"""MRtrix3 tractography parameter extraction.
Reads parameters from :class:`thesis.core.config.TractographyConfig` (the
MRtrix-specific fields added there) and produces a flat ``TypedDict`` that
the node builders consume.
"""
from typing import Optional, TypedDict
from thesis.core.config import PipelineConfig
DEFAULT_TCKGEN_ALGORITHM = "iFOD2"
DEFAULT_TCKGEN_SELECT = 5000
DEFAULT_TCKGEN_SEEDS = 5_000_000
DEFAULT_TCKGEN_MINLENGTH = 30.0
DEFAULT_TCKGEN_MAXLENGTH = 250.0
DEFAULT_RESPONSE_ALGORITHM = "dhollander"
DEFAULT_FOD_ALGORITHM = "msmt_csd"
DEFAULT_FIVETT_ALGORITHM = "fsl"
DEFAULT_MASK_SOURCE = "fsl_nodif"
DEFAULT_MASK_DILATE_VOXELS = 1
DEFAULT_SEED_STRATEGY = "roi"
[docs]
class MRtrix3Params(TypedDict):
"""Runtime parameters for MRtrix3 tractography nodes."""
tckgen_algorithm: str
tckgen_select: int
tckgen_seeds: int
tckgen_minlength: float
tckgen_maxlength: float
tckgen_backtrack: bool
tckgen_crop_at_gmwmi: bool
tckgen_cutoff: Optional[float]
response_algorithm: str
fod_algorithm: str
use_mtnormalise: bool
fivett_algorithm: str
mask_source: str
mask_dilate_voxels: int
use_sift2: bool
seed_strategy: str
gmwmi_apply_roi_filters: bool
[docs]
def prepare_mrtrix3_params(config: PipelineConfig) -> MRtrix3Params:
"""Extract MRtrix3 tractography parameters from the pipeline config.
Args:
config: Validated pipeline configuration.
Returns:
Flat dictionary of parameters consumed by MRtrix3 node builders.
"""
tract_cfg = getattr(config, "tractography", None)
return {
"tckgen_algorithm": getattr(tract_cfg, "tckgen_algorithm", DEFAULT_TCKGEN_ALGORITHM),
"tckgen_select": int(getattr(tract_cfg, "tckgen_select", DEFAULT_TCKGEN_SELECT)),
"tckgen_seeds": int(getattr(tract_cfg, "tckgen_seeds", DEFAULT_TCKGEN_SEEDS)),
"tckgen_minlength": float(getattr(tract_cfg, "tckgen_minlength", DEFAULT_TCKGEN_MINLENGTH)),
"tckgen_maxlength": float(getattr(tract_cfg, "tckgen_maxlength", DEFAULT_TCKGEN_MAXLENGTH)),
"tckgen_backtrack": bool(getattr(tract_cfg, "tckgen_backtrack", True)),
"tckgen_crop_at_gmwmi": bool(getattr(tract_cfg, "tckgen_crop_at_gmwmi", True)),
"tckgen_cutoff": getattr(tract_cfg, "tckgen_cutoff", None),
"response_algorithm": getattr(tract_cfg, "response_algorithm", DEFAULT_RESPONSE_ALGORITHM),
"fod_algorithm": getattr(tract_cfg, "fod_algorithm", DEFAULT_FOD_ALGORITHM),
"use_mtnormalise": bool(getattr(tract_cfg, "use_mtnormalise", True)),
"fivett_algorithm": getattr(tract_cfg, "fivett_algorithm", DEFAULT_FIVETT_ALGORITHM),
"mask_source": getattr(tract_cfg, "mask_source", DEFAULT_MASK_SOURCE),
"mask_dilate_voxels": int(
getattr(tract_cfg, "mask_dilate_voxels", DEFAULT_MASK_DILATE_VOXELS)
),
"use_sift2": bool(getattr(tract_cfg, "use_sift2", True)),
"seed_strategy": getattr(tract_cfg, "seed_strategy", DEFAULT_SEED_STRATEGY),
"gmwmi_apply_roi_filters": bool(getattr(tract_cfg, "gmwmi_apply_roi_filters", True)),
}
