.. _scil_volume_validate_correct_strides:

scil_volume_validate_correct_strides
====================================

::

	usage: __main__.py [-h] [--in_bvec IN_BVEC] [--out_bvec OUT_BVEC]
	                   [--validate_bvec] [--in_bval IN_BVAL] [--b0_threshold thr]
	                   [--skip_b0_check] [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   in_data out_data
	
	Detect when data strides are different from [1, 2, 3] and correct them.
	The script takes as input a nifti file and outputs a nifti file with the
	corrected strides if needed.
	
	Input file can be 3D or 4D. Only the first 3 dimensions are considered
	for the stride correction. In the case of DWI data, we recommand to also input
	the b-values and b-vectors files to correct the b-vectors accordingly. If the
	--validate_bvecs is set, the script first detects sign flips and/or axes swaps
	in the b-vectors from a fiber coherence index [1] and corrects the b-vectors.
	Then, the b-vectors are permuted and sign flipped to match the new strides.
	
	A typical pipeline could be:
	>>> scil_volume_validate_correct_strides t1.nii.gz t1_restride.nii.gz
	>>> scil_volume_validate_correct_strides dwi.nii.gz dwi_restride.nii.gz
	    --in_bvec dwi.bvec --out_bvec dwi_restride.bvec --validate_bvec
	    --in_bval dwi.bval
	
	------------------------------------------------------------------------------
	Reference:
	[1] Schilling KG, Yeh FC, Nath V, Hansen C, Williams O, Resnick S, Anderson AW,
	    Landman BA. A fiber coherence index for quality control of B-table
	    orientation in diffusion MRI scans. Magn Reson Imaging. 2019 May;58:82-89.
	    doi: 10.1016/j.mri.2019.01.018.
	------------------------------------------------------------------------------
	
	positional arguments:
	  in_data               Path to input nifti file.
	  out_data              Path to output nifti file with corrected strides.
	
	options:
	  -h, --help            show this help message and exit
	  --in_bvec IN_BVEC     Path to bvec file (FSL format). If provided, the bvecs will 
	                        be permuted and sign flipped to match the new strides.
	  --out_bvec OUT_BVEC   Path to output bvec file (FSL format). Must be provided if --in_bvec is used.
	  --validate_bvec       If set, the script first detects sign flips and/or axes swaps 
	                        in the b-vectors from a fiber coherence index [1] and corrects 
	                        the b-vectors before permuting/sign flipping them to match the new strides. 
	                        If not set, the b-vectors are only permuted and sign flipped to match the new strides.
	  --in_bval IN_BVAL     Path to bval file. Must be provided if --validate_bvecs is used.
	  --b0_threshold thr    Threshold under which b-values are considered to be b0s.
	                        [Default: 20] 
	                        * Note. We would expect to find at least one b-value in the 
	                          range [0, b0_threshold]. To skip this check, use --skip_b0_check.
	  --skip_b0_check       By default, we supervise that at least one b0 exists in your data
	                        (i.e. b-values below the default --b0_threshold). Use this option to 
	                        allow continuing even if the minimum b-value is suspiciously high.
	                        If no b-value is found below the threshold, the script will continue 
	                        with your minimal b-value as new --b0_threshold.
	                        Use with care, and only if you understand your data.
	  -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.
	
	2.2.2