usage: __main__.py [-h] [--out_prefix OUT_PREFIX] [--mask MASK]
[--processes NBR]
[--sh_basis {descoteaux07,tournier07,descoteaux07_legacy,tournier07_legacy}]
[-v [{DEBUG,INFO,WARNING}]] [-f]
in_prefix in_volume
Use the NUFO map information to select the plausible number of tensors
in the Multi-Resolution Discrete Search (MRDS).
https://link.springer.com/chapter/10.1007/978-3-031-47292-3_4
scil_mrds_select_number_of_tensors.py uses the output from mdtmrds command.
Some mdtmrds output files will be named differently from the expected input:
COMP_SIZE becomes signal_fraction
NUM_COMP becomes num_tensors
PDDs_CARTESIAN becomes evecs
Eigenvalues becomes evals
mdtmrds: information available soon (not part of scilpy).
Input:
Inputs are a list of 5 files for each MRDS solution (D1, D2, D3).
- Signal fraction of each tensor ([in_prefix]_D[1,2,3]_signal_fraction.nii.gz)
- Eigenvalues ($in_prefix]_D[1,2,3]_evals.nii.gz)
- Isotropic ([in_prefix]_D[1,2,3]_isotropic.nii.gz)
- Number of tensors ([in_prefix]_D[1,2,3]_num_tensors.nii.gz)
- Eigenvectors ([in_prefix]_D[1,2,3]_evecs.nii.gz)
Example:
scil_mrds_select_number_of_tensors.py sub-01 nufo.nii.gz
positional arguments:
in_prefix Prefix used for all MRDS solutions.
in_volume Volume with the number of expected tensors. (Example: NUFO volume)
options:
-h, --help show this help message and exit
--out_prefix OUT_PREFIX
Prefix of the MRDS results [results].
--mask MASK Optional mask filename.
--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.
Scilpy version: 2.0.2