usage: __main__.py [-h] [--sphere string] [--mask] [--at A_THRESHOLD]
[--rt R_THRESHOLD] [--abs_peaks_and_values]
[--sh_basis {descoteaux07,tournier07,descoteaux07_legacy,tournier07_legacy}]
[-v [{DEBUG,INFO,WARNING}]] [--processes NBR] [-f]
[--not_all] [--afd_max file] [--afd_total file]
[--afd_sum file] [--nufo file] [--rgb file] [--peaks file]
[--peak_values file] [--peak_indices file]
in_fODF
Script to compute the maximum Apparent Fiber Density (AFD), the fiber ODFs
orientations, values and indices (peaks, peak_values, peak_indices), the Number
of Fiber Orientations (NuFO) maps from fiber ODFs and the RGB map.
AFD_max map is the maximal fODF amplitude for each voxel.
NuFO is the the number of maxima of the fODF with an ABSOLUTE amplitude above
the threshold set using --at, AND an amplitude above the RELATIVE threshold
set using --rt.
The --at argument should be set to a value which is 1.5 times the maximal
value of the fODF in the ventricules. This can be obtained with the
scil_fodf_max_in_ventricles.py script.
If the --abs_peaks_and_values argument is set, the peaks are all normalized
and the peak_values are equal to the actual fODF amplitude of the peaks. By
default, the script max-normalizes the peak_values for each voxel and
multiplies the peaks by peak_values.
By default, will output all possible files, using default names. Specific names
can be specified using the file flags specified in the "File flags" section.
If --not_all is set, only the files specified explicitly by the flags will be
output.
See [Raffelt et al. NeuroImage 2012] and [Dell'Acqua et al HBM 2013] for the
definitions.
Formerly: scil_compute_fodf_metrics.py
positional arguments:
in_fODF Path of the fODF volume in spherical harmonics (SH).
options:
-h, --help show this help message and exit
--sphere string Discrete sphere to use in the processing [repulsion724].
--mask Path to a binary mask. Only the data inside the mask
will beused for computations and reconstruction [None].
--at A_THRESHOLD Absolute threshold on fODF amplitude. This value should be set to
approximately 1.5 to 2 times the maximum fODF amplitude in isotropic voxels
(ie. ventricles).
Use scil_fodf_max_in_ventricles.py to find the maximal value.
See [Dell'Acqua et al HBM 2013] [0.0].
--rt R_THRESHOLD Relative threshold on fODF amplitude in percentage [0.1].
--abs_peaks_and_values
If set, the peak_values are not max-normalized for each voxel,
but rather they keep the actual fODF amplitude of the peaks.
Also, the peaks are given as unit directions instead of being proportional to peak_values. [False]
--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.
--processes NBR Number of sub-processes to start.
Default: [1]
-f Force overwriting of the output files.
--not_all If set, only saves the files specified using the file flags [False].
File flags:
--afd_max file Output filename for the AFD_max map.
--afd_total file Output filename for the AFD_total map(SH coeff = 0).
--afd_sum file Output filename for the sum of all peak contributions
(sum of fODF lobes on the sphere).
--nufo file Output filename for the NuFO map.
--rgb file Output filename for the RGB map.
--peaks file Output filename for the extracted peaks.
--peak_values file Output filename for the extracted peaks values.
--peak_indices file Output filename for the generated peaks indices on the sphere.