usage: __main__.py [-h] [--fa_threshold FA_THRESHOLD]
[--md_threshold MD_THRESHOLD] [--max_value_output file]
[--mask_output file] [--small_dims]
[--sh_basis {descoteaux07,tournier07,descoteaux07_legacy,tournier07_legacy}]
[-v [{DEBUG,INFO,WARNING}]] [-f]
fODFs FA MD
Script to compute the maximum fODF in the ventricles. The ventricules are
estimated from an MD and FA threshold.
This allows to clip the noise of fODF using an absolute thresold.
Formerly: scil_compute_fodf_max_in_ventricles.py
positional arguments:
fODFs Path of the fODF volume in spherical harmonics (SH).
FA Path to the FA volume.
MD Path to the mean diffusivity (MD) volume.
options:
-h, --help show this help message and exit
--fa_threshold FA_THRESHOLD
Maximal threshold of FA (voxels under that threshold are considered
for evaluation. [0.1]).
--md_threshold MD_THRESHOLD
Minimal threshold of MD in mm2/s (voxels above that threshold are
considered for evaluation. [0.003]).
--max_value_output file
Output path for the text file containing the value. If not set the
file will not be saved.
--mask_output file Output path for the ventricule mask. If not set, the mask
will not be saved.
--small_dims If set, takes the full range of data to search the max fodf amplitude
in ventricles. Useful when the data has small dimensions.
--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.
-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.
[1] Dell'Acqua, Flavio, et al. "Can spherical deconvolution provide more
information than fiber orientations? Hindrance modulated orientational
anisotropy, a true-tract specific index to characterize white matter
diffusion." Human brain mapping 34.10 (2013): 2464-2483.