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author
Shoshana Berleant
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pull from nipy/nipype master
1 parent 7f84dff commit b3187f3

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5 files changed

+12
-17
lines changed

5 files changed

+12
-17
lines changed

.travis.yml

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -24,8 +24,8 @@ before_install:
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fsl afni elastix fsl-atlases; fi &&
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if $INSTALL_DEB_DEPENDECIES; then
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source /etc/fsl/fsl.sh;
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source /etc/afni/afni.sh; fi &&
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export FSLOUTPUTTYPE=NIFTI_GZ; }
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source /etc/afni/afni.sh;
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export FSLOUTPUTTYPE=NIFTI_GZ; fi }
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- travis_retry bef_inst
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install:
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# Add install of vtk and mayavi to test mesh (disabled): conda install -y vtk mayavi &&

nipype/algorithms/confounds.py

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -281,8 +281,7 @@ def _list_outputs(self):
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class CompCorInputSpec(BaseInterfaceInputSpec):
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realigned_file = File(exists=True, mandatory=True,
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desc='already realigned brain image (4D)')
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mask_file = File(exists=True,
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desc='mask file that determines ROI (3D)')
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mask_file = File(exists=True, desc='mask file that determines ROI (3D)')
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components_file = File('components_file.txt', exists=False,
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usedefault=True,
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desc='filename to store physiological components')

nipype/interfaces/fsl/possum.py

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -79,6 +79,7 @@ class B0Calc(FSLCommand):
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>>> b0calc = B0Calc()
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>>> b0calc.inputs.in_file = 'tissue+air_map.nii'
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>>> b0calc.inputs.z_b0 = 3.0
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>>> b0calc.inputs.output_type = "NIFTI_GZ"
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>>> b0calc.cmdline # doctest: +IGNORE_UNICODE
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'b0calc -i tissue+air_map.nii -o tissue+air_map_b0field.nii.gz --b0=3.00'
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nipype/interfaces/nilearn.py

Lines changed: 4 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -38,20 +38,19 @@ class SignalExtractionInputSpec(BaseInterfaceInputSpec):
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'corresponds to the class labels in label_file '
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'in ascending order')
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out_file = File('signals.tsv', usedefault=True, exists=False,
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mandatory=False, desc='The name of the file to output to. '
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desc='The name of the file to output to. '
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'signals.tsv by default')
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incl_shared_variance = traits.Bool(True, usedefault=True, mandatory=False, desc='By default '
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incl_shared_variance = traits.Bool(True, usedefault=True, desc='By default '
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'(True), returns simple time series calculated from each '
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'region independently (e.g., for noise regression). If '
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'False, returns unique signals for each region, discarding '
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'shared variance (e.g., for connectivity. Only has effect '
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'with 4D probability maps.')
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include_global = traits.Bool(False, usedefault=True, mandatory=False,
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include_global = traits.Bool(False, usedefault=True,
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desc='If True, include an extra column '
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'labeled "global", with values calculated from the entire brain '
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'(instead of just regions).')
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detrend = traits.Bool(False, usedefault=True, mandatory=False,
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desc='If True, perform detrending using nilearn.')
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detrend = traits.Bool(False, usedefault=True, desc='If True, perform detrending using nilearn.')
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class SignalExtractionOutputSpec(TraitedSpec):
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out_file = File(exists=True, desc='tsv file containing the computed '

nipype/interfaces/tests/test_auto_SignalExtraction.py

Lines changed: 4 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -6,24 +6,20 @@
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def test_SignalExtraction_inputs():
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input_map = dict(class_labels=dict(mandatory=True,
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),
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detrend=dict(mandatory=False,
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usedefault=True,
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detrend=dict(usedefault=True,
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),
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ignore_exception=dict(nohash=True,
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usedefault=True,
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),
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in_file=dict(mandatory=True,
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),
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incl_shared_variance=dict(mandatory=False,
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usedefault=True,
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incl_shared_variance=dict(usedefault=True,
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),
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include_global=dict(mandatory=False,
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usedefault=True,
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include_global=dict(usedefault=True,
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),
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label_files=dict(mandatory=True,
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),
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out_file=dict(mandatory=False,
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usedefault=True,
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out_file=dict(usedefault=True,
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),
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)
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inputs = SignalExtraction.input_spec()

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