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Merge pull request #2339 from salma1601/afni_unifize_more_options
more input parameters in afni.Unifize
2 parents 373bddd + cbc904d commit 3ed2840

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lines changed

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nipype/interfaces/afni/tests/test_auto_Unifize.py

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@@ -6,6 +6,8 @@
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def test_Unifize_inputs():
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input_map = dict(args=dict(argstr='%s',
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),
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cl_frac=dict(argstr='-clfrac %f',
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),
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environ=dict(nohash=True,
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usedefault=True,
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),
@@ -31,14 +33,19 @@ def test_Unifize_inputs():
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),
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out_file=dict(argstr='-prefix %s',
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name_source='in_file',
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name_template='%s_unifized',
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),
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outputtype=dict(),
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quiet=dict(argstr='-quiet',
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),
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rbt=dict(argstr='-rbt %f %f %f',
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),
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scale_file=dict(argstr='-ssave %s',
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),
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t2=dict(argstr='-T2',
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),
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t2_up=dict(argstr='-T2up %f',
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),
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terminal_output=dict(deprecated='1.0.0',
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nohash=True,
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),

nipype/interfaces/afni/utils.py

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@@ -2291,6 +2291,7 @@ class UnifizeInputSpec(AFNICommandInputSpec):
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exists=True,
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copyfile=False)
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out_file = File(
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name_template='%s_unifized',
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desc='output image file name',
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argstr='-prefix %s',
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name_source='in_file')
@@ -2337,6 +2338,22 @@ class UnifizeInputSpec(AFNICommandInputSpec):
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'b = bottom percentile of normalizing data range, [default=70.0]\n'
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'r = top percentile of normalizing data range, [default=80.0]\n',
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argstr='-rbt %f %f %f')
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t2_up = traits.Float(
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desc='Option for AFNI experts only.'
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'Set the upper percentile point used for T2-T1 inversion. '
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'Allowed to be anything between 90 and 100 (inclusive), with '
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'default to 98.5 (for no good reason).',
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argstr='-T2up %f')
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cl_frac = traits.Float(
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desc='Option for AFNI experts only.'
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'Set the automask \'clip level fraction\'. Must be between '
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'0.1 and 0.9. A small fraction means to make the initial '
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'threshold for clipping (a la 3dClipLevel) smaller, which '
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'will tend to make the mask larger. [default=0.1]',
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argstr='-clfrac %f')
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quiet = traits.Bool(
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desc='Don\'t print the progress messages.',
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argstr='-quiet')
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class UnifizeOutputSpec(TraitedSpec):

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