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Merge pull request #3613 from lbutry/added_mrtrix3_functions
[ENH]: Add functions to mrtrix3 interface
2 parents 1b5793a + 5599348 commit 28973c5

10 files changed

+436
-12
lines changed

‎.zenodo.json

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@@ -891,16 +891,6 @@
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"name": "Mihai, Paul Glad",
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"orcid": "0000-0001-5715-6442"
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},
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{
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"affiliation": "Department of Psychology, Stanford University",
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"name": "Gorgolewski, Krzysztof J.",
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"orcid": "0000-0003-3321-7583"
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},
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{
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"affiliation": "MIT, HMS",
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"name": "Ghosh, Satrajit",
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"orcid": "0000-0002-5312-6729"
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},
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{
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"affiliation": "University of Tübingen and MPI for Biological Cybernertics",
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"name": "Bannert, Michael M.",
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{
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"affiliation": "Research Centre Juelich",
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"name": "Wu, Jianxiao",
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"orcid": "0000-0002-4866-272X",
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"orcid": "0000-0002-4866-272X"
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},
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{
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"affiliation": "Department of Neurology, BG-University Hospital Bergmannsheil Bochum, Germany",
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"name": "Butry, Lionel"
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},
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{
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"affiliation": "Lund University",
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"name": "Anijärv, Toomas Erik",
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"orcid": "0000-0002-3650-4230",
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"orcid": "0000-0002-3650-4230"
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},
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{
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"affiliation": "Department of Psychology, Stanford University",
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"name": "Gorgolewski, Krzysztof J.",
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"orcid": "0000-0003-3321-7583"
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},
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{
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"affiliation": "MIT, HMS",
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"name": "Ghosh, Satrajit",
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"orcid": "0000-0002-5312-6729"
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}
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],
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"keywords": [
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"neuroimaging",

‎nipype/interfaces/mrtrix3/__init__.py

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@@ -30,4 +30,7 @@
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SHConv,
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TensorMetrics,
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TransformFSLConvert,
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MaskFilter,
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MTNormalise,
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Generate5tt2gmwmi,
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)

‎nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt2gmwmi.py

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# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
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from ..utils import Generate5tt2gmwmi
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def test_Generate5tt2gmwmi_inputs():
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input_map = dict(
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args=dict(
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argstr="%s",
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),
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bval_scale=dict(
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argstr="-bvalue_scaling %s",
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),
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environ=dict(
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nohash=True,
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usedefault=True,
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),
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grad_file=dict(
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argstr="-grad %s",
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extensions=None,
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xor=["grad_fsl"],
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),
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grad_fsl=dict(
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argstr="-fslgrad %s %s",
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xor=["grad_file"],
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),
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in_bval=dict(
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extensions=None,
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),
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in_bvec=dict(
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argstr="-fslgrad %s %s",
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extensions=None,
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),
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in_file=dict(
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argstr="%s",
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extensions=None,
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mandatory=True,
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position=-2,
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),
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mask_in=dict(
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argstr="-mask_in %s",
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extensions=None,
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position=-3,
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),
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mask_out=dict(
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argstr="%s",
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extensions=None,
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mandatory=True,
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position=-1,
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),
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nthreads=dict(
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argstr="-nthreads %d",
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nohash=True,
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),
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out_bval=dict(
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extensions=None,
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),
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out_bvec=dict(
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argstr="-export_grad_fsl %s %s",
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extensions=None,
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),
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)
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inputs = Generate5tt2gmwmi.input_spec()
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for key, metadata in list(input_map.items()):
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for metakey, value in list(metadata.items()):
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assert getattr(inputs.traits()[key], metakey) == value
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def test_Generate5tt2gmwmi_outputs():
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output_map = dict(
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mask_out=dict(
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extensions=None,
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),
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)
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outputs = Generate5tt2gmwmi.output_spec()
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for key, metadata in list(output_map.items()):
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for metakey, value in list(metadata.items()):
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assert getattr(outputs.traits()[key], metakey) == value

‎nipype/interfaces/mrtrix3/tests/test_auto_MTNormalise.py

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# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
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from ..utils import MTNormalise
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def test_MTNormalise_inputs():
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input_map = dict(
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args=dict(
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argstr="%s",
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),
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bval_scale=dict(
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argstr="-bvalue_scaling %s",
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),
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csf_fod=dict(
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argstr="%s",
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extensions=None,
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position=5,
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),
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environ=dict(
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nohash=True,
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usedefault=True,
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),
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gm_fod=dict(
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argstr="%s",
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extensions=None,
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position=3,
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),
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grad_file=dict(
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argstr="-grad %s",
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extensions=None,
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xor=["grad_fsl"],
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),
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grad_fsl=dict(
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argstr="-fslgrad %s %s",
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xor=["grad_file"],
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),
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in_bval=dict(
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extensions=None,
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),
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in_bvec=dict(
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argstr="-fslgrad %s %s",
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extensions=None,
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),
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mask=dict(
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argstr="-mask %s",
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extensions=None,
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position=-1,
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),
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nthreads=dict(
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argstr="-nthreads %d",
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nohash=True,
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),
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out_bval=dict(
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extensions=None,
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),
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out_bvec=dict(
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argstr="-export_grad_fsl %s %s",
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extensions=None,
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),
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out_file_csf=dict(
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argstr="%s",
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extensions=None,
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position=6,
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),
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out_file_gm=dict(
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argstr="%s",
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extensions=None,
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position=4,
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),
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out_file_wm=dict(
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argstr="%s",
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extensions=None,
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position=2,
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),
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wm_fod=dict(
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argstr="%s",
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extensions=None,
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position=1,
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),
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)
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inputs = MTNormalise.input_spec()
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for key, metadata in list(input_map.items()):
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for metakey, value in list(metadata.items()):
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assert getattr(inputs.traits()[key], metakey) == value
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def test_MTNormalise_outputs():
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output_map = dict(
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out_file_csf=dict(
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extensions=None,
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),
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out_file_gm=dict(
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extensions=None,
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),
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out_file_wm=dict(
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extensions=None,
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),
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)
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outputs = MTNormalise.output_spec()
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for key, metadata in list(output_map.items()):
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for metakey, value in list(metadata.items()):
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assert getattr(outputs.traits()[key], metakey) == value

‎nipype/interfaces/mrtrix3/tests/test_auto_MaskFilter.py

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# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
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from ..utils import MaskFilter
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def test_MaskFilter_inputs():
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input_map = dict(
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args=dict(
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argstr="%s",
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),
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environ=dict(
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nohash=True,
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usedefault=True,
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),
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filter=dict(
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argstr="%s",
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mandatory=True,
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position=-2,
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),
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in_file=dict(
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argstr="%s",
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extensions=None,
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mandatory=True,
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position=-3,
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),
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npass=dict(
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argstr="-npass %d",
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position=1,
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),
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out_file=dict(
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argstr="%s",
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extensions=None,
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mandatory=True,
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name_source=["input_image"],
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position=-1,
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),
36+
)
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inputs = MaskFilter.input_spec()
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for key, metadata in list(input_map.items()):
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for metakey, value in list(metadata.items()):
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assert getattr(inputs.traits()[key], metakey) == value
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def test_MaskFilter_outputs():
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output_map = dict(
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out_file=dict(
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extensions=None,
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),
49+
)
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outputs = MaskFilter.output_spec()
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for key, metadata in list(output_map.items()):
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for metakey, value in list(metadata.items()):
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assert getattr(outputs.traits()[key], metakey) == value

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