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FIX: parsing of filename in AlignEpiAnatPy when filename does not have + #2909

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Merged
merged 2 commits into from
Apr 18, 2019
Merged

FIX: parsing of filename in AlignEpiAnatPy when filename does not have + #2909

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db623d6
BUGFIX when filename does not have +
gpiantoni Apr 5, 2019
e384080
match _overload_extension in AFNItoNIFTI
gpiantoni Apr 5, 2019
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12 changes: 7 additions & 5 deletions nipype/interfaces/afni/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -168,15 +168,17 @@ class AlignEpiAnatPy(AFNIPythonCommand):

def _list_outputs(self):
outputs = self.output_spec().get()
anat_prefix = ''.join(
self._gen_fname(self.inputs.anat).split('+')[:-1])
epi_prefix = ''.join(
self._gen_fname(self.inputs.in_file).split('+')[:-1])
anat_prefix = self._gen_fname(self.inputs.anat)
epi_prefix = self._gen_fname(self.inputs.in_file)
if '+' in anat_prefix:
anat_prefix = ''.join(anat_prefix.split('+')[:-1])
if '+' in epi_prefix:
epi_prefix = ''.join(epi_prefix.split('+')[:-1])
outputtype = self.inputs.outputtype
if outputtype == 'AFNI':
ext = '.HEAD'
else:
Info.output_type_to_ext(outputtype)
ext = Info.output_type_to_ext(outputtype)
matext = '.1D'
suffix = self.inputs.suffix
if self.inputs.anat2epi:
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2 changes: 1 addition & 1 deletion nipype/interfaces/afni/utils.py
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Expand Up @@ -143,7 +143,7 @@ class AFNItoNIFTI(AFNICommand):
input_spec = AFNItoNIFTIInputSpec
output_spec = AFNICommandOutputSpec

def _overload_extension(self, value):
def _overload_extension(self, value, name=None):
path, base, ext = split_filename(value)
if ext.lower() not in ['.nii', '.nii.gz', '.1d', '.1D']:
ext += '.nii'
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