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‎pydra/tasks/fsl/__init__.py

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@@ -7,5 +7,6 @@
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"""
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from ._version import get_versions
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__version__ = get_versions()['version']
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del get_versions

‎pydra/tasks/fsl/conftest.py

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@@ -2,20 +2,19 @@
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import shutil
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from tempfile import mkdtemp
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import pytest
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#import numpy
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# import numpy
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import py.path as pp
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8-
NIPYPE_DATADIR = os.path.realpath(
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os.path.join(os.path.dirname(__file__), "tests/data")
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)
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NIPYPE_DATADIR = os.path.realpath(os.path.join(os.path.dirname(__file__), "tests/data"))
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temp_folder = mkdtemp()
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data_dir = os.path.join(temp_folder, "data")
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shutil.copytree(NIPYPE_DATADIR, data_dir)
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@pytest.fixture(autouse=True)
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def add_np(doctest_namespace):
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# doctest_namespace["np"] = numpy
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# doctest_namespace["np"] = numpy
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doctest_namespace["os"] = os
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doctest_namespace["pytest"] = pytest
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doctest_namespace["datadir"] = data_dir

‎pydra/tasks/fsl/preprocess/applywarp.py

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@@ -115,9 +115,7 @@
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},
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),
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]
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ApplyWarp_input_spec = specs.SpecInfo(
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name="Input", fields=input_fields, bases=(specs.ShellSpec,)
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)
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ApplyWarp_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
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output_fields = []
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ApplyWarp_output_spec = specs.SpecInfo(

‎pydra/tasks/fsl/preprocess/bet.py

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@@ -183,9 +183,7 @@
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},
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),
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]
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BET_input_spec = specs.SpecInfo(
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name="Input", fields=input_fields, bases=(specs.ShellSpec,)
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)
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BET_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
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output_fields = [
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(
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},
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),
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]
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BET_output_spec = specs.SpecInfo(
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name="Output", fields=output_fields, bases=(specs.ShellOutSpec,)
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)
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BET_output_spec = specs.SpecInfo(name="Output", fields=output_fields, bases=(specs.ShellOutSpec,))
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class BET(ShellCommandTask):

‎pydra/tasks/fsl/preprocess/fast.py

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Original file line numberDiff line numberDiff line change
@@ -228,9 +228,7 @@ def FAST_output_nclass(field, in_files, nclasses, out_basename):
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{"help_string": "outputs individual probability maps", "argstr": "-p"},
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),
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]
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FAST_input_spec = specs.SpecInfo(
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name="Input", fields=input_fields, bases=(specs.ShellSpec,)
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)
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FAST_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
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output_fields = [
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(
@@ -263,9 +261,7 @@ def FAST_output_nclass(field, in_files, nclasses, out_basename):
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{"requires": [("probability_maps", True)], "callable": "FAST_output_nclass"},
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),
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]
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FAST_output_spec = specs.SpecInfo(
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name="Output", fields=output_fields, bases=(specs.ShellOutSpec,)
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)
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FAST_output_spec = specs.SpecInfo(name="Output", fields=output_fields, bases=(specs.ShellOutSpec,))
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class FAST(ShellCommandTask):

‎pydra/tasks/fsl/preprocess/first.py

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},
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),
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]
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FIRST_input_spec = specs.SpecInfo(
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name="Input", fields=input_fields, bases=(specs.ShellSpec,)
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)
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FIRST_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
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output_fields = [
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(

‎pydra/tasks/fsl/preprocess/flirt.py

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{"help_string": "value of bbr slope", "argstr": "-bbrslope {bbrslope}"},
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),
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]
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FLIRT_input_spec = specs.SpecInfo(
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name="Input", fields=input_fields, bases=(specs.ShellSpec,)
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)
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FLIRT_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
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output_fields = []
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FLIRT_output_spec = specs.SpecInfo(

‎pydra/tasks/fsl/preprocess/fnirt.py

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},
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),
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]
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FNIRT_input_spec = specs.SpecInfo(
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name="Input", fields=input_fields, bases=(specs.ShellSpec,)
356-
)
354+
FNIRT_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
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358356
output_fields = [
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(

‎pydra/tasks/fsl/preprocess/mcflirt.py

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},
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),
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]
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MCFLIRT_input_spec = specs.SpecInfo(
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name="Input", fields=input_fields, bases=(specs.ShellSpec,)
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)
137+
MCFLIRT_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
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output_fields = [
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(

‎pydra/tasks/fsl/preprocess/prelude.py

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},
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),
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]
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PRELUDE_input_spec = specs.SpecInfo(
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name="Input", fields=input_fields, bases=(specs.ShellSpec,)
146-
)
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PRELUDE_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
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148146
output_fields = []
149147
PRELUDE_output_spec = specs.SpecInfo(

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