usage: __main__.py [-h] [--mask MASK] [--asi_map ASI_MAP]
[--odd_power_map ODD_POWER_MAP] [--peaks PEAKS]
[--peak_values PEAK_VALUES] [--peak_indices PEAK_INDICES]
[--nufid NUFID] [--not_all] [--at A_THRESHOLD]
[--rt R_THRESHOLD]
[--sphere {repulsion100,repulsion200,repulsion724,symmetric362,symmetric642,symmetric724}]
[--processes NBR]
[--sh_basis {descoteaux07,tournier07,descoteaux07_legacy,tournier07_legacy}]
[-v [{DEBUG,INFO,WARNING}]] [-f]
in_sh
Script to compute various metrics derivated from asymmetric ODF.
These metrics include the asymmetric peak directions image, a number of fiber
directions (nufid) map [1], the asymmetry index (ASI) map [2] and an odd-power
map [3].
The asymmetric peak directions image contains peaks per hemisphere, considering
antipodal sphere directions as distinct. On a symmetric signal, the number of
asymmetric peaks extracted is then twice the number of symmetric peaks.
The nufid map is the asymmetric alternative to NuFO maps. It counts the
number of asymmetric peaks extracted and ranges in [0..N] with N the maximum
number of peaks.
The asymmetric index is a cosine-based metric in the range [0..1], with 0
corresponding to a perfectly symmetric signal and 1 to a perfectly asymmetric
signal.
The odd-power map is also in the range [0..1], with 0 corresponding to a
perfectly symmetric signal and 1 to a perfectly anti-symmetric signal. It is
given as the ratio of the L2-norm of odd SH coefficients on the L2-norm of all
SH coefficients.
Formerly: scil_compute_asym_odf_metrics.py
positional arguments:
in_sh Input SH image.
options:
-h, --help show this help message and exit
--mask MASK Optional mask.
--asi_map ASI_MAP Output asymmetry index (ASI) map.
--odd_power_map ODD_POWER_MAP
Output odd power map.
--peaks PEAKS Output filename for the extracted peaks.
--peak_values PEAK_VALUES
Output filename for the extracted peaks values.
--peak_indices PEAK_INDICES
Output filename for the generated peaks indices on the sphere.
--nufid NUFID Output filename for the nufid file.
--not_all If set, only saves the files specified using the file flags [False].
--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].
--sphere {repulsion100,repulsion200,repulsion724,symmetric362,symmetric642,symmetric724}
Sphere to use for peak directions estimation [symmetric724].
--processes NBR Number of sub-processes to start.
Default: [1]
--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.
References:
[1] C. Poirier and M. Descoteaux, "Filtering Methods for Asymmetric ODFs:
Where and How Asymmetry Occurs in the White Matter." bioRxiv. 2022 Jan 1;
2022.12.18.520881. doi: https://doi.org/10.1101/2022.12.18.520881
[2] S. Cetin Karayumak, E. Özarslan, and G. Unal,
"Asymmetric Orientation Distribution Functions (AODFs) revealing intravoxel
geometry in diffusion MRI," Magnetic Resonance Imaging, vol. 49, pp. 145-158,
Jun. 2018, doi: https://doi.org/10.1016/j.mri.2018.03.006.
[3] C. Poirier, E. St-Onge, and M. Descoteaux, "Investigating the Occurence of
Asymmetric Patterns in White Matter Fiber Orientation Distribution Functions"
[Abstract], In: Proc. Intl. Soc. Mag. Reson. Med. 29 (2021), 2021 May 15-20,
Vancouver, BC, Abstract number 0865.