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Merged
merged 15 commits into from
Mar 23, 2018
Merged

Fix/dcm2niix #2498

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6ecd4a9
ref: dcm2niix interface
mgxd Mar 16, 2018
26d82fe
tst: add datalad/dcm2niix to testing
mgxd Mar 16, 2018
b60b4d8
fix: dcm2niix doctest
mgxd Mar 16, 2018
6d7bb8d
tst: move dcm2niix test to circle
mgxd Mar 16, 2018
43c43a7
fix: forgotten changes
mgxd Mar 16, 2018
4c2e885
tst: remove dcm2niix and datalad testing until neurodocker fixes
mgxd Mar 16, 2018
ec72e99
tst: add check for dcm2niix executable
mgxd Mar 16, 2018
140b715
enh: add version checking
mgxd Mar 17, 2018
e904bbb
fix: version parsing
mgxd Mar 17, 2018
7ba24f1
doc: add test [skip-ci]
mgxd Mar 19, 2018
333c5a3
Merge branch 'fix/dcm2niix' of github.com:mgxd/nipype into fix/dcm2niix
mgxd Mar 19, 2018
715de9c
Merge branch 'master' of git://github.com/nipy/nipype into fix/dcm2niix
mgxd Mar 19, 2018
dd0503f
fix: address review comments
mgxd Mar 23, 2018
c92289b
Merge branch 'master' of git://github.com/nipy/nipype into fix/dcm2niix
mgxd Mar 23, 2018
41c45b9
fix: argstr and doctest
mgxd Mar 23, 2018
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11 changes: 4 additions & 7 deletions nipype/interfaces/dcm2nii.py
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Original file line number Diff line number Diff line change
Expand Up @@ -277,7 +277,7 @@ class Dcm2niixInputSpec(CommandLineInputSpec):
argstr="-f %s",
desc="Output filename")
output_dir = Directory(
os.getcwd(),
".",
usedefault=True,
exists=True,
argstr='-o %s',
Expand Down Expand Up @@ -323,7 +323,7 @@ class Dcm2niixInputSpec(CommandLineInputSpec):
desc="Flag if text notes includes private patient details")
compression = traits.Enum(
1, 2, 3, 4, 5, 6, 7, 8, 9,
argstr='-%s',
argstr='-%d',
desc="Gz compression level (1=fastest, 9=smallest)")
comment = traits.Str(
argstr='-c %s',
Expand Down Expand Up @@ -360,11 +360,6 @@ class Dcm2niix(CommandLine):
>>> converter.inputs.output_dir = 'ds005'
>>> converter.cmdline
'dcm2niix -b y -z y -5 -x n -t n -m n -o ds005 -s n -v n dicomdir'
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perhaps add:

>>> converter.run() # doctest: +SKIP

after this


>>> flags = '-'.join([val.strip() + ' ' for val in sorted(' '.join(converter.cmdline.split()[1:-1]).split('-'))])
>>> flags
' -5 -b y -m n -o ds005 -s n -t n -v n -x n -z y '
>>> converter.run() # doctest: +SKIP
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I think we did still want the converter.run() line, though.

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😅

"""

input_spec = Dcm2niixInputSpec
Expand All @@ -387,6 +382,8 @@ def _format_arg(self, opt, spec, val):
val = True
if opt == 'source_names':
return spec.argstr % val[0]
if opt == 'series_numbers':
return ' '.join([spec.argstr % v for v in val])
return super(Dcm2niix, self)._format_arg(opt, spec, val)

def _run_interface(self, runtime):
Expand Down