usage: __main__.py [-h] [-f] [--sh_order SH_ORDER] [--mask MASK] [--use_qball]
[--not_all] [--gfa GFA] [--peaks PEAKS]
[--peak_indices PEAK_INDICES] [--sh SH] [--nufo NUFO]
[--a_power A_POWER] [--b0_threshold thr] [--skip_b0_check]
[--sh_basis {descoteaux07,tournier07,descoteaux07_legacy,tournier07_legacy}]
[--processes NBR] [-v [{DEBUG,INFO,WARNING}]]
in_dwi in_bval in_bvec
Script to compute the Constant Solid Angle (CSA) or Analytical Q-ball model,
the generalized fractional anisotropy (GFA) and the peaks of the model.
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 [Descoteaux et al MRM 2007, Aganj et al MRM 2009] for details and
[Cote et al MEDIA 2013] for quantitative comparisons.
Formerly: scil_compute_qball_metrics.py
positional arguments:
in_dwi Path of the input diffusion volume.
in_bval Path of the bvals file, in FSL format.
in_bvec Path of the bvecs file, in FSL format.
options:
-h, --help show this help message and exit
-f Force overwriting of the output files.
--sh_order SH_ORDER Spherical harmonics order. Must be a positive even number [4].
--mask MASK Path to a binary mask. Only data inside the mask will be used for computations and reconstruction [None].
--use_qball If set, qball will be used as the odf reconstruction model instead of CSA.
--not_all If set, will only save the files specified using the following flags.
--b0_threshold thr Threshold under which b-values are considered to be b0s.
[Default: 20]
* Note. We would expect to find at least one b-value in the
range [0, b0_threshold]. To skip this check, use --skip_b0_check.
--skip_b0_check By default, we supervise that at least one b0 exists in your data
(i.e. b-values below the default --b0_threshold). Use this option to
allow continuing even if the minimum b-value is suspiciously high.
If no b-value is found below the threshold, the script will continue
with your minimal b-value as new --b0_threshold.
Use with care, and only if you understand your data.
--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.
--processes NBR Number of sub-processes to start.
Default: [1]
-v [{DEBUG,INFO,WARNING}]
Produces verbose output depending on the provided level.
Default level is warning, default when using -v is info.
File flags:
--gfa GFA Output filename for the generalized fractional anisotropy [gfa.nii.gz].
--peaks PEAKS Output filename for the extracted peaks [peaks.nii.gz].
--peak_indices PEAK_INDICES
Output filename for the generated peaks indices on the sphere [peaks_indices.nii.gz].
--sh SH Output filename for the spherical harmonics coefficients [sh.nii.gz].
--nufo NUFO Output filename for the NUFO map [nufo.nii.gz].
--a_power A_POWER Output filename for the anisotropic power map[anisotropic_power.nii.gz].