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Error generated by Automask in nipype.interfaces.afni #586

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Error generated by Automask in nipype.interfaces.afni #586

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bc33651
Function Automask raises error due to string '-apply_prefix <undefine…
mick-d Jun 24, 2013
a5728b5
Merge remote-tracking branch 'upstream/master'
mick-d Jun 27, 2013
12841c2
Added the option for resampling with isotropic voxels as available in…
mick-d Jun 27, 2013
4f70bdf
Update
mick-d Jul 3, 2013
c5c11e9
Postpone FSL Flirt apply_isoxfm for a different PR
mick-d Jul 3, 2013
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22 changes: 11 additions & 11 deletions nipype/interfaces/afni/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -508,12 +508,12 @@ class AutomaskInputSpec(AFNICommandInputSpec):
argstr="-erode %s")

mask_suffix = traits.Str(
desc="out_file suffix", depracated=0.8, new_name="out_file")
desc="out_file suffix", deprecated=0.8, new_name="out_file")
apply_suffix = traits.Str(
desc="out_file suffix", depracated=0.8, new_name="brain_file")
apply_mask = File(desc="output file from 3dAutomask",
argstr='-apply_prefix %s',
name_source="in_file", depracated=0.8, new_name="brain_file")
desc="out_file suffix", deprecated=0.8, new_name="brain_file")
#apply_mask = File(desc="output file from 3dAutomask",
#argstr='-apply_prefix %s',
#name_source="in_file", deprecated=0.8, new_name="brain_file")


class AutomaskOutputSpec(TraitedSpec):
Expand Down Expand Up @@ -580,12 +580,12 @@ def _gen_filename(self, name):
return super(Automask, self)._gen_filename(name)
return Undefined

def _list_outputs(self):
outputs = super(Automask, self)._list_outputs()
if isdefined(self.inputs.apply_mask):
outputs['brain_file'] = os.path.abspath(
self._gen_filename('apply_mask'))
return outputs
#def _list_outputs(self):
#outputs = super(Automask, self)._list_outputs()
#if isdefined(self.inputs.apply_mask):
#outputs['brain_file'] = os.path.abspath(
#self._gen_filename('apply_mask'))
#return outputs


class VolregInputSpec(AFNICommandInputSpec):
Expand Down