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fixed refit #702

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Merged
satra merged 3 commits into from
Oct 25, 2013
Merged

fixed refit #702

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5b843f9
fixed refit
chrisgorgo Oct 24, 2013
4f962e1
fixed doctests
chrisgorgo Oct 24, 2013
8f47a12
fixed more bugs
chrisgorgo Oct 24, 2013
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16 changes: 9 additions & 7 deletions nipype/interfaces/afni/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@
from nipype.utils.filemanip import fname_presuffix
from .base import AFNICommand, AFNICommandInputSpec,\
AFNICommandOutputSpec
from nipype.interfaces.base import CommandLineInputSpec, CommandLine

warn = warnings.warn
warnings.filterwarnings('always', category=UserWarning)
Expand Down Expand Up @@ -149,17 +150,14 @@ class TShift(AFNICommand):
output_spec = AFNICommandOutputSpec


class RefitInputSpec(AFNICommandInputSpec):
class RefitInputSpec(CommandLineInputSpec):
in_file = File(desc='input file to 3drefit',
argstr='%s',
position=-1,
mandatory=True,
exists=True,
copyfile=True)

out_file = File(name_template="%s_refit", desc='output image file name, should be the same as input',
argstr='%s', name_source="in_file")

deoblique = traits.Bool(desc='replace current transformation' +
' matrix with cardinal matrix',
argstr='-deoblique')
Expand All @@ -173,7 +171,7 @@ class RefitInputSpec(AFNICommandInputSpec):
argstr='-zorigin %s')


class Refit(AFNICommand):
class Refit(CommandLine):
"""Changes some of the information inside a 3D dataset's header

For complete details, see the `3drefit Documentation.
Expand All @@ -186,16 +184,20 @@ class Refit(AFNICommand):
>>> refit = afni.Refit()
>>> refit.inputs.in_file = 'structural.nii'
>>> refit.inputs.deoblique = True
>>> refit.inputs.outputtype = "NIFTI_GZ"
>>> refit.cmdline
'3drefit -deoblique structural_refit.nii.gz structural.nii'
'3drefit -deoblique structural.nii'
>>> res = refit.run() # doctest: +SKIP

"""

_cmd = '3drefit'
input_spec = RefitInputSpec
output_spec = AFNICommandOutputSpec

def _list_outputs(self):
outputs = super(AFNICommand, self)._list_outputs()
outputs["out_file"] = os.path.abspath(self.inputs.in_file)
return outputs


class WarpInputSpec(AFNICommandInputSpec):
Expand Down