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
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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.
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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