10000 ENH: Add inputs to mrtrix3.DWIPreprocInputSpec and remove mandatory annotation for pe_dir by GalKepler · Pull Request #3470 · nipy/nipype · GitHub
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ENH: Add inputs to mrtrix3.DWIPreprocInputSpec and remove mandatory annotation for pe_dir #3470

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Merged
merged 10 commits into from
Jul 23, 2022
Merged

ENH: Add inputs to mrtrix3.DWIPreprocInputSpec and remove mandatory annotation for pe_dir #3470

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735c712
fixed some bugs in the interface to dwifslpreproc
GalKepler May 11, 2022
411e577
updated my ORCID in zenodo
GalKepler May 11, 2022
285f187
reformatted to pass pre-commit hooks
GalKepler May 11, 2022
9d37260
removed default values for gradients' files outputs
GalKepler May 12, 2022
443f7f4
edited pre-existing tests to match the new keyword arguments
GalKepler May 12, 2022
9306be7
reformatted to match project's settings
GalKepler May 12, 2022
87e8704
changes dwifslpreproc outputs' configuration and reset tests to match…
GalKepler May 13, 2022
e726ac4
updated docstrings to match the new configurations
GalKepler May 13, 2022
4ab9084
Apply suggestions from code review
effigies Jul 13, 2022
43edc43
Merge branch 'master' into dwifslpreproc
GalKepler Jul 15, 2022
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removed default values for gradients' files outputs
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@GalKepler
GalKepler committed May 12, 2022
commit 9d372603aa76811b6cca41217a535eac7d8cdbdc
25 changes: 17 additions & 8 deletions nipype/interfaces/mrtrix3/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -192,7 +192,9 @@ class DWIBiasCorrectInputSpec(MRTrix3BaseInputSpec):
mandatory=True,
desc="input DWI image",
)
in_mask = File(argstr="-mask %s", desc="input mask image for bias field estimation")
in_mask = File(
argstr="-mask %s", desc="input mask image for bias field estimation"
)
use_ants = traits.Bool(
argstr="ants",
mandatory=True,
Expand Down Expand Up @@ -343,13 +345,12 @@ class DWIPreprocInputSpec(MRTrix3BaseInputSpec):
out_grad_mrtrix = File(
"grad.b",
argstr="%s",
usedefault=True,
requires=["export_grad_mrtrix"],
desc="name of new gradient file",
)
out_grad_fsl = traits.Tuple(
File("grad.bvecs", usedefault=True, desc="bvecs"),
File("grad.bvals", usedefault=True, desc="bvals"),
File("grad.bvecs", desc="bvecs"),
File("grad.bvals", desc="bvals"),
argstr="%s, %s",
requires=["export_grad_fsl"],
desc="Output (bvecs, bvals) gradients FSL format",
Expand Down Expand Up @@ -410,7 +411,9 @@ def _list_outputs(self):
outputs = self.output_spec().get()
outputs["out_file"] = op.abspath(self.inputs.out_file)
if self.inputs.export_grad_mrtrix:
outputs["out_grad_mrtrix"] = op.abspath(self.inputs.out_grad_mrtrix)
outputs["out_grad_mrtrix"] = op.abspath(
self.inputs.out_grad_mrtrix
)
if self.inputs.export_grad_fsl:
outputs["out_fsl_bvec"] = op.abspath(self.inputs.out_grad_fsl[0])
outputs["out_fsl_bval"] = op.abspath(self.inputs.out_grad_fsl[1])
Expand Down Expand Up @@ -444,9 +447,15 @@ class ResponseSDInputSpec(MRTrix3BaseInputSpec):
usedefault=True,
desc="output WM response text file",
)
gm_file = File(argstr="%s", position=-2, desc="output GM response text file")
csf_file = File(argstr="%s", position=-1, desc="output CSF response text file")
in_mask = File(exists=True, argstr="-mask %s", desc="provide initial mask image")
gm_file = File(
argstr="%s", position=-2, desc="output GM response text file"
)
csf_file = File(
argstr="%s", position=-1, desc="output CSF response text file"
)
in_mask = File(
exists=True, argstr="-mask %s", desc="provide initial mask image"
)
max_sh = InputMultiObject(
traits.Int,
argstr="-lmax %s",
Expand Down
0