usage: __main__.py [-h]
[--sh_basis {descoteaux07,tournier07,descoteaux07_legacy,tournier07_legacy}]
[--todi_sigma {0,1,2,3,4}] [--sf_threshold SF_THRESHOLD]
[--out_prefix OUT_PREFIX] [--out_dir OUT_DIR]
[--reference REFERENCE] [-v [{DEBUG,INFO,WARNING}]] [-f]
in_bundle in_fodf in_mask
Generation of priors and enhanced-FOD from an example/template bundle.
The bundle must have been cleaned thorougly before use. The E-FOD can then
be used for bundle-specific tractography, but not for FOD metrics.
Formerly: scil_generate_priors_from_bundle.py
positional arguments:
in_bundle Input bundle filename.
in_fodf Input FOD filename.
in_mask Mask to constrain the TODI spatial smoothing,
for example a WM mask.
options:
-h, --help show this help message and exit
--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.
--todi_sigma {0,1,2,3,4}
Smooth the orientation histogram.
--sf_threshold SF_THRESHOLD
Relative threshold for sf masking (0.0-1.0).
--out_prefix OUT_PREFIX
Add a prefix to all output filename,
default is no prefix.
--out_dir OUT_DIR Output directory for all generated files,
default is current directory.
--reference REFERENCE
Reference anatomy for tck/vtk/fib/dpy file
support (.nii or .nii.gz).
-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] Rheault, Francois, et al. "Bundle-specific tractography with
incorporated anatomical and orientational priors."
NeuroImage 186 (2019): 382-398