usage: __main__.py [-h] [--fa_threshold FA_THRESHOLD]
[--md_threshold MD_THRESHOLD] [--in_mask file]
[--max_value_output file] [--out_mask file] [--small_dims]
[--use_median]
[--sh_basis {descoteaux07,tournier07,descoteaux07_legacy,tournier07_legacy}]
[-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
fODFs FA MD
Script to compute the mean/median 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.
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Reference:
[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.
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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]).
--in_mask file Path to a binary mask. Only the data inside the mask will be used
for evaluation. Useful if the FA and MD thresholds are not good enough.
--max_value_output file
Output path for the text file containing the value. If not set the
file will not be saved.
--out_mask 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.
--use_median If set, use the median value instead of the mean.
--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,ERROR}]
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.
2.2.2