usage: __main__.py [-h] [--fa_min_single_fiber FA_MIN_SINGLE_FIBER]
[--fa_max_ventricles FA_MAX_VENTRICLES]
[--md_min_ventricles MD_MIN_VENTRICLES]
[--roi_radius ROI_RADIUS] [--roi_center pos pos pos]
[--out_txt_1fiber_para FILE] [--out_txt_1fiber_perp FILE]
[--out_mask_1fiber FILE] [--out_txt_ventricles FILE]
[--out_mask_ventricles FILE] [-v [{DEBUG,INFO,WARNING}]]
[-f]
in_FA in_AD in_RD in_MD
Compute the axial (para_diff), radial (perp_diff), and mean (iso_diff)
diffusivity priors for NODDI.
Formerly: scil_compute_NODDI_priors.py
positional arguments:
in_FA Path to the FA volume.
in_AD Path to the axial diffusivity (AD) volume.
in_RD Path to the radial diffusivity (RD) volume.
in_MD Path to the mean diffusivity (MD) volume.
options:
-h, --help show this help message and exit
-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.
Metrics options:
--fa_min_single_fiber FA_MIN_SINGLE_FIBER
Minimal threshold of FA (voxels above that threshold are considered in
the single fiber mask). [0.7]
--fa_max_ventricles FA_MAX_VENTRICLES
Maximal threshold of FA (voxels under that threshold are considered in
the ventricles). [0.1]
--md_min_ventricles MD_MIN_VENTRICLES
Minimal threshold of MD in mm2/s (voxels above that threshold are considered
for in the ventricles). [0.003]
Regions options:
--roi_radius ROI_RADIUS
Radius of the region used to estimate the priors. The roi will be a cube spanning
from ROI_CENTER in each direction. [20]
--roi_center pos pos pos
Center of the roi of size roi_radius used to estimate the priors; a 3-value coordinate.
If not set, uses the center of the 3D volume.
Outputs:
--out_txt_1fiber_para FILE
Output path for the text file containing the single fiber average value of AD.
If not set, the file will not be saved.
--out_txt_1fiber_perp FILE
Output path for the text file containing the single fiber average value of RD.
If not set, the file will not be saved.
--out_mask_1fiber FILE
Output path for single fiber mask. If not set, the mask will not be saved.
--out_txt_ventricles FILE
Output path for the text file containing the ventricles average value of MD.
If not set, the file will not be saved.
--out_mask_ventricles FILE
Output path for the ventricule mask.
If not set, the mask will not be saved.
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.