usage: __main__.py [-h] [--relative RELATIVE] [--absolute ABSOLUTE]
[--sh_basis {descoteaux07,tournier07,descoteaux07_legacy,tournier07_legacy}]
[--sphere {repulsion100,repulsion200,repulsion724,symmetric362,symmetric642,symmetric724}]
[-f] [-v [{DEBUG,INFO,WARNING,ERROR}]]
in_odf out_mask
Compute a binary mask based on a global SF threshold.
The script masks voxels where the maximum SF amplitude is below
either a relative factor or an absolute threshold (or both).
When fODFs are evaluated on a sphere (SF), the amplitude of the lobes
corresponds to the strength of the diffusion signal in those directions.
Thresholding these amplitudes is a common practice to filter out spurious
peaks arising from noise or the deconvolution process (e.g., ringing effects).
The absolute threshold can be estimated from the mean/median maximum fODF
in the ventricles, computed with scil_fodf_max_in_ventricles.
If both --relative and --absolute are provided, the final threshold is the
maximum of the two resulting values.
positional arguments:
in_odf Input ODF file (SH or Peaks) (.nii.gz).
out_mask Output binary mask (.nii.gz).
options:
-h, --help show this help message and exit
--sh_basis {descoteaux07,tournier07,descoteaux07_legacy,tournier07_legacy}
Spherical harmonics basis used for the SH coefficients.
Must be either descoteaux07', 'tournier07',
'descoteaux07_legacy' or 'tournier07_legacy' [['descoteaux07_legacy']]:
'descoteaux07' : SH basis from the Descoteaux et al.
MRM 2007 paper
'tournier07' : SH basis from the new Tournier et al.
NeuroImage 2019 paper, as in MRtrix 3.
'descoteaux07_legacy': SH basis from the legacy Dipy implementation
of the Descoteaux et al. MRM 2007 paper
'tournier07_legacy' : SH basis from the legacy Tournier et al.
NeuroImage 2007 paper.
--sphere {repulsion100,repulsion200,repulsion724,symmetric362,symmetric642,symmetric724}
Dipy sphere; set of possible directions.
Default: [repulsion724]
-f Force overwriting of the output files.
-v [{DEBUG,INFO,WARNING,ERROR}]
Produces verbose output depending on the provided level.
Default level is warning, default when using -v is info.
Threshold options:
--relative RELATIVE Global SF threshold relative factor (0-1).
--absolute ABSOLUTE Global SF absolute threshold.
2.3.0