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TEST/FIX: Implement argstr handling for mri_gtmpvc --mg
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nipype/interfaces/freesurfer/petsurfer.py

Lines changed: 12 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -296,7 +296,7 @@ class GTMPVCInputSpec(FSTraitedSpec):
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mg = traits.Tuple(
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traits.Float,
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traits.List(traits.String),
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argstr="--mg %f %s...",
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argstr="--mg %g %s",
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desc="gmthresh RefId1 RefId2 ...: perform Mueller-Gaertner PVC, gmthresh is min gm pvf bet 0 and 1",
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)
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@@ -484,6 +484,15 @@ class GTMPVC(FSCommand):
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--i sub-01_ses-baseline_pet.nii.gz --km-hb 11 12 50 51 --km-ref 8 47 --no-rescale \
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--psf 4.000000 --o pvc --reg sub-01_ses-baseline_pet_mean_reg.lta --save-input \
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--seg gtmseg.mgz'
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>>> gtmpvc = GTMPVC()
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>>> gtmpvc.inputs.in_file = 'sub-01_ses-baseline_pet.nii.gz'
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>>> gtmpvc.inputs.segmentation = 'gtmseg.mgz'
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>>> gtmpvc.inputs.regheader = True
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>>> gtmpvc.inputs.pvc_dir = 'pvc'
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>>> gtmpvc.inputs.mg = (0.5, ["ROI1", "ROI2"])
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>>> gtmpvc.cmdline # doctest: +NORMALIZE_WHITESPACE
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'mri_gtmpvc --i sub-01_ses-baseline_pet.nii.gz --mg 0.5 ROI1 ROI2 --o pvc --regheader --seg gtmseg.mgz'
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"""
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_cmd = "mri_gtmpvc"
@@ -507,6 +516,8 @@ def _format_arg(self, name, spec, val):
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"MB3": 8,
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}[val]
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)
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if name == 'mg':
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return spec.argstr % (val[0], ' '.join(val[1]))
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return super(GTMPVC, self)._format_arg(name, spec, val)
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def _list_outputs(self):

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