usage: __main__.py [-h]
(--sphere {repulsion100,repulsion200,repulsion724,symmetric362,symmetric642,symmetric724} | --in_bvec IN_BVEC)
[--dtype {float32,float64}] [--in_bval IN_BVAL]
[--in_b0 IN_B0] [--out_bval OUT_BVAL] [--out_bvec OUT_BVEC]
[--b0_scaling]
[--sh_basis {descoteaux07,tournier07,descoteaux07_legacy,tournier07_legacy}]
[--full_basis] [--b0_threshold thr] [--processes NBR]
[-v [{DEBUG,INFO,WARNING}]] [-f]
in_sh out_sf
Script to sample SF values from a Spherical Harmonics signal. Outputs a Nifti
file with the SF values and an associated .bvec file with the chosen
directions.
If converting from SH to a DWI-like SF volume, --in_bval and --in_b0 need
to be provided to concatenate the b0 image to the SF, and to generate the new
bvals file. Otherwise, no .bval file will be created.
Formerly: scil_compute_sf_from_sh.py
positional arguments:
in_sh Path of the SH volume.
out_sf Name of the output SF file to save (bvals/bvecs will be automatically named when necessary).
options:
-h, --help show this help message and exit
--sphere {repulsion100,repulsion200,repulsion724,symmetric362,symmetric642,symmetric724}
Sphere used for the SH to SF projection.
--in_bvec IN_BVEC Directions used for the SH to SF projection.
If given, --in_bval must also be provided.
--dtype {float32,float64}
Datatype to use for SF computation and output array.'[float32]'
--in_bval IN_BVAL b-value file, in FSL format, used to assign a b-value to the
output SF and generate a `.bval` file.
- If used, --out_bval is required.
- The output bval will contain one b-value per point in the SF
output (i.e. one per point on the --sphere or one per --in_bvec.)
- The values of the output bval will all be set to the same b-value:
the average of your in_bval. (Any b0 found in this file, i.e
b-values under --b0_threshold, will be removed beforehand.)
- To add b0s to both the SF volume and the --out_bval file, use --in_b0.
--in_b0 IN_B0 b0 volume to concatenate to the final SF volume.
--out_bval OUT_BVAL Optional output bval file.
--out_bvec OUT_BVEC Optional output bvec file.
--b0_scaling Scale resulting SF by the b0 image (--in_b0 mustbe given).
--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.
--full_basis If true, use a full basis for the input SH coefficients.
--b0_threshold thr Threshold under which b-values are considered to be b0s.
Default if not set is 20.
This value is used with option --in_bval only: any b0 found in the in_bval will be removed.
--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.