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[FIX] Fix input specs for eddy #67

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Sep 14, 2023
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[FIX] Fix input specs for eddy #67

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121 changes: 87 additions & 34 deletions src/pydra/tasks/fsl/eddy/eddy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,8 +17,8 @@
... fieldmap_image="fieldmap.nii",
... )
>>> task.cmdline # doctest: +ELLIPSIS
'eddy --imain input.nii --mask brain.nii --acqp params.txt --index index.txt \
--bvecs input.bvec --bvals input.bval --field fieldmap.nii --out eddy ...'
'eddy --imain=input.nii --mask=brain.nii --acqp=params.txt --index=index.txt \
--bvecs=input.bvec --bvals=input.bval --field=fieldmap.nii --out=eddy ...'
"""

__all__ = ["Eddy"]
Expand All @@ -37,41 +37,59 @@ class EddySpec(ShellSpec):

# Parameters that specify input files.
input_image: PathLike = field(
metadata={"help_string": "input image as a 4D volume", "mandatory": True, "argstr": "--imain"}
metadata={
"help_string": "input image as a 4D volume",
"mandatory": True,
"argstr": "--imain={input_image}",
}
)

brain_mask: PathLike = field(
metadata={"help_string": "brain mask as a single volume image", "mandatory": True, "argstr": "--mask"}
metadata={
"help_string": "brain mask as a single volume image",
"mandatory": True,
"argstr": "--mask={brain_mask}",
}
)

encoding_file: PathLike = field(
metadata={
"help_string": "acquisition parameters for the diffusion protocol",
"mandatory": True,
"argstr": "--acqp",
"argstr": "--acqp={encoding_file}",
}
)

index_file: PathLike = field(
metadata={
"help_string": "mapping from volume index to encoding parameters",
"mandatory": True,
"argstr": "--index",
"argstr": "--index={index_file}",
}
)

bvec_file: PathLike = field(
metadata={"help_string": "diffusion directions", "mandatory": True, "argstr": "--bvecs"}
metadata={
"help_string": "diffusion directions",
"mandatory": True,
"argstr": "--bvecs={bvec_file}",
}
)

bval_file: PathLike = field(metadata={"help_string": "diffusion weighting", "mandatory": True, "argstr": "--bvals"})
bval_file: PathLike = field(
metadata={
"help_string": "diffusion weighting",
"mandatory": True,
"argstr": "--bvals={bval_file}",
}
)

fieldmap_image: PathLike = field(metadata={"help_string": "fieldmap image", "argstr": "--field"})
fieldmap_image: PathLike = field(metadata={"help_string": "fieldmap image", "argstr": "--field={fieldmap_image}"})

fieldmap_matrix: PathLike = field(
metadata={
"help_string": "rigid-body transformation matrix from fieldmap to first input volume",
"argstr": "--field_mat",
"argstr": "--field_mat={fieldmap_matrix}",
"requires": {"fieldmap_image"},
}
)
Expand All @@ -82,15 +100,19 @@ class EddySpec(ShellSpec):

# Parameters specifying names of output-files.
output_basename: str = field(
default="eddy", metadata={"help_string": "basename for output files", "argstr": "--out"}
default="eddy",
metadata={
"help_string": "basename for output files",
"argstr": "--out={output_basename}",
},
)

# Parameters specifying how eddy should be run.
first_level_model: str = field(
default="quadratic",
metadata={
"help_string": "model for the magnetic field generated by Eddy currents",
"argstr": "--flm",
"argstr": "--flm={first_level_model}",
"allowed_values": {"movement", "linear", "quadratic", "cubic"},
},
)
Expand All @@ -99,7 +121,7 @@ class EddySpec(ShellSpec):
default="none",
metadata={
"help_string": "model for how diffusion gradients generate Eddy currents",
"argstr": "--slm",
"argstr": "--slm={second_level_model}",
"allowed_values": {"none", "linear", "quadratic"},
},
)
Expand All @@ -108,12 +130,16 @@ class EddySpec(ShellSpec):
default=0,
metadata={
"help_string": "filter width used for pre-conditioning data prior to estimating distortions",
"argstr": "--fwhm",
"argstr": "--fwhm={fwhm}",
},
)

num_iterations: int = field(
default=5, metadata={"help_string": "number of iterations for eddy", "argstr": "--niter"}
default=5,
metadata={
"help_string": "number of iterations for eddy",
"argstr": "--niter={num_iterations}",
},
)

fill_empty_planes: bool = field(metadata={"help_string": "detect and fill empty planes", "argstr": "--fep"})
Expand All @@ -122,23 +148,34 @@ class EddySpec(ShellSpec):
default="spline",
metadata={
"help_string": "interpolation method for the estimation phase",
"argstr": "--interp",
"argstr": "--interp={interpolation}",
"allowed_values": {"spline", "trilinear"},
},
)

resampling: str = field(
default="jac",
metadata={"help_string": "final resampling strategy", "argstr": "--resamp", "allowed_values": {"jac", "lsr"}},
metadata={
"help_string": "final resampling strategy",
"argstr": "--resamp={resampling}",
"allowed_values": {"jac", "lsr"},
},
)

num_voxels: int = field(
default=1000,
metadata={"help_string": "number of voxels to use for GP hyperparameter estimation", "argstr": "--nvoxhp"},
metadata={
"help_string": "number of voxels to use for GP hyperparameter estimation",
"argstr": "--nvoxhp={num_voxels}",
},
)

fudge_factor: int = field(
default=10, metadata={"help_string": "fudge factor for Q-space smoothing during estimation", "argstr": "--ff"}
default=10,
metadata={
"help_string": "fudge factor for Q-space smoothing during estimation",
"argstr": "--ff={fudge_factor}",
},
)

