_volume_resample.
	    - pad or crop the volume to match the desired shape, use
	      scil_volume_reshape.
	    - reshape a volume to match the resolution of another, use
	      scil_volume_reslice_to_reference.
	
	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,ERROR}]
	                        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 json file from which to take the bounding box to crop input file.
	  --output_bbox OUTPUT_BBOX
	                        Path of the json file where to write the computed bounding box.
	  --use_deprecated_pickle
	                        Enable to use .pkl bounding boxes instead of .json.
	
	2.2.2