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Commit 28973c5

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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

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10 files changed

+436
-12
lines changed

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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)
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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(
11+
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
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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"],
31+
),
32+
grad_fsl=dict(
33+
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,
38+
),
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in_bvec=dict(
40+
argstr="-fslgrad %s %s",
41+
extensions=None,
42+
),
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mask=dict(
44+
argstr="-mask %s",
45+
extensions=None,
46+
position=-1,
47+
),
48+
nthreads=dict(
49+
argstr="-nthreads %d",
50+
nohash=True,
51+
),
52+
out_bval=dict(
53+
extensions=None,
54+
),
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out_bvec=dict(
56+
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,
62+
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",
71+
extensions=None,
72+
position=2,
73+
),
74+
wm_fod=dict(
75+
argstr="%s",
76+
extensions=None,
77+
position=1,
78+
),
79+
)
80+
inputs = MTNormalise.input_spec()
81+
82+
for key, metadata in list(input_map.items()):
83+
for metakey, value in list(metadata.items()):
84+
assert getattr(inputs.traits()[key], metakey) == value
85+
86+
87+
def test_MTNormalise_outputs():
88+
output_map = dict(
89+
out_file_csf=dict(
90+
extensions=None,
91+
),
92+
out_file_gm=dict(
93+
extensions=None,
94+
),
95+
out_file_wm=dict(
96+
extensions=None,
97+
),
98+
)
99+
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
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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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4+
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def test_MaskFilter_inputs():
6+
input_map = dict(
7+
args=dict(
8+
argstr="%s",
9+
),
10+
environ=dict(
11+
nohash=True,
12+
usedefault=True,
13+
),
14+
filter=dict(
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argstr="%s",
16+
mandatory=True,
17+
position=-2,
18+
),
19+
in_file=dict(
20+
argstr="%s",
21+
extensions=None,
22+
mandatory=True,
23+
position=-3,
24+
),
25+
npass=dict(
26+
argstr="-npass %d",
27+
position=1,
28+
),
29+
out_file=dict(
30+
argstr="%s",
31+
extensions=None,
32+
mandatory=True,
33+
name_source=["input_image"],
34+
position=-1,
35+
),
36+
)
37+
inputs = MaskFilter.input_spec()
38+
39+
for key, metadata in list(input_map.items()):
40+
for metakey, value in list(metadata.items()):
41+
assert getattr(inputs.traits()[key], metakey) == value
42+
43+
44+
def test_MaskFilter_outputs():
45+
output_map = dict(
46+
out_file=dict(
47+
extensions=None,
48+
),
49+
)
50+
outputs = MaskFilter.output_spec()
51+
52+
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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