# Parameters for outlier replacement (ol)
Expand All @@ -147,67 +184,81 @@ class EddySpec(ShellSpec):
outlier_num_stdevs: int = field(
metadata={
"help_string": "number of times off the standard deviation to qualify as outlier",
"argstr": "--ol_nstd",
"argstr": "--ol_nstd={outlier_num_stdevs}",
"requires": {"replace_outliers"},
}
)

outlier_num_voxels: int = field(
metadata={
"help_string": "minimum number of voxels in a slice to qualify for outlier detection",
"argstr": "--ol_nvox",
"argstr": "--ol_nvox={outlier_num_voxels}",
"requires": {"replace_outliers"},
}
)

outlier_type: str = field(
metadata={
"help_string": "type of outliers detected",
"argstr": "--ol_type",
"argstr": "--ol_type={outlier_type}",
"allowed_values": {"both", "gw", "sw"},
"requires": {"replace_outliers"},
}
)

multiband_factor: int = field(metadata={"help_string": "multiband factor", "argstr": "--mb"})
multiband_factor: int = field(metadata={"help_string": "multiband factor", "argstr": "--mb={multiband_factor}"})

multiband_offset: int = field(
metadata={"help_string": "multiband slice offset", "argstr": "--mb_offs", "requires": {"multiband_factor"}}
metadata={
"help_string": "multiband slice offset",
"argstr": "--mb_offs={multiband_offset}",
"requires": {"multiband_factor"},
}
)

# Parameters for intra-volume movement correction (s2v)
movement_prediction_order: int = field(
default=0, metadata={"help_string": "order of movement prediction model", "argstr": "--mporder"}
default=0,
metadata={
"help_string": "order of movement prediction model",
"argstr": "--mporder={movement_prediction_order}",
},
)

s2v_num_iterations: int = field(
metadata={"help_string": "number of iterations for s2v movement estimation", "argstr": "--s2v_niter"}
metadata={
"help_string": "number of iterations for s2v movement estimation",
"argstr": "--s2v_niter={s2v_num_iterations}",
}
)

s2v_lambda: float = field(
metadata={"help_string": "weighting of regularization for s2v movement estimation", "argstr": "--s2v_lambda"}
metadata={
"help_string": "weighting of regularization for s2v movement estimation",
"argstr": "--s2v_lambda={s2v_lambda}",
}
)

s2v_interpolation: str = field(
metadata={
"help_string": "interpolation method for s2v movement estimation.",
"argstr": "--s2v_interp",
"argstr": "--s2v_interp={s2v_interpolation}",
"allowed_values": {"spline", "trilinear"},
}
)

slice_grouping_file: PathLike = field(
metadata={
"help_string": "file containing slice grouping information",
"argstr": "--slspec",
"argstr": "--slspec={slice_grouping_file}",
"xor": {"slice_timing_file"},
}
)

slice_timing_file: PathLike = field(
metadata={
"help_string": "file containing slice timing information",
"argstr": "--json",
"argstr": "--json={slice_timing_file}",
"xor": {"slice_grouping_file"},
}
)
Expand All @@ -223,23 +274,23 @@ class EddySpec(ShellSpec):
mbs_num_iterations: int = field(
metadata={
"help_string": "number of iterations for MBS field estimation",
"argstr": "--mbs_niter",
"argstr": "--mbs_niter={mbs_num_iterations}",
"requires": {"estimate_move_by_susceptibility"},
}
)

mbs_lambda: int = field(
metadata={
"help_string": "weighting of regularization for MBS field estimation",
"argstr": "--mbs_lambda",
"argstr": "--mbs_lambda={mbs_lambda}",
"requires": {"estimate_move_by_susceptibility"},
}
)

mbs_knot_spacing: int = field(
metadata={
"help_string": "knot-spacing for MBS field estimation",
"argstr": "--mbs_ksp",
"argstr": "--mbs_ksp={mbs_knot_spacing}",
"requires": {"estimate_move_by_susceptibility"},
}
)
Expand All @@ -249,7 +300,9 @@ class EddySpec(ShellSpec):
metadata={"help_string": "bypass checks for data shelling", "argstr": "--data_is_shelled"}
)

random_seed: int = field(metadata={"help_string": "random seed for voxel selection", "argstr": "--initrand"})
random_seed: int = field(
metadata={"help_string": "random seed for voxel selection", "argstr": "--initrand={random_seed}"}
)

save_cnr_maps: bool = field(metadata={"help_string": "save shell-wise CNR maps", "argstr": "--cnr_maps"})

Expand Down