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[FIX] Doctest of antsJointFusion failing #1879

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Merged
merged 1 commit into from
Mar 14, 2017
Merged

[FIX] Doctest of antsJointFusion failing #1879

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19 changes: 10 additions & 9 deletions nipype/interfaces/ants/segmentation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1130,28 +1130,29 @@ def _format_arg(self, opt, spec, val):
if not isdefined(self.inputs.out_label_fusion):
retval = '-o {0}'.format(self.inputs.out_intensity_fusion_name_format)
elif opt == 'atlas_image':
atlas_image_cmd=" ".join(
[ '-g [{0}]'.format(",".join(
fn for fn in ai) ) for ai in self.inputs.atlas_image]
atlas_image_cmd = " ".join(
['-g [{0}]'.format(", ".join("'%s'" % fn for fn in ai))
for ai in self.inputs.atlas_image]
)
retval = atlas_image_cmd
elif opt == 'target_image':
target_image_cmd=" ".join(
[ '-t [{0}]'.format(",".join(
fn for fn in ai) ) for ai in self.inputs.target_image]
target_image_cmd = " ".join(
['-t [{0}]'.format(", ".join("'%s'" % fn for fn in ai))
for ai in self.inputs.target_image]
)
retval = target_image_cmd
elif opt == 'atlas_segmentation_image':
assert len(val) == len(self.inputs.atlas_image), "Number of specified " \
"segmentations should be identical to the number of atlas image " \
"sets {0}!={1}".format(len(val), len(self.inputs.atlas_image))
atlas_segmentation_image_cmd=" ".join(
[ '-t [{0}]'.format( fn ) for fn in self.inputs.atlas_segmentation_image ]

atlas_segmentation_image_cmd = " ".join(
['-l {0}'.format(fn) for fn in self.inputs.atlas_segmentation_image]
)
retval = atlas_segmentation_image_cmd
else:

return super(ANTSCommand, self)._format_arg(opt, spec, val)
return super(AntsJointFusion, self)._format_arg(opt, spec, val)
return retval

def _list_outputs(self):
Expand Down