usage: __main__.py [-h] [--sh_order int] [--mask] [--b0_threshold thr]
[--skip_b0_check]
[--sh_basis {descoteaux07,tournier07,descoteaux07_legacy,tournier07_legacy}]
[--processes NBR] [-v [{DEBUG,INFO,WARNING}]] [-f]
in_dwi in_bval in_bvec frf_file out_fODF
Script to compute Constrained Spherical Deconvolution (CSD) fiber ODFs.
See [Tournier et al. NeuroImage 2007]
Formerly: scil_compute_ssst_fodf.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.
frf_file Path of the FRF file
out_fODF Output path for the fiber ODF coefficients.
options:
-h, --help show this help message and exit
--sh_order int SH order used for the CSD. (Default: 8)
--mask Path to a binary mask. Only the data inside the mask will be used
for computations and reconstruction.
--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.
-f Force overwriting of the output files.