usage: __main__.py [-h] [--std_scale STD_SCALE] [--b0_threshold thr]
[--skip_b0_check] [-v [{DEBUG,INFO,WARNING}]]
in_dwi in_bval in_bvec
This script simply finds the 3 closest angular neighbors of each direction
(per shell) and compute the voxel-wise correlation.
If the angles or correlations to neighbors are below the shell average (by
args.std_scale x STD) it will flag the volume as a potential outlier.
This script supports multi-shells, but each shell is independant and detected
using the --b0_threshold parameter.
This script can be run before any processing to identify potential problem
before launching pre-processing.
positional arguments:
in_dwi The DWI file (.nii) to concatenate.
in_bval The b-values files in FSL format (.bval).
in_bvec The b-vectors files in FSL format (.bvec).
options:
-h, --help show this help message and exit
--std_scale STD_SCALE
How many deviation from the mean are required to be considered an outlier. [2.0]
--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}]
Produces verbose output depending on the provided level.
Default level is warning, default when using -v is info.