usage: __main__.py [-h] [--mask MASK] [--out_dir OUT_DIR] [--tolerance tol]
[--skip_b0_check] [--para_diff PARA_DIFF]
[--iso_diff ISO_DIFF] [--lambda1 LAMBDA1]
[--lambda2 LAMBDA2]
[--save_kernels DIRECTORY | --load_kernels DIRECTORY]
[--compute_only] [--processes NBR]
[-v [{DEBUG,INFO,WARNING}]] [-f]
in_dwi in_bval in_bvec
Compute NODDI [1] maps using AMICO.
Multi-shell DWI necessary.
Formerly: scil_compute_NODDI.py
---------------------------------------------------------------
Reference:
[1] Zhang H, Schneider T, Wheeler-Kingshott CA, Alexander DC.
NODDI: practical in vivo neurite orientation dispersion
and density imaging of the human brain.
NeuroImage. 2012 Jul 16;61:1000-16.
---------------------------------------------------------------
positional arguments:
in_dwi DWI file acquired with a NODDI compatible protocol (single-shell data not suited).
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 NODDI results. [results]
--tolerance tol The tolerated gap between the b-values to extract and the current b-value.
[Default: 20]
* Note. We would expect to find at least one b-value in the
range [0, tolerance]. 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 --tolerance). 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 the original --tolerance and no b0 volumes.
Use with care, and only if you understand your data.
--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. [0.0017]
--iso_diff ISO_DIFF Mean diffusivity (MD) in ventricles. [0.003]
--lambda1 LAMBDA1 First regularization parameter. [0.5]
--lambda2 LAMBDA2 Second regularization parameter. [0.001]
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.
Scilpy version: 2.0.2