usage: __main__.py [-h] [--mask MASK] [--out_dir OUT_DIR] [--b_thr B_THR]
[--para_diff PARA_DIFF] [--iso_diff ISO_DIFF]
[--perp_diff_min PERP_DIFF_MIN]
[--perp_diff_max PERP_DIFF_MAX] [--lambda1 LAMBDA1]
[--lambda2 LAMBDA2]
[--save_kernels DIRECTORY | --load_kernels DIRECTORY]
[--compute_only] [--mouse] [--processes NBR]
[-v [{DEBUG,INFO,WARNING}]] [-f]
in_dwi in_bval in_bvec
Compute Free Water maps [1] using AMICO.
This script supports both single and multi-shell data.
Formerly: scil_compute_freewater.py
positional arguments:
in_dwi DWI file.
in_bval b-values filename, in FSL format (.bval).
in_bvec b-vectors filename, in FSL format (.bvec).
options:
-h, --help show this help message and exit
--mask MASK Brain mask filename.
--out_dir OUT_DIR Output directory for the Free Water results. [results]
--b_thr B_THR Limit value to consider that a b-value is on an
existing shell. Above this limit, the b-value is
placed on a new shell. This includes b0s values.
--mouse If set, use mouse fitting profile.
--processes NBR Number of sub-processes to start. Default: [1]
-v [{DEBUG,INFO,WARNING}]
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.
Model options:
--para_diff PARA_DIFF
Axial diffusivity (AD) in the CC. [0.0015]
--iso_diff ISO_DIFF Mean diffusivity (MD) in ventricles. [0.003]
--perp_diff_min PERP_DIFF_MIN
Radial diffusivity (RD) minimum. [0.0001]
--perp_diff_max PERP_DIFF_MAX
Radial diffusivity (RD) maximum. [0.0007]
--lambda1 LAMBDA1 First regularization parameter. [0.0]
--lambda2 LAMBDA2 Second regularization parameter. [0.25]
Kernels options:
--save_kernels DIRECTORY
Output directory for the COMMIT kernels.
--load_kernels DIRECTORY
Input directory where the COMMIT kernels are located.
--compute_only Compute kernels only, --save_kernels must be used.
Reference:
[1] Pasternak 0, Sochen N, Gur Y, Intrator N, Assaf Y.
Free water elimination and mapping from diffusion mri.
Magn Reson Med. 62 (3) (2009) 717-730.