usage: __main__.py [-h] [-f] [--mask file] [--b0_thr B0_THR]
[--shells SHELLS [SHELLS ...]] [--shell_thr SHELL_THR]
[-v [{DEBUG,INFO,WARNING}]]
in_dwi in_bval out_avg
Script to compute powder average (mean diffusion weighted image) from set of
diffusion images.
By default will output an average image calculated from all images with
non-zero bvalue.
Specify --bvalue to output an image for a single shell
Script currently does not take into account the diffusion gradient directions
being averaged.
Formerly: scil_compute_powder_average.py
positional arguments:
in_dwi Path of the input diffusion volume.
in_bval Path of the bvals file, in FSL format.
out_avg Path of the output file.
options:
-h, --help show this help message and exit
-f Force overwriting of the output files.
--mask file Path to a binary mask.
Only data inside the mask will be used for powder avg. (Default: None)
--b0_thr B0_THR Exclude b0 volumes from powder average with bvalue less than specified threshold.
(Default: remove volumes with bvalue < 50
--shells SHELLS [SHELLS ...]
bvalue (shells) to include in powder average passed as a list
(e.g. --shells 1000 2000). If not specified will include all volumes with a non-zero bvalue.
--shell_thr SHELL_THR
Include volumes with bvalue +- the specified threshold.
(Default: [50]
-v [{DEBUG,INFO,WARNING}]
Produces verbose output depending on the provided level.
Default level is warning, default when using -v is info.